51
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Schlame M, Xu Y, Erdjument-Bromage H, Neubert TA, Ren M. Lipidome-wide 13C flux analysis: a novel tool to estimate the turnover of lipids in organisms and cultures. J Lipid Res 2020; 61:95-104. [PMID: 31712250 PMCID: PMC6939592 DOI: 10.1194/jlr.d119000318] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 11/07/2019] [Indexed: 01/12/2023] Open
Abstract
Lipid metabolism plays an important role in the regulation of cellular homeostasis. However, because it is difficult to measure the actual rates of synthesis and degradation of individual lipid species, lipid compositions are often used as a surrogate to evaluate lipid metabolism even though they provide only static snapshots of the lipodome. Here, we designed a simple method to determine the turnover rate of phospholipid and acylglycerol species based on the incorporation of 13C6-glucose combined with LC-MS/MS. We labeled adult Drosophila melanogaster with 13C6-glucose that incorporates into the entire lipidome, derived kinetic parameters from mass spectra, and studied effects of deletion of CG6718, the fly homolog of the calcium-independent phospholipase A2β, on lipid metabolism. Although 13C6-glucose gave rise to a complex pattern of 13C incorporation, we were able to identify discrete isotopomers in which 13C atoms were confined to the glycerol group. With these isotopomers, we calculated turnover rate constants, half-life times, and fluxes of the glycerol backbone of multiple lipid species. To perform these calculations, we estimated the fraction of labeled molecules in glycerol-3-phosphate, the lipid precursor, by mass isotopomer distribution analysis of the spectra of phosphatidylglycerol. When we applied this method to D. melanogaster, we found a range of lipid half-lives from 2 to 200 days, demonstrated tissue-specific fluxes of individual lipid species, and identified a novel function of CG6718 in triacylglycerol metabolism. This method provides fluxomics-type data with significant potential to improve the understanding of complex lipid regulation in a variety of research models.
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Affiliation(s)
- Michael Schlame
- Departments of Anesthesiology, New York University School of Medicine, New York, NY 10016; Cell Biology, New York University School of Medicine, New York, NY 10016.
| | - Yang Xu
- Departments of Anesthesiology, New York University School of Medicine, New York, NY 10016
| | - Hediye Erdjument-Bromage
- Cell Biology, New York University School of Medicine, New York, NY 10016; Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY 10016
| | - Thomas A Neubert
- Cell Biology, New York University School of Medicine, New York, NY 10016; Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY 10016
| | - Mindong Ren
- Departments of Anesthesiology, New York University School of Medicine, New York, NY 10016; Cell Biology, New York University School of Medicine, New York, NY 10016
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52
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Hervás G, Frutos P, Toral P. Endogenous synthesis of milk cis-9,trans-11 conjugated linoleic acid in dairy ewes: Quantification using 13C-labeled vaccenic acid and comparison with estimates based on cobalt administration. J Dairy Sci 2020; 103:368-378. [DOI: 10.3168/jds.2019-17050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 10/01/2019] [Indexed: 01/16/2023]
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53
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Allen DK, Young JD. Tracing metabolic flux through time and space with isotope labeling experiments. Curr Opin Biotechnol 2019; 64:92-100. [PMID: 31864070 PMCID: PMC7302994 DOI: 10.1016/j.copbio.2019.11.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 12/11/2022]
Abstract
Metabolism is dynamic and must function in context-specific ways to adjust to changes in the surrounding cellular and ecological environment. When isotopic tracers are used, metabolite flow (i.e. metabolic flux) can be quantified through biochemical networks to assess metabolic pathway operation. The cellular activities considered across multiple tissues and organs result in the observed phenotype and can be analyzed to discover emergent, whole-system properties of biology and elucidate misconceptions about network operation. However, temporal and spatial challenges remain significant hurdles and require novel approaches and creative solutions. We survey current investigations in higher plant and animal systems focused on dynamic isotope labeling experiments, spatially resolved measurement strategies, and observations from re-analysis of our own studies that suggest prospects for future work. Related discoveries will be necessary to push the frontier of our understanding of metabolism to suggest novel solutions to cure disease and feed a growing future world population.
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Affiliation(s)
- Doug K Allen
- United States Department of Agriculture-Agricultural Research Service, Plant Genetics Research Unit, 975 North Warson Road, St. Louis, MO 63132, United States; Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, United States.
| | - Jamey D Young
- Department of Chemical & Biomolecular Engineering, Vanderbilt University, PMB 351604, 2301 Vanderbilt Place, Nashville, TN 37235, United States; Department of Molecular Physiology & Biophysics, Vanderbilt University, PMB 351604, 2301 Vanderbilt Place, Nashville, TN 37235, United States.
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54
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Gokhale S, Lu W, Zhu S, Liu Y, Hart RP, Rabinowitz JD, Xie P. Elevated Choline Kinase α-Mediated Choline Metabolism Supports the Prolonged Survival of TRAF3-Deficient B Lymphocytes. THE JOURNAL OF IMMUNOLOGY 2019; 204:459-471. [PMID: 31826940 DOI: 10.4049/jimmunol.1900658] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/13/2019] [Indexed: 12/27/2022]
Abstract
Specific deletion of the tumor suppressor TRAF3 from B lymphocytes in mice leads to the prolonged survival of mature B cells and expanded B cell compartments in secondary lymphoid organs. In the current study, we investigated the metabolic basis of TRAF3-mediated regulation of B cell survival by employing metabolomic, lipidomic, and transcriptomic analyses. We compared the polar metabolites, lipids, and metabolic enzymes of resting splenic B cells purified from young adult B cell-specific Traf3 -/- and littermate control mice. We found that multiple metabolites, lipids, and enzymes regulated by TRAF3 in B cells are clustered in the choline metabolic pathway. Using stable isotope labeling, we demonstrated that phosphocholine and phosphatidylcholine biosynthesis was markedly elevated in Traf3 -/- mouse B cells and decreased in TRAF3-reconstituted human multiple myeloma cells. Furthermore, pharmacological inhibition of choline kinase α, an enzyme that catalyzes phosphocholine synthesis and was strikingly increased in Traf3 -/- B cells, substantially reversed the survival phenotype of Traf3 -/- B cells both in vitro and in vivo. Taken together, our results indicate that enhanced phosphocholine and phosphatidylcholine synthesis supports the prolonged survival of Traf3 -/- B lymphocytes. Our findings suggest that TRAF3-regulated choline metabolism has diagnostic and therapeutic value for B cell malignancies with TRAF3 deletions or relevant mutations.
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Affiliation(s)
- Samantha Gokhale
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854.,Graduate Program in Cellular and Molecular Pharmacology, Rutgers University, Piscataway, NJ 08854
| | - Wenyun Lu
- Department of Chemistry, Princeton University, Princeton, NJ 08544.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901; and
| | - Sining Zhu
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854.,Graduate Program in Cellular and Molecular Pharmacology, Rutgers University, Piscataway, NJ 08854
| | - Yingying Liu
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901; and.,W.M. Keck Center for Collaborative Neuroscience, Rutgers University, Piscataway, NJ 08854
| | - Joshua D Rabinowitz
- Department of Chemistry, Princeton University, Princeton, NJ 08544.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901; and
| | - Ping Xie
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854; .,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901; and
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55
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Dietary Bioactive Fatty Acids as Modulators of Immune Function: Implications on Human Health. Nutrients 2019; 11:nu11122974. [PMID: 31817430 PMCID: PMC6950193 DOI: 10.3390/nu11122974] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/05/2019] [Accepted: 11/20/2019] [Indexed: 12/11/2022] Open
Abstract
Diet is major modifiable risk factor for cardiovascular disease that can influence the immune status of the individual and contribute to persistent low-grade inflammation. In recent years, there has been an increased appreciation of the role of polyunsaturated fatty acids (PUFA) in improving immune function and reduction of systemic inflammation via the modulation of pattern recognition receptors (PRR) on immune cells. Extensive research on the use of bioactive lipids such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) and their metabolites have illustrated the importance of these pro-resolving lipid mediators in modulating signaling through PRRs. While their mechanism of action, bioavailability in the blood, and their efficacy for clinical use forms an active area of research, they are found widely administered as marine animal-based supplements like fish oil and krill oil to promote health. The focus of this review will be to discuss the effect of these bioactive fatty acids and their metabolites on immune cells and the resulting inflammatory response, with a brief discussion about modern methods for their analysis using mass spectrometry-based methods.
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56
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Xia Z, Zhou X, Li J, Li L, Ma Y, Wu Y, Huang Z, Li X, Xu P, Xue M. Multiple-Omics Techniques Reveal the Role of Glycerophospholipid Metabolic Pathway in the Response of Saccharomyces cerevisiae Against Hypoxic Stress. Front Microbiol 2019; 10:1398. [PMID: 31316482 PMCID: PMC6610297 DOI: 10.3389/fmicb.2019.01398] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/04/2019] [Indexed: 11/13/2022] Open
Abstract
Although the biological processes of organism under hypoxic stress had been elucidated, the whole physiological changes of Saccharomyces cerevisiae are still unclear. In this work, we investigated the changes of biological process of S. cerevisiae under hypoxia by the methods of transcriptomics, proteomics, metabolomics, and bioinformatics. The results showed that the expression of a total of 1017 mRNA in transcriptome, 213 proteins in proteome, and 51 metabolites in metabolome had been significantly changed between the hypoxia and normoxia conditions. Moreover, based on the integration of system-omics data, we found that the carbohydrate, amino acids, fatty acid biosynthesis, lipid metabolic pathway, and oxidative phosphorylation were significantly changed in hypoxic stress. Among these pathways, the glycerophospholipid metabolic pathway was remarkably up-regulated from the mRNA, protein, and metabolites levels under hypoxic stress, and the expression of relevant mRNA was also confirmed by the qPCR. The metabolites of glycerophospholipid pathway such as phosphatidylcholine, phosphatidylethanolamine, phosphoinositide, and phosphatidic acids probably maintained the stability of cell membranes against hypoxic stress to relieve the cell injury, and kept S. cerevisiae survive with energy production. These findings in the hypoxic omics and integrated networks provide very useful information for further exploring the molecular mechanism of hypoxic stress.
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Affiliation(s)
- Zhengchao Xia
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Xuelin Zhou
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Jingyi Li
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China.,Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Lei Li
- Central Laboratory, Capital Medical University, Beijing, China
| | - Yi Ma
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Yi Wu
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Zhong Huang
- Health Branch College, Lanzhou Modern Vocational College, Lanzhou, China
| | - Xiaorong Li
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Pingxiang Xu
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Ming Xue
- Department of Pharmacology, Beijing Laboratory for Biomedical Detection Technology and Instrument, School of Basic Medical Sciences, Capital Medical University, Beijing, China.,Beijing Engineering Research Center for Nerve System Drugs, Beijing, China
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57
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Watkins OC, Islam MO, Selvam P, Pillai RA, Cazenave-Gassiot A, Bendt AK, Karnani N, Godfrey KM, Lewis RM, Wenk MR, Chan SY. Metabolism of 13C-Labeled Fatty Acids in Term Human Placental Explants by Liquid Chromatography-Mass Spectrometry. Endocrinology 2019; 160:1394-1408. [PMID: 30920585 DOI: 10.1210/en.2018-01020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/21/2019] [Indexed: 12/18/2022]
Abstract
Placental lipid transport and metabolism are poorly understood despite the importance for fetal development and lifelong health. We aimed to explore fatty acid (FA) processing in human villous placental explants from seven uncomplicated term singleton pregnancies delivered by elective cesarean section. Explants were treated with stable isotope-labeled palmitic acid (13C-PA), oleic acid (13C-OA), or docosahexaenoic acid (13C-DHA) for 3, 24, or 48 hours. Stable isotope-labeled lipids synthesized by placental explants from labeled FA were quantified, alongside endogenous unlabeled placental lipids, by liquid chromatography-mass spectrometry. Labeled phosphatidylcholines (PCs), triacylglycerols (TAGs), and phosphatidylethanolamines were detected in explants, whereas labeled lysophosphatidylcholines were found in both explants and conditioned media. 13C-PA was primarily directed into PC synthesis (74% of 13C-PA-labeled lipids), whereas 13C-OA was directed almost equally into PC and TAG synthesis (45% and 53%, respectively, of 13C-OA-labeled lipids). 13C-DHA was only detectable in TAGs. TAGs demonstrated the highest isotopic enrichment for all 13C-FAs with 13C-OA-TAGs comprising >50% of total OA-TAGs (unlabeled and labeled), consistent with TAGs being a labile and accessible reservoir for FA storage. Variations in lipid incorporation were correlated to maternal glycemia and body mass index, suggesting that this experimental model could be used to investigate the effect of maternal factors on placental lipid metabolism. We conclude that lipid metabolic partitioning of freshly imported FAs into labile and less labile lipid reservoirs in placenta is FA dependent. This process may partly mediate the physiological preferential transplacental transfer of particular FAs to the fetus, but may also be implicated in the fetoplacental pathophysiology of maternal metabolic dysfunction.
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Affiliation(s)
- Oliver C Watkins
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mohammad Omedul Islam
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Preben Selvam
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Reshma Appukuttan Pillai
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Amaury Cazenave-Gassiot
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Anne K Bendt
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Neerja Karnani
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Singapore
| | - Keith M Godfrey
- MRC Lifecourse Epidemiology Unit and NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Rohan M Lewis
- MRC Lifecourse Epidemiology Unit and NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Markus R Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Shiao-Yng Chan
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore, Singapore
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58
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Liebisch G, Ecker J, Roth S, Schweizer S, Öttl V, Schött HF, Yoon H, Haller D, Holler E, Burkhardt R, Matysik S. Quantification of Fecal Short Chain Fatty Acids by Liquid Chromatography Tandem Mass Spectrometry-Investigation of Pre-Analytic Stability. Biomolecules 2019; 9:E121. [PMID: 30925749 PMCID: PMC6523859 DOI: 10.3390/biom9040121] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/13/2019] [Accepted: 03/25/2019] [Indexed: 01/12/2023] Open
Abstract
Short chain fatty acids (SCFAs) are generated by the degradation and fermentation of complex carbohydrates, (i.e., dietary fiber) by the gut microbiota relevant for microbe⁻host communication. Here, we present a method for the quantification of SCFAs in fecal samples by liquid chromatography tandem mass spectrometry (LC-MS/MS) upon derivatization to 3-nitrophenylhydrazones (3NPH). The method includes acetate, propionate, butyrate, and isobutyrate with a run time of 4 min. The reproducible (coefficients of variation (CV) below 10%) quantification of SCFAs in human fecal samples was achieved by the application of stable isotope labelled internal standards. The specificity was demonstrated by the introduction of a quantifier and qualifier ions. The method was applied to investigate the pre-analytic stability of SCFAs in human feces. Concentrations of SCFA may change substantially within hours; the degree and kinetics of these changes revealed huge differences between the donors. The fecal SCFA level could be preserved by the addition of organic solvents like isopropanol. An analysis of the colon content of mice either treated with antibiotics or fed with a diet containing a non-degradable and -fermentable fiber source showed decreased SCFA concentrations. In summary, this fast and reproducible method for the quantification of SCFA in fecal samples provides a valuable tool for both basic research and large-scale studies.
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Affiliation(s)
- Gerhard Liebisch
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany.
| | - Josef Ecker
- Nutritional Physiology, Technical University of Munich, 85354 Freising, Germany.
- ZIEL-Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
| | - Sebastian Roth
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany.
| | - Sabine Schweizer
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany.
| | - Veronika Öttl
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany.
| | - Hans-Frieder Schött
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany.
| | - Hongsup Yoon
- ZIEL-Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
- Chair of Nutrition and Immunology, Technical University of Munich, 85354 Freising, Germany.
| | - Dirk Haller
- ZIEL-Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
- Chair of Nutrition and Immunology, Technical University of Munich, 85354 Freising, Germany.
| | - Ernst Holler
- Department of Hematology and Oncology, Internal Medicine III, University Hospital Regensburg, 93053 Regensburg, Germany.
| | - Ralph Burkhardt
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany.
| | - Silke Matysik
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany.
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59
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Shi G, Chen L, Chen G, Zou C, Li J, Li M, Fang C, Li C. Identification and Functional Prediction of Long Intergenic Non-coding RNAs Related to Subcutaneous Adipose Development in Pigs. Front Genet 2019; 10:160. [PMID: 30886630 PMCID: PMC6409335 DOI: 10.3389/fgene.2019.00160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/14/2019] [Indexed: 12/19/2022] Open
Abstract
An increasing number of studies have shown that long intergenic non-coding RNAs (lincRNAs) are a very important class of non-coding RNAs that plays a vital role in many biological processes. Adipose tissue is an important place for storing energy, but few studies on lincRNAs were related to pig subcutaneous fat development. Here, we used published RNA-seq data from subcutaneous adipose tissue of Italian Large White pigs and identified 252 putative lincRNAs, wherein 34 were unannotated. These lincRNAs had relatively shorter length, lower number of exons, and lower expression level compared with protein-coding transcripts. Gene ontology and pathway analysis indicated that the adjacent genes of lincRNAs were involved in lipid metabolism. In addition, differentially expressed lincRNAs (DELs) between low and high backfat thickness pigs were identified. Through the detection of quantitative trait locus (QTL), DELs were mainly located in QTLs related to adipose development. Based on the expression correlation of DEL genes and their differentially expressed potential target genes, we constructed a co-expression network and a potential pathway of DEL's effect on lipid metabolism. Our study identified and analyzed lincRNAs in subcutaneous adipose tissue, and results suggested that lincRNAs may be involved in the regulation of subcutaneous fat development. Our findings provided new insights into the biological function of porcine lincRNAs.
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Affiliation(s)
- Gaoli Shi
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Lin Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Guoting Chen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Cheng Zou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Jingxuan Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Mengxun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Chengchi Fang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China
| | - Changchun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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60
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Artegoitia VM, Foote AP, Lewis RM, Freetly HC. Metabolomics Profile and Targeted Lipidomics in Multiple Tissues Associated with Feed Efficiency in Beef Steers. ACS OMEGA 2019; 4:3973-3982. [PMID: 31459606 PMCID: PMC6648084 DOI: 10.1021/acsomega.8b02494] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 12/14/2018] [Indexed: 05/13/2023]
Abstract
A study of multiple tissues was conducted to identify potential metabolic differences in cattle differing in feed efficiency. Individual feed intake and body weight was measured on 144 steers during 105 days on a high-concentrate ration. Steers were selected according to differences in average daily gain (ADG) with those with the greatest ADG (n = 8; 1.96 ± 0.02 kg/day) and least ADG (n = 8; 1.57 ± 0.02 kg/day), whose dry matter intake was within 0.32 SD of the mean intake (10.10 ± 0.05 kg/day). Duodenum, liver, adipose, and longissimus-dorsi were collected at slaughter, and metabolomics profiles were performed by ultra performance liquid chromatography quadrupole-time of-flight mass spectrometry. Principal components analyses, t-tests, and fold changes in tissues profile were used to identify differential metabolites between ADG groups. These were primarily involved in α-linolenic metabolism, which was downregulated in the greatest ADG as compared to least-ADG group in duodenum, adipose, and longissimus-dorsi. However, taurine and glycerophospholipids metabolisms were both upregulated in the greatest ADG compared with least-ADG group in the liver. The phospholipids and cholesterol were quantified in the tissues. Lipid transport and oxidation were the main common metabolic mechanisms associated with cattle feed efficiency. Combining analyses of multiple tissues may offer a powerful approach for defining the molecular basis of differences in performance among cattle for key production attributes.
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Affiliation(s)
- Virginia M. Artegoitia
- Department
of Animal Science, University of Nebraska-Lincoln, Lincoln, Nebraska 68583, United States
- E-mail:
| | - Andrew P. Foote
- ARS,
U.S. Meat Animal Research Center, USDA, Clay Center, Nebraska 68933, United States
| | - Ronald M. Lewis
- Department
of Animal Science, University of Nebraska-Lincoln, Lincoln, Nebraska 68583, United States
| | - Harvey C. Freetly
- ARS,
U.S. Meat Animal Research Center, USDA, Clay Center, Nebraska 68933, United States
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61
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Li H, Wang Y, Meng Q, Wang Y, Xia G, Xia X, Shen J. Comprehensive proteomic and metabolomic profiling of mcr-1-mediated colistin resistance in Escherichia coli. Int J Antimicrob Agents 2019; 53:795-804. [PMID: 30811973 DOI: 10.1016/j.ijantimicag.2019.02.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 02/15/2019] [Accepted: 02/16/2019] [Indexed: 12/15/2022]
Abstract
Spread of the mcr-1 gene in human and veterinary medicine has jeopardised the use of polymyxins, last-resort antibiotics against life-threatening multidrug-resistant Gram-negative bacteria. As a lipid-modifying gene, whether mcr-1 causes proteomic and metabolomic changes in bacteria and affects the corresponding metabolic pathway is largely unknown. In this study, label-free quantitative proteomics and untargeted metabolomics were used to profile comprehensive proteome and metabolome characteristics of mcr-1-mediated colistin-resistant and -susceptible Escherichia coli in order to gain further insight into the colistin resistance mechanism. Large sets of differentially expressed proteins (DEPs) and metabolites were identified that contributed to mcr-1-mediated antimicrobial resistance, predominantly in different growth conditions with and without colistin. mcr-1 caused downregulated expression of most proteins in order to adapt to drug pressure. Pathway analysis showed that metabolic processes were significantly affected, mainly related to glycerophospholipid metabolism, thiamine metabolism and lipopolysaccharide (LPS) biosynthesis. The substrate phosphoethanolamine (PEA) for mcr-1 to mediate colistin resistance was accumulated in colistin-resistant E. coli. Notably, mcr-1 not only caused PEA modification of the bacterial cell membrane lipid A but also affected the biosynthesis and transport of lipoprotein in colistin resistance by disturbing the expression of efflux pump proteins involved in the cationic antimicrobial peptide (CAMP) resistance pathway. Overall, disturbed glycerophospholipid metabolism and LPS biosynthesis as well as accumulation of the substrate PEA was closely related with mcr-1-mediated colistin resistance. These findings could provide further valuable information to inhibit colistin resistance by blocking this metabolic process.
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Affiliation(s)
- Hui Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China; Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing Center for Disease Prevention and Control, Beijing, China
| | - Yingyu Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qingshi Meng
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yang Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, China Agricultural University, Beijing, China
| | - Guoliang Xia
- State Key Laboratory of Agrobiotechnology, College of Biological Science, China Agricultural University, Beijing, China
| | - Xi Xia
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.
| | - Jianzhong Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.
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62
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Retention time bracketing for targeted sphingolipidomics by liquid chromatography-tandem mass spectrometry. Bioanalysis 2019; 11:185-201. [PMID: 30661375 DOI: 10.4155/bio-2018-0036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Aim: In complex biological matrixes, many sphingolipids are present with multiple reaction monitoring traces or lack of standard for verification, potentially leading to inaccurate identification and quantitation. Results/methodology: Based on these retention times of available standards, we devised a retention time bracketing approach to identify and predict sphingolipids of the same homologous series. Excellent concordance of predicted and observed retention times (<0.1 min) of sphingolipids were demonstrated. We also showed that many odd- and/or short-chain sphingolipids, commonly used as internal standards, are present in biological matrices including human serum, peritoneal fluid and cells. Conclusion: A retention time table, and a list of appropriate standards are presented, which are expected to be useful resources in targeted sphingolipidomics.
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63
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Liu L, Yin TL, Chen Y, Li Y, Yin L, Ding J, Yang J, Feng HL. Follicular dynamics of glycerophospholipid and sphingolipid metabolisms in polycystic ovary syndrome patients. J Steroid Biochem Mol Biol 2019; 185:142-149. [PMID: 30121347 DOI: 10.1016/j.jsbmb.2018.08.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 07/28/2018] [Accepted: 08/14/2018] [Indexed: 01/09/2023]
Abstract
Polycystic ovary syndrome (PCOS) is a common heterogeneous disease, affecting up to 5-10% women at reproductive age. Although PCOS patients could produce morphologically normal metaphase II oocytes undergoing assisted reproductive techniques (ART), oocyte developmental competence and embryo development have been impaired in following in-vitro fertilization (IVF) steps. Follicular fluid (FF) provides a variety of information in oocyte environment when oocytes grow. In the present work, based on ultra-performance liquid chromatography coupled with mass spectrometry (UPLC-MS), the metabolic signatures of PCOS FF have been compared with healthy women using untargeted metabolomics approach. Significant abundance differences of a series of glycerolipid, glycerophospholipids, sphingolipids, and carboxylic acids have been discovered. Among them, reduced levels of phosphatidylglycerolphosphate (PGP) and a triglyceride (TG) were highly related to the lower fertilization rate in PCOS; increased abundance of lysoPE and decreased amount of PC were significantly correlated with LH/FSH (ratio of luteinizing hormone to follicle stimulating hormone). Some metabolites, including decreased sphingolipids, glycerophospholipids, and fluctuated fatty acyls, also performed close relationship with other ART and clinical results. We concluded that dysfunctions in the metabolism of glycerolipid, glycerophospholipid, sphingolipid, and glycosphingolipid biosynthesis in PCOS patients' follicles play a non-ignorable role in declining the 2 pronuclei (PN) fertilization rate during IVF procedure.
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Affiliation(s)
- Lingyan Liu
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, College of Pharmaceutical Sciences, Capital Medical University, Beijing 100069, PR China
| | - Tai-Lang Yin
- Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China.
| | - Yu Chen
- Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China; Reproductive Medicine Center, Wuhan Children's Hospital(Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Yinghuan Li
- Beijing Area Major Laboratory of Peptide and Small Molecular Drugs, Engineering Research Center of Endogenous Prophylactic of Ministry of Education of China, College of Pharmaceutical Sciences, Capital Medical University, Beijing 100069, PR China
| | - Lu Yin
- Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Jinli Ding
- Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China
| | - Jing Yang
- Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China.
| | - Huai-L Feng
- The New York Fertility Center, New York-Presbyterian Queens Affiliate with Weill Medical College of Cornell University, NY, United States.
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64
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Russo R, Haange SB, Rolle-Kampczyk U, von Bergen M, Becker JM, Liess M. Identification of pesticide exposure-induced metabolic changes in mosquito larvae. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 643:1533-1541. [PMID: 30189569 DOI: 10.1016/j.scitotenv.2018.06.282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/22/2018] [Accepted: 06/22/2018] [Indexed: 06/08/2023]
Abstract
The European regulatory framework for pesticides generally applies an assessment factor of up to 100 below the acute median lethal concentration (LC50) in laboratory tests to predict the regulatory acceptable concentrations (RACs). However, long-term detrimental effects of pesticides in the environment occur far below the RACs. Here, we explored the metabolic changes induced by exposure to the neonicotinoid insecticide clothianidin in larvae of the mosquito Culex pipiens. We exposed the test organisms to the insecticide for 24 h and then measured the levels of 184 metabolites immediately and 48 h after the pulse contamination. We established a link between the exposure to clothianidin and changes in the level of three specific classes of metabolites involved in energy metabolism, namely, glycerophospholipids, acylcarnitines and biogenic amines. Remarkably, exposure to concentrations considered to be safe according to the regulatory framework (2-4 orders of magnitude lower than the acute LC50), induced longer-term effects than exposure to the highest concentration. These results suggest that a specific detoxification mechanism was only triggered by the highest concentration. We conclude that even very low insecticide concentrations increase the energy demands of exposed organisms, which potentially translates into a decline in sensitive species in the field.
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Affiliation(s)
- Renato Russo
- UFZ, Helmholtz Centre for Environmental Research, Department of System-Ecotoxicology, Permoserstraße 15, 04318 Leipzig, Germany; RWTH Aachen University, Institute for Environmental Research (Biology V), Worringerweg 1, 52074 Aachen, Germany
| | - Sven-Bastiaan Haange
- UFZ, Helmholtz Centre for Environmental Research, Department of Molecular System Biology, Permoserstraße 15, 04318 Leipzig, Germany; University of Leipzig, Institute of Biochemistry, Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- UFZ, Helmholtz Centre for Environmental Research, Department of Molecular System Biology, Permoserstraße 15, 04318 Leipzig, Germany
| | - Martin von Bergen
- UFZ, Helmholtz Centre for Environmental Research, Department of Molecular System Biology, Permoserstraße 15, 04318 Leipzig, Germany
| | - Jeremias Martin Becker
- UFZ, Helmholtz Centre for Environmental Research, Department of System-Ecotoxicology, Permoserstraße 15, 04318 Leipzig, Germany; RWTH Aachen University, Institute for Environmental Research (Biology V), Worringerweg 1, 52074 Aachen, Germany
| | - Matthias Liess
- UFZ, Helmholtz Centre for Environmental Research, Department of System-Ecotoxicology, Permoserstraße 15, 04318 Leipzig, Germany; RWTH Aachen University, Institute for Environmental Research (Biology V), Worringerweg 1, 52074 Aachen, Germany.
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65
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Triebl A, Wenk MR. Analytical Considerations of Stable Isotope Labelling in Lipidomics. Biomolecules 2018; 8:biom8040151. [PMID: 30453585 PMCID: PMC6315579 DOI: 10.3390/biom8040151] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 12/26/2022] Open
Abstract
Over the last two decades, lipids have come to be understood as far more than merely components of cellular membranes and forms of energy storage, and are now also being implicated to play important roles in a variety of diseases, with lipid biomarker research one of the most widespread applications of lipidomic techniques both in research and in clinical settings. Stable isotope labelling has become a staple technique in the analysis of small molecule metabolism and dynamics, as it is the only experimental setup by which biosynthesis, remodelling and degradation of biomolecules can be directly measured. Using state-of-the-art analytical technologies such as chromatography-coupled high resolution tandem mass spectrometry, the stable isotope label can be precisely localized and quantified within the biomolecules. The application of stable isotope labelling to lipidomics is however complicated by the diversity of lipids and the complexity of the necessary data analysis. This article discusses key experimental aspects of stable isotope labelling in the field of mass spectrometry-based lipidomics, summarizes current applications and provides an outlook on future developments and potential.
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Affiliation(s)
- Alexander Triebl
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore; Singapore 117596, Singapore.
| | - Markus R Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore; Singapore 117596, Singapore.
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66
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Kindt A, Liebisch G, Clavel T, Haller D, Hörmannsperger G, Yoon H, Kolmeder D, Sigruener A, Krautbauer S, Seeliger C, Ganzha A, Schweizer S, Morisset R, Strowig T, Daniel H, Helm D, Küster B, Krumsiek J, Ecker J. The gut microbiota promotes hepatic fatty acid desaturation and elongation in mice. Nat Commun 2018; 9:3760. [PMID: 30218046 PMCID: PMC6138742 DOI: 10.1038/s41467-018-05767-4] [Citation(s) in RCA: 167] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 07/05/2018] [Accepted: 07/25/2018] [Indexed: 02/06/2023] Open
Abstract
Interactions between the gut microbial ecosystem and host lipid homeostasis are highly relevant to host physiology and metabolic diseases. We present a comprehensive multi-omics view of the effect of intestinal microbial colonization on hepatic lipid metabolism, integrating transcriptomic, proteomic, phosphoproteomic, and lipidomic analyses of liver and plasma samples from germfree and specific pathogen-free mice. Microbes induce monounsaturated fatty acid generation by stearoyl-CoA desaturase 1 and polyunsaturated fatty acid elongation by fatty acid elongase 5, leading to significant alterations in glycerophospholipid acyl-chain profiles. A composite classification score calculated from the observed alterations in fatty acid profiles in germfree mice clearly differentiates antibiotic-treated mice from untreated controls with high sensitivity. Mechanistic investigations reveal that acetate originating from gut microbial degradation of dietary fiber serves as precursor for hepatic synthesis of C16 and C18 fatty acids and their related glycerophospholipid species that are also released into the circulation.
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Affiliation(s)
- Alida Kindt
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, 85764, Germany.,Department of Analytical Biosciences, Leiden Academic Centre for Drug Research, Leiden University, Leiden, 2333, Netherlands
| | - Gerhard Liebisch
- Institute of Clinical Chemistry, Universitätsklinikum Regensburg, Regensburg, 93053, Germany
| | - Thomas Clavel
- Functional Microbiome Research Group, Institute of Medical Microbiology, Universitätsklinikum Aachen, Aachen, 52074, Germany.,ZIEL Institute for Food and Health, Technische Universität München (TUM), Freising, 85354, Germany
| | - Dirk Haller
- ZIEL Institute for Food and Health, Technische Universität München (TUM), Freising, 85354, Germany.,Ernährung und Immunologie, Technische Universität München (TUM), Freising, 85354, Germany
| | - Gabriele Hörmannsperger
- ZIEL Institute for Food and Health, Technische Universität München (TUM), Freising, 85354, Germany.,Ernährung und Immunologie, Technische Universität München (TUM), Freising, 85354, Germany
| | - Hongsup Yoon
- ZIEL Institute for Food and Health, Technische Universität München (TUM), Freising, 85354, Germany.,Ernährung und Immunologie, Technische Universität München (TUM), Freising, 85354, Germany
| | - Daniela Kolmeder
- Ernährungsphysiologie, Technische Universität München (TUM), Freising, 85354, Germany
| | - Alexander Sigruener
- Institute of Clinical Chemistry, Universitätsklinikum Regensburg, Regensburg, 93053, Germany
| | - Sabrina Krautbauer
- Institute of Clinical Chemistry, Universitätsklinikum Regensburg, Regensburg, 93053, Germany
| | - Claudine Seeliger
- Ernährungsphysiologie, Technische Universität München (TUM), Freising, 85354, Germany
| | - Alexandra Ganzha
- Ernährungsphysiologie, Technische Universität München (TUM), Freising, 85354, Germany
| | - Sabine Schweizer
- Ernährungsphysiologie, Technische Universität München (TUM), Freising, 85354, Germany
| | - Rosalie Morisset
- Ernährungsphysiologie, Technische Universität München (TUM), Freising, 85354, Germany
| | - Till Strowig
- Research Group Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, 38124, Germany
| | - Hannelore Daniel
- Ernährungsphysiologie, Technische Universität München (TUM), Freising, 85354, Germany
| | - Dominic Helm
- Proteomics and Bioanalytics, Technische Universität München (TUM), Freising, 85354, Germany
| | - Bernhard Küster
- Proteomics and Bioanalytics, Technische Universität München (TUM), Freising, 85354, Germany
| | - Jan Krumsiek
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, 85764, Germany. .,German Center for Diabetes Research (DZD), Neuherberg, 85764, Germany. .,Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, 10021, USA.
| | - Josef Ecker
- Ernährungsphysiologie, Technische Universität München (TUM), Freising, 85354, Germany.
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67
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Zhang ZH, Li MH, Liu D, Chen H, Chen DQ, Tan NH, Ma SC, Zhao YY. Rhubarb Protect Against Tubulointerstitial Fibrosis by Inhibiting TGF-β/Smad Pathway and Improving Abnormal Metabolome in Chronic Kidney Disease. Front Pharmacol 2018; 9:1029. [PMID: 30271345 PMCID: PMC6146043 DOI: 10.3389/fphar.2018.01029] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 08/24/2018] [Indexed: 12/01/2022] Open
Abstract
Tubulointerstitial fibrosis is the final common pathway for all kidney diseases leading to chronic kidney disease (CKD). TGF-β/Smad signaling pathway plays a key role in renal fibrosis. Previous studies have revealed that rhubarb extracts attenuated the increase of transforming growth factor-β 1 (TGF-β1) in CKD rats. To gain an in-depth insight into the mechanism of the anti-fibrotic activities of the rhubarb extracts, we investigated the influence of rhubarb extracts on TGF-β/Smad signaling pathway and the influence on metabolome in a rat model of CKD with adenine-induced chronic tubulointerstitial nephropathy. Male Sprague-Dawley rats were divided into four groups, including control, CKD, CKD + petroleum ether extract, CKD + ethyl acetate extract, and CKD + n-butanol extract groups. Kidneys harvested on the week three were evaluated for renal fibrosis, the expression of proteins in TGF-β/Smad signaling pathway and metabolomic study. We found rhubarb extracts suppressed TGF-β/Smad3-mediated renal fibrosis by reducing the TGF-β1, transforming growth factor-β receptor I (TGF-β RI), transforming growth factor-β receptor II (TGF-β RII), Smad2, p-Smad2, Smad3, p-Smad3, and Smad4, meanwhile increased Smad7. In addition, rhubarb extracts mitigated renal injury and dysfunction, and either fully or partially reversed the abnormalities of tissue metabolites. Thus, rebalancing the disorder of TGF-β/Smad signaling and metabolic dysfunction by treatment with rhubarb extracts may represent as an effective therapy for CKD associated with fibrosis.
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Affiliation(s)
- Zhi-Hao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China.,State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Ming-Hua Li
- National Institutes for Food and Drug Control, State Food and Drug Administration, Beijing, China
| | - Dan Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
| | - Hua Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
| | - Dan-Qian Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
| | - Ning-Hua Tan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Shuang-Cheng Ma
- National Institutes for Food and Drug Control, State Food and Drug Administration, Beijing, China
| | - Ying-Yong Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Sciences, Northwest University, Xi'an, China
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68
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Chen Y, Berejnaia O, Liu J, Wang SP, Daurio NA, Yin W, Mayoral R, Petrov A, Kasumov T, Zhang GF, Previs SF, Kelley DE, McLaren DG. Quantifying ceramide kinetics in vivo using stable isotope tracers and LC-MS/MS. Am J Physiol Endocrinol Metab 2018; 315:E416-E424. [PMID: 29509438 DOI: 10.1152/ajpendo.00457.2017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Numerous studies have implicated dyslipidemia as a key factor in mediating insulin resistance. Ceramides have received special attention since their levels are inversely associated with normal insulin signaling and positively associated with factors that are involved in cardiometabolic disease. Despite the growing literature surrounding ceramide biology, there are limited data regarding the activity of ceramide synthesis and turnover in vivo. Herein, we demonstrate the ability to measure ceramide kinetics by coupling the administration of [2H]water with LC-MS/MS analyses. As a "proof-of-concept" we determined the effect of a diet-induced alteration on ceramide flux; studies also examined the effect of myriocin (a known inhibitor of serine palmitoyltransferase, the first step in sphingosine biosynthesis). Our data suggest that one can estimate ceramide synthesis and draw conclusions regarding the source of fatty acids; we discuss caveats in regards to method development in this area.
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Affiliation(s)
- Ying Chen
- MRL, Merck & Co., Inc., Kenilworth, New Jersey
| | | | - Jinqi Liu
- MRL, Merck & Co., Inc., Kenilworth, New Jersey
| | | | | | - Wu Yin
- MRL, Merck & Co., Inc., Kenilworth, New Jersey
| | | | | | - Takhar Kasumov
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio
| | - Guo-Fang Zhang
- Division of Endocrinology, Metabolism and Nutrition, Duke Molecular Physiology Institute, and Department of Medicine, Duke University , Durham, North Carolina
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69
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Gu J, Ji C, Yue S, Shu D, Su F, Zhang Y, Xie Y, Zhang Y, Liu W, Zhao M. Enantioselective Effects of Metalaxyl Enantiomers in Adolescent Rat Metabolic Profiles Using NMR-Based Metabolomics. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5438-5447. [PMID: 29683314 DOI: 10.1021/acs.est.7b06540] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
More than 30% of the registered pesticides are chiral with one or more chiral centers and exist as two or more enantiomers. The frequency of chiral chemicals and their environmental safety has been considered in their risk assessment in recent decades. Despite the fact that metabolic disturbance is an important sensitive molecular initiating event of toxicology effects, the potential mechanisms of how chiral compounds affect metabolism phenotypes in organisms remain unclear. As a typical chiral pesticide, metalaxyl is an acylalanine fungicide with systemic function. Although the fungicidal activity almost comes from the R-enantiomer, the toxicity of both enantiomers in animals and human beings is not yet clear. In this study, a nuclear magnetic resonance (NMR)-based metabolomics approach was adopted to evaluate the enantioselectivity in metabolic perturbations in adolescent rats. On the basis of multivariate statistical results, stable and evident metabolic profiles of the enantiomers were obtained. When rats were exposed to R-metalaxyl, the significantly perturbed metabolic pathways were biosynthesis of valine, leucine, and isoleucine, synthesis and degradation of ketone bodies, and metabolism of glycerolipid. In contrast, more significantly perturbed metabolic pathways were obtained when the rats were exposed to S-metalaxyl, including glycolysis, biosynthesis of valine, leucine, and isoleucine, metabolism of glycine, serine, and threonine, synthesis and degradation of ketone bodies, metabolism of glycerophospholipid and glycerolipid. These abnormal metabolic pathways were closely related to liver metabolism. These results offer more detailed information about the enantioselective metabolic effects of metalaxyl in adolescent development and provide data for the health risk assessment of metalaxyl at molecular level.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Weiping Liu
- College of Environment & Resource Sciences , Zhejiang University , Hangzhou 310058 , China
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70
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Atzrodt J, Derdau V, Kerr WJ, Reid M. Deuterium- und tritiummarkierte Verbindungen: Anwendungen in den modernen Biowissenschaften. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201704146] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jens Atzrodt
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry; Industriepark Höchst, G876 65926 Frankfurt Deutschland
| | - Volker Derdau
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry; Industriepark Höchst, G876 65926 Frankfurt Deutschland
| | - William J. Kerr
- Department of Pure and Applied Chemistry, WestCHEM; University of Strathclyde; 295 Cathedral Street Glasgow Scotland G1 1XL Großbritannien
| | - Marc Reid
- Department of Pure and Applied Chemistry, WestCHEM; University of Strathclyde; 295 Cathedral Street Glasgow Scotland G1 1XL Großbritannien
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71
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Atzrodt J, Derdau V, Kerr WJ, Reid M. Deuterium- and Tritium-Labelled Compounds: Applications in the Life Sciences. Angew Chem Int Ed Engl 2018; 57:1758-1784. [PMID: 28815899 DOI: 10.1002/anie.201704146] [Citation(s) in RCA: 407] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/27/2017] [Indexed: 12/19/2022]
Abstract
Hydrogen isotopes are unique tools for identifying and understanding biological and chemical processes. Hydrogen isotope labelling allows for the traceless and direct incorporation of an additional mass or radioactive tag into an organic molecule with almost no changes in its chemical structure, physical properties, or biological activity. Using deuterium-labelled isotopologues to study the unique mass-spectrometric patterns generated from mixtures of biologically relevant molecules drastically simplifies analysis. Such methods are now providing unprecedented levels of insight in a wide and continuously growing range of applications in the life sciences and beyond. Tritium (3 H), in particular, has seen an increase in utilization, especially in pharmaceutical drug discovery. The efforts and costs associated with the synthesis of labelled compounds are more than compensated for by the enhanced molecular sensitivity during analysis and the high reliability of the data obtained. In this Review, advances in the application of hydrogen isotopes in the life sciences are described.
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Affiliation(s)
- Jens Atzrodt
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry, Industriepark Höchst, G876, 65926, Frankfurt, Germany
| | - Volker Derdau
- Isotope Chemistry and Metabolite Synthesis, Integrated Drug Discovery, Medicinal Chemistry, Industriepark Höchst, G876, 65926, Frankfurt, Germany
| | - William J Kerr
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, Scotland, G1 1XL, UK
| | - Marc Reid
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow, Scotland, G1 1XL, UK
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72
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Wilkinson DJ. Historical and contemporary stable isotope tracer approaches to studying mammalian protein metabolism. MASS SPECTROMETRY REVIEWS 2018; 37:57-80. [PMID: 27182900 PMCID: PMC5763415 DOI: 10.1002/mas.21507] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 04/22/2016] [Indexed: 06/05/2023]
Abstract
Over a century ago, Frederick Soddy provided the first evidence for the existence of isotopes; elements that occupy the same position in the periodic table are essentially chemically identical but differ in mass due to a different number of neutrons within the atomic nucleus. Allied to the discovery of isotopes was the development of some of the first forms of mass spectrometers, driven forward by the Nobel laureates JJ Thomson and FW Aston, enabling the accurate separation, identification, and quantification of the relative abundance of these isotopes. As a result, within a few years, the number of known isotopes both stable and radioactive had greatly increased and there are now over 300 stable or radioisotopes presently known. Unknown at the time, however, was the potential utility of these isotopes within biological disciplines, it was soon discovered that these stable isotopes, particularly those of carbon (13 C), nitrogen (15 N), oxygen (18 O), and hydrogen (2 H) could be chemically introduced into organic compounds, such as fatty acids, amino acids, and sugars, and used to "trace" the metabolic fate of these compounds within biological systems. From this important breakthrough, the age of the isotope tracer was born. Over the following 80 yrs, stable isotopes would become a vital tool in not only the biological sciences, but also areas as diverse as forensics, geology, and art. This progress has been almost exclusively driven through the development of new and innovative mass spectrometry equipment from IRMS to GC-MS to LC-MS, which has allowed for the accurate quantitation of isotopic abundance within samples of complex matrices. This historical review details the development of stable isotope tracers as metabolic tools, with particular reference to their use in monitoring protein metabolism, highlighting the unique array of tools that are now available for the investigation of protein metabolism in vivo at a whole body down to a single protein level. Importantly, it will detail how this development has been closely aligned to the technological development within the area of mass spectrometry. Without the dedicated development provided by these mass spectrometrists over the past century, the use of stable isotope tracers within the field of protein metabolism would not be as widely applied as it is today, this relationship will no doubt continue to flourish in the future and stable isotope tracers will maintain their importance as a tool within the biological sciences for many years to come. © 2016 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc. Mass Spec Rev.
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Affiliation(s)
- Daniel James Wilkinson
- MRC‐ARUK Centre for Musculoskeletal Ageing Research, Clinical, Metabolic and Molecular PhysiologyUniversity of Nottingham, Royal Derby Hospital CentreDerbyUnited Kingdom
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73
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Schuhmann K, Srzentić K, Nagornov KO, Thomas H, Gutmann T, Coskun Ü, Tsybin YO, Shevchenko A. Monitoring Membrane Lipidome Turnover by Metabolic 15N Labeling and Shotgun Ultra-High-Resolution Orbitrap Fourier Transform Mass Spectrometry. Anal Chem 2017; 89:12857-12865. [PMID: 29111682 DOI: 10.1021/acs.analchem.7b03437] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lipidomes undergo permanent extensive remodeling, but how the turnover rate differs between lipid classes and molecular species is poorly understood. We employed metabolic 15N labeling and shotgun ultra-high-resolution mass spectrometry (sUHR) to quantify the absolute (molar) abundance and determine the turnover rate of glycerophospholipids and sphingolipids by direct analysis of total lipid extracts. sUHR performed on a commercial Orbitrap Elite instrument at the mass resolution of 1.35 × 106 (m/z 200) baseline resolved peaks of 13C isotopes of unlabeled and monoisotopic peaks of 15N labeled lipids (Δm = 0.0063 Da). Therefore, the rate of metabolic 15N labeling of individual lipid species could be determined without compromising the scope, accuracy, and dynamic range of full-lipidome quantitative shotgun profiling. As a proof of concept, we employed sUHR to determine the lipidome composition and fluxes of 62 nitrogen-containing membrane lipids in human hepatoma HepG2 cells.
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Affiliation(s)
- Kai Schuhmann
- Max Planck Institute of Molecular Cell Biology and Genetics , Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Kristina Srzentić
- Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | | | - Henrik Thomas
- Max Planck Institute of Molecular Cell Biology and Genetics , Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Theresia Gutmann
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden , Fetscher Strasse 74, 01307 Dresden, Germany.,German Center for Diabetes Research , Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Ünal Coskun
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden , Fetscher Strasse 74, 01307 Dresden, Germany.,German Center for Diabetes Research , Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Yury O Tsybin
- Spectroswiss , EPFL Innovation Park, Building I, 1015 Lausanne, Switzerland
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics , Pfotenhauerstrasse 108, 01307 Dresden, Germany
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74
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Pauling JK, Hermansson M, Hartler J, Christiansen K, Gallego SF, Peng B, Ahrends R, Ejsing CS. Proposal for a common nomenclature for fragment ions in mass spectra of lipids. PLoS One 2017; 12:e0188394. [PMID: 29161304 PMCID: PMC5697860 DOI: 10.1371/journal.pone.0188394] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/20/2017] [Indexed: 12/16/2022] Open
Abstract
Advances in mass spectrometry-based lipidomics have in recent years prompted efforts to standardize the annotation of the vast number of lipid molecules that can be detected in biological systems. These efforts have focused on cataloguing, naming and drawing chemical structures of intact lipid molecules, but have provided no guidelines for annotation of lipid fragment ions detected using tandem and multi-stage mass spectrometry, albeit these fragment ions are mandatory for structural elucidation and high confidence lipid identification, especially in high throughput lipidomics workflows. Here we propose a nomenclature for the annotation of lipid fragment ions, describe its implementation and present a freely available web application, termed ALEX123 lipid calculator, that can be used to query a comprehensive database featuring curated lipid fragmentation information for more than 430,000 potential lipid molecules from 47 lipid classes covering five lipid categories. We note that the nomenclature is generic, extendable to stable isotope-labeled lipid molecules and applicable to automated annotation of fragment ions detected by most contemporary lipidomics platforms, including LC-MS/MS-based routines.
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Affiliation(s)
- Josch K. Pauling
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Martin Hermansson
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Jürgen Hartler
- Institute of Computational Biotechnology, Graz University of Technology, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Graz, Austria
| | - Klaus Christiansen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Sandra F. Gallego
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Bing Peng
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Dortmund, Germany
| | - Christer S. Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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75
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Hu T, Zhang JL. Mass-spectrometry-based lipidomics. J Sep Sci 2017; 41:351-372. [PMID: 28859259 DOI: 10.1002/jssc.201700709] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 01/09/2023]
Abstract
Lipids, which have a core function in energy storage, signalling and biofilm structures, play important roles in a variety of cellular processes because of the great diversity of their structural and physiochemical properties. Lipidomics is the large-scale profiling and quantification of biogenic lipid molecules, the comprehensive study of their pathways and the interpretation of their physiological significance based on analytical chemistry and statistical analysis. Lipidomics will not only provide insight into the physiological functions of lipid molecules but will also provide an approach to discovering important biomarkers for diagnosis or treatment of human diseases. Mass-spectrometry-based analytical techniques are currently the most widely used and most effective tools for lipid profiling and quantification. In this review, the field of mass-spectrometry-based lipidomics was discussed. Recent progress in all essential steps in lipidomics was carefully discussed in this review, including lipid extraction strategies, separation techniques and mass-spectrometry-based analytical and quantitative methods in lipidomics. We also focused on novel resolution strategies for difficult problems in determining C=C bond positions in lipidomics. Finally, new technologies that were developed in recent years including single-cell lipidomics, flux-based lipidomics and multiomics technologies were also reviewed.
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Affiliation(s)
- Ting Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, PR China
| | - Jin-Lan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, PR China
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76
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Brandsma J, Bailey AP, Koster G, Gould AP, Postle AD. Stable isotope analysis of dynamic lipidomics. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:792-796. [PMID: 28302590 DOI: 10.1016/j.bbalip.2017.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/07/2017] [Accepted: 03/09/2017] [Indexed: 11/28/2022]
Abstract
Metabolic pathway flux is a fundamental element of biological activity, which can be quantified using a variety of mass spectrometric techniques to monitor incorporation of stable isotope-labelled substrates into metabolic products. This article contrasts developments in electrospray ionisation mass spectrometry (ESI-MS) for the measurement of lipid metabolism with more established gas chromatography mass spectrometry and isotope ratio mass spectrometry methodologies. ESI-MS combined with diagnostic tandem MS/MS scans permits the sensitive and specific analysis of stable isotope-labelled substrates into intact lipid molecular species without the requirement for lipid hydrolysis and derivatisation. Such dynamic lipidomic methodologies using non-toxic stable isotopes can be readily applied to quantify lipid metabolic fluxes in clinical and metabolic studies in vivo. However, a significant current limitation is the absence of appropriate software to generate kinetic models of substrate incorporation into multiple products in the time domain. Finally, we discuss the future potential of stable isotope-mass spectrometry imaging to quantify the location as well as the extent of lipid synthesis. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein.
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Affiliation(s)
- Joost Brandsma
- Academic Unit of Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Andrew P Bailey
- The Francis Crick Institute, 1 Midland Road, London, United Kingdom
| | - Grielof Koster
- Academic Unit of Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; National Institute of Health Research Biomedical Research Unit in Respiratory Medicine, University Hospitals Southampton NHS Foundation Trust, United Kingdom
| | - Alex P Gould
- The Francis Crick Institute, 1 Midland Road, London, United Kingdom
| | - Anthony D Postle
- Academic Unit of Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.
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77
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Lipidomics in research on yeast membrane lipid homeostasis. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:797-799. [PMID: 28219720 DOI: 10.1016/j.bbalip.2017.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 11/21/2022]
Abstract
Mass spectrometry is increasingly used in research on membrane lipid homeostasis, both in analyses of the steady state lipidome at the level of molecular lipid species, and in pulse-chase approaches employing stable isotope-labeled lipid precursors addressing the dynamics of lipid metabolism. Here my experience with, and view on mass spectrometry-based lipid analysis is presented, with emphasis on aspects of quantification of membrane lipid composition of the yeast Saccharomyces cerevisiae. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein.
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78
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Homeoviscous Adaptation and the Regulation of Membrane Lipids. J Mol Biol 2016; 428:4776-4791. [DOI: 10.1016/j.jmb.2016.08.013] [Citation(s) in RCA: 207] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/05/2016] [Accepted: 08/08/2016] [Indexed: 11/23/2022]
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79
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A Simple Method for Measuring Carbon-13 Fatty Acid Enrichment in the Major Lipid Classes of Microalgae Using GC-MS. Metabolites 2016; 6:metabo6040042. [PMID: 27845718 PMCID: PMC5192448 DOI: 10.3390/metabo6040042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/29/2016] [Accepted: 11/07/2016] [Indexed: 12/14/2022] Open
Abstract
A simple method for tracing carbon fixation and lipid synthesis in microalgae was developed using a combination of solid-phase extraction (SPE) and negative ion chemical ionisation gas chromatography mass spectrometry (NCI-GC-MS). NCI-GC-MS is an extremely sensitive technique that can produce an unfragmented molecular ion making this technique particularly useful for stable isotope enrichment studies. Derivatisation of fatty acids using pentafluorobenzyl bromide (PFBBr) allows the coupling of the high separation efficiency of GC and the measurement of unfragmented molecular ions for each of the fatty acids by single quadrupole MS. The key is that isotope spectra can be measured without interference from co-eluting fatty acids or other molecules. Pre-fractionation of lipid extracts by SPE allows the measurement of 13C isotope incorporation into the three main lipid classes (phospholipids, glycolipids, neutral lipids) in microalgae thus allowing the study of complex lipid biochemistry using relatively straightforward analytical technology. The high selectivity of GC is necessary as it allows the collection of mass spectra for individual fatty acids, including cis/trans isomers, of the PFB-derivatised fatty acids. The combination of solid-phase extraction and GC-MS enables the accurate determination of 13C incorporation into each lipid pool. Three solvent extraction protocols that are commonly used in lipidomics were also evaluated and are described here with regard to extraction efficiencies for lipid analysis in microalgae.
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80
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Kuchař L, Asfaw B, Rybová J, Ledvinová J. Tandem Mass Spectrometry of Sphingolipids: Applications for Diagnosis of Sphingolipidoses. Adv Clin Chem 2016; 77:177-219. [PMID: 27717417 DOI: 10.1016/bs.acc.2016.06.004] [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: 02/08/2023]
Abstract
In recent years, mass spectrometry (MS) has become the dominant technology in lipidomic analysis. It is widely used in diagnosis and research of lipid metabolism disorders including those characterized by impairment of lysosomal functions and storage of nondegraded-degraded substrates. These rare diseases, which include sphingolipidoses, have severe and often fatal clinical consequences. Modern MS methods have contributed significantly to achieve a definitive diagnosis, which is essential in clinical practice to begin properly targeted patient care. Here we summarize MS and tandem MS methods used for qualitative and quantitative analysis of sphingolipids (SL) relative to the diagnostic process for sphingolipidoses and studies focusing on alterations in cell functions due to these disorders. This review covers the following topics: Tandem MS is sensitive and robust in determining the composition of sphingolipid classes in various biological materials. Its ability to establish SL metabolomic profiles using MS bench-top analyzers, significantly benefits the first stages of a diagnosis as well as metabolic studies of these disorders. It can thus contribute to a better understanding of the biological significance of SL.
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Affiliation(s)
- L Kuchař
- Charles University in Prague and General University Hospital, Prague, Czech Republic.
| | - B Asfaw
- Charles University in Prague and General University Hospital, Prague, Czech Republic
| | - J Rybová
- Charles University in Prague and General University Hospital, Prague, Czech Republic
| | - J Ledvinová
- Charles University in Prague and General University Hospital, Prague, Czech Republic.
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81
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Yang K, Han X. Lipidomics: Techniques, Applications, and Outcomes Related to Biomedical Sciences. Trends Biochem Sci 2016; 41:954-969. [PMID: 27663237 DOI: 10.1016/j.tibs.2016.08.010] [Citation(s) in RCA: 341] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/16/2016] [Accepted: 08/19/2016] [Indexed: 12/16/2022]
Abstract
Lipidomics is a newly emerged discipline that studies cellular lipids on a large scale based on analytical chemistry principles and technological tools, particularly mass spectrometry. Recently, techniques have greatly advanced and novel applications of lipidomics in the biomedical sciences have emerged. This review provides a timely update on these aspects. After briefly introducing the lipidomics discipline, we compare mass spectrometry-based techniques for analysis of lipids and summarize very recent applications of lipidomics in health and disease. Finally, we discuss the status of the field, future directions, and advantages and limitations of the field.
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Affiliation(s)
- Kui Yang
- Division of Bioorganic Chemistry and Molecular Pharmacology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Xianlin Han
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, Florida 32827, USA; College of Basic Medical Sciences, Zhejiang Chinese Medical University, 548 Bingwen Road, Hangzhou, Zhejiang 310053, China.
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82
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Kong Z, Li M, An J, Chen J, Bao Y, Francis F, Dai X. The fungicide triadimefon affects beer flavor and composition by influencing Saccharomyces cerevisiae metabolism. Sci Rep 2016; 6:33552. [PMID: 27629523 PMCID: PMC5024320 DOI: 10.1038/srep33552] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/24/2016] [Indexed: 12/13/2022] Open
Abstract
Despite the fact that beer is produced on a large scale, the effects of pesticide residues on beer have been rarely investigated. In this study, we used micro-brewing settings to determine the effect of triadimefon on the growth of Saccharomyces cerevisiae and beer flavor. The yeast growth in medium was significantly inhibited (45%) at concentrations higher than 5 mg L(-1), reaching 80% and 100% inhibition at 10 mg L(-1) and 50 mg L(-1), respectively. There were significant differences in sensory quality between beer samples fermented with and without triadimefon based on data obtained with an electronic tongue and nose. Such an effect was most likely underlain by changes in yeast fermentation activity, including decreased utilization of maltotriose and most amino acids, reduced production of isobutyl and isoamyl alcohols, and increased ethyl acetate content in the fungicide treated samples. Furthermore, yeast metabolic profiling by phenotype microarray and UPLC/TOF-MS showed that triadimefon caused significant changes in the metabolism of glutathione, phenylalanine and sphingolipids, and in sterol biosynthesis. Thus, triadimefon negatively affects beer sensory qualities by influencing the metabolic activity of S. cerevisiae during fermentation, emphasizing the necessity of stricter control over fungicide residues in brewing by the food industry.
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Affiliation(s)
- Zhiqiang Kong
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing/Laboratory of Agro-products Quality Safety Risk Assessment, Ministry of Agriculture, Beijing 100193, P. R. China
- Functional and Evolutionary Entomology, Gembloux Agro-Bio-Tech, University of Liège, Passage des Déportés 2, 5030 Gembloux, Belgium
| | - Minmin Li
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing/Laboratory of Agro-products Quality Safety Risk Assessment, Ministry of Agriculture, Beijing 100193, P. R. China
| | - Jingjing An
- College of Food Science, Northeast Agricultural University, Key Laboratory of Dairy Science, Ministry of Education, Harbin 150030, China
| | - Jieying Chen
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing/Laboratory of Agro-products Quality Safety Risk Assessment, Ministry of Agriculture, Beijing 100193, P. R. China
| | - Yuming Bao
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing/Laboratory of Agro-products Quality Safety Risk Assessment, Ministry of Agriculture, Beijing 100193, P. R. China
| | - Frédéric Francis
- Functional and Evolutionary Entomology, Gembloux Agro-Bio-Tech, University of Liège, Passage des Déportés 2, 5030 Gembloux, Belgium
| | - Xiaofeng Dai
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences/Key Laboratory of Agro-Products Processing/Laboratory of Agro-products Quality Safety Risk Assessment, Ministry of Agriculture, Beijing 100193, P. R. China
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83
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Determining the Turnover of Glycosphingolipid Species by Stable-Isotope Tracer Lipidomics. J Mol Biol 2016; 428:4856-4866. [PMID: 27363608 DOI: 10.1016/j.jmb.2016.06.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 01/08/2023]
Abstract
In this study, we used water-soluble stable mass isotope precursors to measure the turnover of endogenous ceramide (Cer) and glycosphingolipids (GSLs) in HEp-2 cells. Cells incubated in the presence of [13C-U]glucose showed rapid incorporation of hexose residues with an increased mass of 6Da into GSLs. Different turnover rates of GSL classes and their molecular species were observed. Approximately 30% of the glucosylceramide, 50% of the lactosylceramide, and 50% of the globotriaosylceramide species showed a much slower turnover than the rest. This demonstrates the existence of different lipid pools, where a certain fraction of species survived for a long time in the cells. The species with the shortest N-amidated fatty acyl groups (C16:0 and C18:0) showed a more rapid turnover than those with the longest N-amidated fatty acids (C24:0 and C24:1). Experiments with addition of [13C-U]serine were performed to study de novo synthesis of Cer from serine and palmitoyl-CoA. These experiments revealed that de novo synthesis contributes to a minor extent to the total synthesis of new sphingolipids and showed that there is a more rapid formation of the longest Cer species (C24:0 and C24:1) than of the shortest species (C16:0), that is, the opposite as observed for the GSLs in the experiments with [13C-U]glucose. In conclusion, this FLUX lipidomics experimental approach with the addition of [13C-U]glucose to cells allows us to not only study the total turnover but also permit observations of lipid intermediates and metabolic flow of endogenous GSL species at the molecular lipid level.
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84
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Martínez-Montañés F, Schneiter R. Tools for the analysis of metabolic flux through the sphingolipid pathway. Biochimie 2016; 130:76-80. [PMID: 27208414 DOI: 10.1016/j.biochi.2016.05.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 05/13/2016] [Indexed: 01/26/2023]
Abstract
Discerning the complex regulation of the enzymatic steps necessary for sphingolipid biosynthesis is facilitated by the utilization of tracers that allow a time-resolved analysis of the pathway dynamics without affecting the metabolic flux. Different strategies have been used and new tools are continuously being developed to probe the various enzymatic conversions that occur within this complex pathway. Here, we provide a short overview of the divergent fungal and mammalian sphingolipid biosynthetic routes, and of the tracers and methods that are frequently employed to follow the flux of intermediates throughout these pathways.
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Affiliation(s)
| | - Roger Schneiter
- University of Fribourg, Department of Biology, 1700 Fribourg, Switzerland.
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85
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Singh A, Del Poeta M. Sphingolipidomics: An Important Mechanistic Tool for Studying Fungal Pathogens. Front Microbiol 2016; 7:501. [PMID: 27148190 PMCID: PMC4830811 DOI: 10.3389/fmicb.2016.00501] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 03/28/2016] [Indexed: 01/28/2023] Open
Abstract
Sphingolipids form of a unique and complex group of bioactive lipids in fungi. Structurally, sphingolipids of fungi are quite diverse with unique differences in the sphingoid backbone, amide linked fatty acyl chain and the polar head group. Two of the most studied and conserved sphingolipid classes in fungi are the glucosyl- or galactosyl-ceramides and the phosphorylinositol containing phytoceramides. Comprehensive structural characterization and quantification of these lipids is largely based on advanced analytical mass spectrometry based lipidomic methods. While separation of complex lipid mixtures is achieved through high performance liquid chromatography, the soft - electrospray ionization tandem mass spectrometry allows a high sensitivity and selectivity of detection. Herein, we present an overview of lipid extraction, chromatographic separation and mass spectrometry employed in qualitative and quantitative sphingolipidomics in fungi.
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Affiliation(s)
- Ashutosh Singh
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony BrookNY, USA; Veterans Administration Medical Center, NorthportNY, USA
| | - Maurizio Del Poeta
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony BrookNY, USA; Veterans Administration Medical Center, NorthportNY, USA
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86
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Allen DK. Assessing compartmentalized flux in lipid metabolism with isotopes. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:1226-1242. [PMID: 27003250 DOI: 10.1016/j.bbalip.2016.03.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 03/13/2016] [Accepted: 03/14/2016] [Indexed: 12/28/2022]
Abstract
Metabolism in plants takes place across multiple cell types and within distinct organelles. The distributions equate to spatial heterogeneity; though the limited means to experimentally assess metabolism frequently involve homogenizing tissues and mixing metabolites from different locations. Most current isotope investigations of metabolism therefore lack the ability to resolve spatially distinct events. Recognition of this limitation has resulted in inspired efforts to advance metabolic flux analysis and isotopic labeling techniques. Though a number of these efforts have been applied to studies in central metabolism; recent advances in instrumentation and techniques present an untapped opportunity to make similar progress in lipid metabolism where the use of stable isotopes has been more limited. These efforts will benefit from sophisticated radiolabeling reports that continue to enrich our knowledge on lipid biosynthetic pathways and provide some direction for stable isotope experimental design and extension of MFA. Evidence for this assertion is presented through the review of several elegant stable isotope studies and by taking stock of what has been learned from radioisotope investigations when spatial aspects of metabolism were considered. The studies emphasize that glycerolipid production occurs across several locations with assembly of lipids in the ER or plastid, fatty acid biosynthesis occurring in the plastid, and the generation of acetyl-CoA and glycerol-3-phosphate taking place at multiple sites. Considering metabolism in this context underscores the cellular and subcellular organization that is important to enhanced production of glycerolipids in plants. An attempt is made to unify salient features from a number of reports into a diagrammatic model of lipid metabolism and propose where stable isotope labeling experiments and further flux analysis may help address questions in the field. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner.
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Affiliation(s)
- Doug K Allen
- United States Department of Agriculture, Agricultural Research Service, 975 North Warson Road, St. Louis, MO 63132, United States; Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, United States.
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87
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To KKW, Lee KC, Wong SSY, Sze KH, Ke YH, Lui YM, Tang BSF, Li IWS, Lau SKP, Hung IFN, Law CY, Lam CW, Yuen KY. Lipid metabolites as potential diagnostic and prognostic biomarkers for acute community acquired pneumonia. Diagn Microbiol Infect Dis 2016; 85:249-54. [PMID: 27105773 PMCID: PMC7173326 DOI: 10.1016/j.diagmicrobio.2016.03.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 03/02/2016] [Accepted: 03/11/2016] [Indexed: 02/03/2023]
Abstract
Early diagnosis of acute community-acquired pneumonia (CAP) is important in patient triage and treatment decisions. To identify biomarkers that distinguish patients with CAP from non-CAP controls, we conducted an untargeted global metabolome analysis for plasma samples from 142 patients with CAP (CAP cases) and 97 without CAP (non-CAP controls). Thirteen lipid metabolites could discriminate between CAP cases and non-CAP controls with area-under-the-receiver-operating-characteristic curve of >0.8 (P ≤ 10−9). The levels of glycosphingolipids, sphingomyelins, lysophosphatidylcholines and L-palmitoylcarnitine were higher, while the levels of lysophosphatidylethanolamines were lower in the CAP cases than those in non-CAP controls. All 13 metabolites could distinguish CAP cases from the non-infection, extrapulmonary infection and non-CAP respiratory tract infection subgroups. The levels of trihexosylceramide (d18:1/16:0) were higher, while the levels of lysophosphatidylethanolamines were lower, in the fatal than those of non-fatal CAP cases. Our findings suggest that lipid metabolites are potential diagnostic and prognostic biomarkers for CAP. Thirteen lipid metabolites could discriminate CAP cases from non-CAP controls. The levels of 2 lipid metabolites differ between fatal and non-fatal CAP cases. Lipid metabolites are potential diagnostic and prognostic biomarkers for CAP.
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Affiliation(s)
- Kelvin K W To
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, China; Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Kim-Chung Lee
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Samson S Y Wong
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, China; Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Kong-Hung Sze
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Yi-Hong Ke
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Yin-Ming Lui
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Bone S F Tang
- Department of Pathology, Hong Kong Sanatorium Hospital, Hong Kong SAR, China
| | - Iris W S Li
- Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Susanna K P Lau
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, China; Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China
| | - Ivan F N Hung
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, China; Department of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Chun-Yiu Law
- Department of Pathology, The University of Hong Kong Hong Kong SAR, China
| | - Ching-Wan Lam
- Department of Pathology, The University of Hong Kong Hong Kong SAR, China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, The University of Hong Kong, Hong Kong SAR, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong SAR, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong SAR, China; Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China.
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88
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Sun ZJ, Jia HM, Qiu GX, Zhou C, Guo S, Zhang JG, Shen JX, Zhao Y, Zou ZM. Identification of candidate diagnostic biomarkers for adolescent idiopathic scoliosis using UPLC/QTOF-MS analysis: a first report of lipid metabolism profiles. Sci Rep 2016; 6:22274. [PMID: 26928931 PMCID: PMC4772092 DOI: 10.1038/srep22274] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 02/10/2016] [Indexed: 11/28/2022] Open
Abstract
Adolescent idiopathic scoliosis (AIS) is a complex spine deformity, affecting approximately 1–3% adolescents. Earlier diagnosis could increase the likelihood of successful conservative treatment and hence reduce the need for surgical intervention. We conducted a serum metabonomic study to explore the potential biomarkers of AIS for early diagnosis. Serum metabolic profiles were firstly explored between 30 AIS patients and 31 healthy controls by ultra high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. Then, the candidate metabolites were validated in an independent cohort including 31 AIS patients and 44 controls. The results showed that metabolic profiles of AIS patients generally deviated from healthy controls in both the discovery set and replication set. Seven differential metabolites were identified as candidate diagnostic biomarkers, including PC(20:4), 2-hexenoylcarnitine, beta-D-glucopyranuronicacid, DG(38:9), MG(20:3), LysoPC(18:2) and LysoPC(16:0). These candidate metabolites indicated disrupted lipid metabolism in AIS, including glycerophospholipid, glycerolipid and fatty acid metabolism. Elevated expressions of adipose triglyceride lipase and hormone sensitive lipase in adipose tissue further corroborated our findings of increased lipid metabolism in AIS. Our findings suggest that differential metabolites discovered in AIS could be used as potential diagnostic biomarkers and that lipid metabolism plays a role in the pathogenesis of AIS.
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Affiliation(s)
- Zhi-jian Sun
- Department of Orthopaedics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng District Shuaifuyuan No. 1, Beijing 100730, China
| | - Hong-mei Jia
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Gui-xing Qiu
- Department of Orthopaedics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng District Shuaifuyuan No. 1, Beijing 100730, China
| | - Chao Zhou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Shigong Guo
- Department of Trauma &Orthopaedic Surgery, Lister Hospital, Stevenage, UK
| | - Jian-guo Zhang
- Department of Orthopaedics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng District Shuaifuyuan No. 1, Beijing 100730, China
| | - Jian-xiong Shen
- Department of Orthopaedics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng District Shuaifuyuan No. 1, Beijing 100730, China
| | - Yu Zhao
- Department of Orthopaedics, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Dongcheng District Shuaifuyuan No. 1, Beijing 100730, China
| | - Zhong-mei Zou
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
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89
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Liu GJ, Xiao GH, Liu NJ, Liu D, Chen PS, Qin YM, Zhu YX. Targeted Lipidomics Studies Reveal that Linolenic Acid Promotes Cotton Fiber Elongation by Activating Phosphatidylinositol and Phosphatidylinositol Monophosphate Biosynthesis. MOLECULAR PLANT 2015; 8:911-921. [PMID: 25731673 DOI: 10.1016/j.molp.2015.02.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/25/2015] [Accepted: 02/14/2015] [Indexed: 06/04/2023]
Abstract
The membrane lipids from fast-elongating wild-type cotton (Gossypium hirsutum) fibers at 10 days post-anthesis, wild-type ovules with fiber cells removed, and ovules from the fuzzless-lintless mutant harvested at the same age, were extracted, separated, and quantified. Fiber cells contained significantly higher amounts of phosphatidylinositol (PI) than both ovule samples with PI 34:3 being the most predominant species. The genes encoding fatty acid desaturases (Δ(15)GhFAD), PI synthase (PIS) and PI kinase (PIK) were expressed in a fiber-preferential manner. Further analysis of phosphatidylinositol monophosphate (PIP) indicated that elongating fibers contained four- to five-fold higher amounts of PIP 34:3 than the ovules. Exogenously applied linolenic acid (C18:3), soybean L-α-PI, and PIPs containing PIP 34:3 promoted significant fiber growth, whereas a liver PI lacking the C18:3 moiety, linoleic acid, and PIP 36:2 were completely ineffective. The growth inhibitory effects of carbenoxolone, 5-hydroxytryptamine, and wortmannin were reverted by C18:3, PI, or PIP, respectively, suggesting that PIP signaling is essential for fiber cell growth. Furthermore, cotton plants expressing virus-induced gene-silencing constructs that specifically suppressed GhΔ(15)FAD, GhPIS, or GhPIK expression, resulted in significantly short-fibered phenotypes. Our data provide the basis for in-depth studies on the roles of PI and PIP in mediating cotton fiber growth.
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Affiliation(s)
- Gao-Jun Liu
- The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Guang-Hui Xiao
- The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Ning-Jing Liu
- The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Dan Liu
- The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Pei-Shuang Chen
- The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Yong-Mei Qin
- The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China.
| | - Yu-Xian Zhu
- The State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
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90
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Multidimensional mass spectrometry-based shotgun lipidomics analysis of vinyl ether diglycerides. Anal Bioanal Chem 2015; 407:5199-210. [PMID: 25822162 DOI: 10.1007/s00216-015-8640-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 10/23/2022]
Abstract
Diglycerides play a central role in lipid metabolism and signaling in mammalian cells. Although diacylglycerol molecular species comprise the majority of cellular diglycerides that are commonly measured using a variety of approaches, identification of extremely low abundance vinyl ether diglycerides has remained challenging. In this work, representative molecular species from the three diglyceride subclasses (diacyl, vinyl ether, and alkyl ether diglycerides; hereafter referred to as diradylglycerols) were interrogated by mass spectrometric analysis. Product ion mass spectra of the synthesized diradylglycerols with varied chain lengths and degrees of unsaturation demonstrated diagnostic fragmentation patterns indicative of each subclass. Multidimensional mass spectrometry-based shotgun lipidomics (MDMS-SL) analysis of mouse brain and heart lipid extracts were performed using the identified informative signature product ions. Through an array of tandem mass spectrometric analyses utilizing the orthogonal characteristics of neutral loss scanning and precursor ion scanning, the differential fragmentation of each subclass was exploited for high-yield structural analyses. Although molecular ion mass spectra readily identified diacylglycerol molecular species directly from the hexane fractions of tissue extracts enriched in nonpolar lipids, molecular ion peaks corresponding to ether-linked diglycerides were not observable. The power of MDMS-SL utilizing the tandem mass spectrometric array analysis was demonstrated by identification and profiling of individual molecular species of vinyl ether diglycerides in mouse brain and heart from their undetectable molecular ion peaks during MS(1) analysis. Collectively, this technology enabled the identification and profiling of previously inaccessible vinyl ether diglyceride molecular species in mammalian tissues directly from extracts of biologic tissues.
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91
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Allen DK, Bates PD, Tjellström H. Tracking the metabolic pulse of plant lipid production with isotopic labeling and flux analyses: Past, present and future. Prog Lipid Res 2015; 58:97-120. [PMID: 25773881 DOI: 10.1016/j.plipres.2015.02.002] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 01/30/2015] [Accepted: 02/11/2015] [Indexed: 11/25/2022]
Abstract
Metabolism is comprised of networks of chemical transformations, organized into integrated biochemical pathways that are the basis of cellular operation, and function to sustain life. Metabolism, and thus life, is not static. The rate of metabolites transitioning through biochemical pathways (i.e., flux) determines cellular phenotypes, and is constantly changing in response to genetic or environmental perturbations. Each change evokes a response in metabolic pathway flow, and the quantification of fluxes under varied conditions helps to elucidate major and minor routes, and regulatory aspects of metabolism. To measure fluxes requires experimental methods that assess the movements and transformations of metabolites without creating artifacts. Isotopic labeling fills this role and is a long-standing experimental approach to identify pathways and quantify their metabolic relevance in different tissues or under different conditions. The application of labeling techniques to plant science is however far from reaching it potential. In light of advances in genetics and molecular biology that provide a means to alter metabolism, and given recent improvements in instrumentation, computational tools and available isotopes, the use of isotopic labeling to probe metabolism is becoming more and more powerful. We review the principal analytical methods for isotopic labeling with a focus on seminal studies of pathways and fluxes in lipid metabolism and carbon partitioning through central metabolism. Central carbon metabolic steps are directly linked to lipid production by serving to generate the precursors for fatty acid biosynthesis and lipid assembly. Additionally some of the ideas for labeling techniques that may be most applicable for lipid metabolism in the future were originally developed to investigate other aspects of central metabolism. We conclude by describing recent advances that will play an important future role in quantifying flux and metabolic operation in plant tissues.
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Affiliation(s)
- Doug K Allen
- United States Department of Agriculture, Agricultural Research Service, 975 North Warson Road, St. Louis, MO 63132, United States; Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, United States.
| | - Philip D Bates
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406, United States
| | - Henrik Tjellström
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, United States; Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, United States
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92
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Mass Spectrometry in Food Quality and Safety. ADVANCED MASS SPECTROMETRY FOR FOOD SAFETY AND QUALITY 2015. [DOI: 10.1016/b978-0-444-63340-8.00001-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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93
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Li H, Xia X, Li X, Naren G, Fu Q, Wang Y, Wu C, Ding S, Zhang S, Jiang H, Li J, Shen J. Untargeted metabolomic profiling of amphenicol-resistant Campylobacter jejuni by ultra-high-performance liquid chromatography-mass spectrometry. J Proteome Res 2014; 14:1060-8. [PMID: 25491530 DOI: 10.1021/pr501061d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Campylobacter jejuni, an important foodborne microorganism, poses severe and emergent threats to human health as antibiotic resistance becomes increasingly prevalent. The mechanisms of drug resistance are hard to decipher, and little is known at the metabolic level. Here we apply metabolomic profiling to discover metabolic changes associated with amphenicol (chloramphenicol and florfenicol) resistance mutations of Campylobacter jejuni. An optimized sample preparation method was combined with ultra-high-performance liquid chromatography-time-of-flight mass spectrometry (UHPLC-TOF/MS) and pattern recognition for the analysis of small-molecule biomarkers of drug resistance. UHPLC-triple quadrupole MS operated in multiple reaction monitoring mode was used for quantitative analysis of metabolic features from UHPLC-TOF/MS profiling. Up to 41 differential metabolites involved in glycerophospholipid metabolism, sphingolipid metabolism, and fatty acid metabolism were observed in a chloramphenicol-resistant mutant strain of Campylobacter jejuni. A panel of 40 features was identified in florfenicol-resistant mutants, demonstrating changes in glycerophospholipid metabolism, sphingolipid metabolism, and tryptophan metabolism. This study shows that the UHPLC-MS-based metabolomics platform is a promising and valuable tool to generate new insights into the drug-resistant mechanism of Campylobacter jejuni.
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Affiliation(s)
- Hui Li
- Department of Veterinary Pharmacology and Toxicology, College of Veterinary Medicine, China Agricultural University , Beijing 100193, P. R. China
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94
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Analysis of biologically-active, endogenous carboxylic acids based on chromatography-mass spectrometry. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2014.05.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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