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Nůsková H, Cortizo FG, Schwenker LS, Sachsenheimer T, Diakonov EE, Tiebe M, Schneider M, Lohbeck J, Reid C, Kopp-Schneider A, Helm D, Brügger B, Miller AK, Teleman AA. Competition for cysteine acylation by C16:0 and C18:0 derived lipids is a global phenomenon in the proteome. J Biol Chem 2023; 299:105088. [PMID: 37495107 PMCID: PMC10470219 DOI: 10.1016/j.jbc.2023.105088] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/16/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023] Open
Abstract
S-acylation is a reversible posttranslational protein modification consisting of attachment of a fatty acid to a cysteine via a thioester bond. Research over the last few years has shown that a variety of different fatty acids, such as palmitic acid (C16:0), stearate (C18:0), or oleate (C18:1), are used in cells to S-acylate proteins. We recently showed that GNAI proteins can be acylated on a single residue, Cys3, with either C16:0 or C18:1, and that the relative proportion of acylation with these fatty acids depends on the level of the respective fatty acid in the cell's environment. This has functional consequences for GNAI proteins, with the identity of the acylating fatty acid affecting the subcellular localization of GNAIs. Unclear is whether this competitive acylation is specific to GNAI proteins or a more general phenomenon in the proteome. We perform here a proteome screen to identify proteins acylated with different fatty acids. We identify 218 proteins acylated with C16:0 and 308 proteins acylated with C18-lipids, thereby uncovering novel targets of acylation. We find that most proteins that can be acylated by C16:0 can also be acylated with C18-fatty acids. For proteins with more than one acylation site, we find that this competitive acylation occurs on each individual cysteine residue. This raises the possibility that the function of many different proteins can be regulated by the lipid environment via differential S-acylation.
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Affiliation(s)
- Hana Nůsková
- Division of Signal Transduction in Cancer and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Fabiola Garcia Cortizo
- Division of Signal Transduction in Cancer and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lena Sophie Schwenker
- Division of Signal Transduction in Cancer and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Egor E Diakonov
- Division of Signal Transduction in Cancer and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Tiebe
- Division of Signal Transduction in Cancer and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Schneider
- Mass Spectrometry Based Protein Analysis Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jasmin Lohbeck
- Research Group Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carissa Reid
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Dominic Helm
- Mass Spectrometry Based Protein Analysis Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Aubry K Miller
- Research Group Cancer Drug Development, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aurelio A Teleman
- Division of Signal Transduction in Cancer and Metabolism, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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2
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Nůsková H, Serebryakova MV, Ferrer-Caelles A, Sachsenheimer T, Lüchtenborg C, Miller AK, Brügger B, Kordyukova LV, Teleman AA. Stearic acid blunts growth-factor signaling via oleoylation of GNAI proteins. Nat Commun 2021; 12:4590. [PMID: 34321466 PMCID: PMC8319428 DOI: 10.1038/s41467-021-24844-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 07/08/2021] [Indexed: 01/13/2023] Open
Abstract
Covalent attachment of C16:0 to proteins (palmitoylation) regulates protein function. Proteins are also S-acylated by other fatty acids including C18:0. Whether protein acylation with different fatty acids has different functional outcomes is not well studied. We show here that C18:0 (stearate) and C18:1 (oleate) compete with C16:0 to S-acylate Cys3 of GNAI proteins. C18:0 becomes desaturated so that C18:0 and C18:1 both cause S-oleoylation of GNAI. Exposure of cells to C16:0 or C18:0 shifts GNAI acylation towards palmitoylation or oleoylation, respectively. Oleoylation causes GNAI proteins to shift out of cell membrane detergent-resistant fractions where they potentiate EGFR signaling. Consequently, exposure of cells to C18:0 reduces recruitment of Gab1 to EGFR and reduces AKT activation. This provides a molecular mechanism for the anti-tumor effects of C18:0, uncovers a mechanistic link how metabolites affect cell signaling, and provides evidence that the identity of the fatty acid acylating a protein can have functional consequences.
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Affiliation(s)
- Hana Nůsková
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Heidelberg, Germany
| | - Marina V Serebryakova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Anna Ferrer-Caelles
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg University, Heidelberg, Germany
| | | | | | - Aubry K Miller
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Larisa V Kordyukova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Aurelio A Teleman
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Heidelberg University, Heidelberg, Germany.
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3
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Wang W, Wei Q, Zhang J, Zhang M, Wang C, Qu R, Wang Y, Yang G, Wang J. A Ratiometric Fluorescent Biosensor Reveals Dynamic Regulation of Long‐Chain Fatty Acyl‐CoA Esters Metabolism. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Weibo Wang
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences Peking University Beijing 100191 China
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education International Joint Research Center for Intelligent Biosensor Technology and Health College of Chemistry Central China Normal University Wuhan 430079 China
| | - Qingpeng Wei
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Jiayuan Zhang
- Wellcome Centre for Human Genetics University of Oxford Roosevelt Dr, Headington Oxford OX3 7BN UK
| | - Meiqi Zhang
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Chuchen Wang
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Renyu Qu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education International Joint Research Center for Intelligent Biosensor Technology and Health College of Chemistry Central China Normal University Wuhan 430079 China
| | - Yuan Wang
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences Peking University Beijing 100191 China
| | - Guangfu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education International Joint Research Center for Intelligent Biosensor Technology and Health College of Chemistry Central China Normal University Wuhan 430079 China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs Department of Chemical Biology School of Pharmaceutical Sciences Peking University Beijing 100191 China
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4
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Wang W, Wei Q, Zhang J, Zhang M, Wang C, Qu R, Wang Y, Yang G, Wang J. A Ratiometric Fluorescent Biosensor Reveals Dynamic Regulation of Long-Chain Fatty Acyl-CoA Esters Metabolism. Angew Chem Int Ed Engl 2021; 60:13996-14004. [PMID: 33837610 DOI: 10.1002/anie.202101731] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/14/2021] [Indexed: 01/28/2023]
Abstract
Despite increasing awareness of the biological impacts of long-chain fatty acyl-CoA esters (LCACoAs), our knowledge about the subcellular distribution and regulatory functions of these acyl-CoA molecules is limited by a lack of methods for detecting LCACoAs in living cells. Here, we report development of a genetically encoded fluorescent sensor that enables ratiometric quantification of LCACoAs in living cells and subcellular compartments. We demonstrate how this FadR-cpYFP fusion "LACSer sensor" undergoes LCACoA-induced conformational changes reflected in easily detectable fluorescence responses, and show proof-of-concept for real-time monitoring of LCACoAs in human cells. Subsequently, we applied LACSer in scientific studies investigating how disruption of ACSL enzymes differentially reduces cytosolic and mitochondrial LCACoA levels, and show how genetic disruption of an acyl-CoA binding protein (ACBP) alters mitochondrial accumulation of LCACoAs.
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Affiliation(s)
- Weibo Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China.,Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Qingpeng Wei
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Jiayuan Zhang
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Dr, Headington, Oxford, OX3 7BN, UK
| | - Meiqi Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Chuchen Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Renyu Qu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Yuan Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Guangfu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
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5
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Li P, Gawaz M, Chatterjee M, Lämmerhofer M. Targeted Profiling of Short-, Medium-, and Long-Chain Fatty Acyl-Coenzyme As in Biological Samples by Phosphate Methylation Coupled to Liquid Chromatography-Tandem Mass Spectrometry. Anal Chem 2021; 93:4342-4350. [PMID: 33620217 DOI: 10.1021/acs.analchem.1c00664] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Fatty acyl-coenzyme As (acyl-CoAs) are of central importance in lipid metabolism pathways. Short-chain acyl-CoAs are usually part of metabolomics, and medium- to (very) long-chain acyl-CoAs are focus of lipidomics studies. However, owing to the specific complex and amphiphilic nature contributed by fatty acyl chains and hydrophilic CoA moiety, lipidomic analysis of acyl-CoAs is still challenging, especially in terms of sample preparation and chromatographic coverage. In this work, we propose a derivatization strategy of acyl-CoAs based on phosphate methylation. After derivatization, full coverage (from free CoA to C25:0-CoA) and good peak shape in liquid chromatography were achieved. At the same time, analyte loss due to the high affinity of phosphate groups to glass and metallic surfaces was resolved, which is beneficial for routine analysis in large-scale lipidomics studies. A sample preparation method based on mixed-mode SPE was developed to optimize extraction recoveries and allow optimal integration of the derivatization process in the analytical workflow. LC-MS/MS was performed with targeted data acquisition by SRM transitions, which were constructed based on similar fragmentation rules observed for all methylated acyl-CoAs. To achieve accurate quantification, uniformly 13C-labeled metabolite extract from yeast cells was taken as internal standards. Odd-chain and stable isotope-labeled acyl-CoAs were used as surrogate calibrants in the same matrix. LOQs were between 16.9 nM (short-chain acyl-CoAs) and 4.2 nM (very-long-chain acyl-CoAs). This method was validated in cultured cells and was applied in HeLa cells and human platelets of coronary artery disease patients. It revealed distinct acyl-CoA profiles in HeLa cells and platelets. The results showed that this method can effectively detect acyl-CoAs in biological samples. Considering their central importance in many de novo lipid biosynthesis and remodeling processes, this targeted method offers a valid foundation for future lipidomics analysis of acyl-CoA profiles in biological samples, particularly those concerning metabolic syndrome.
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Affiliation(s)
- Peng Li
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, 72076 Tübingen, Germany
| | - Meinrad Gawaz
- Department of Cardiology and Angiology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Madhumita Chatterjee
- Department of Cardiology and Angiology, University Hospital Tübingen, 72076 Tübingen, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, 72076 Tübingen, Germany
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6
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Lam SM, Zhou T, Li J, Zhang S, Chua GH, Li B, Shui G. A robust, integrated platform for comprehensive analyses of acyl-coenzyme As and acyl-carnitines revealed chain length-dependent disparity in fatty acyl metabolic fates across Drosophila development. Sci Bull (Beijing) 2020; 65:1840-1848. [PMID: 36659124 DOI: 10.1016/j.scib.2020.07.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/02/2020] [Accepted: 06/15/2020] [Indexed: 01/21/2023]
Abstract
Acyl-coenzyme A thioesters (acyl-CoAs) denote a key class of intermediary metabolites that lies at the hub of major metabolic pathways. The great diversity in polarity between short- and long-chain acyl-CoAs makes it technically challenging to cover an inclusive range of acyl-CoAs within a single method. Levels of acyl-carnitines, which function to convey fatty acyls into mitochondria matrix for β-oxidation, indicate the efficiency of mitochondrial import and utilization of corresponding acyl-CoAs. Herein, we report a robust, integrated platform to allow simultaneous quantitation of endogenous acyl-CoAs and acyl-carnitines. Using this method, we monitored changes in intermediary lipid profiles across Drosophila development under control (ND) and high-fat diet (HFD). We observed specific accumulations of medium-chain (C8-C12) and long-chain (≥C16) acyl-carnitines distinct to L3 larval and pupal stages, respectively. These observations suggested development-specific, chain length-dependent disparity in metabolic fates of acyl-CoAs across Drosophila development, which was validated by deploying the same platform to monitor isotope incorporation introduced from labelled 12:0 and 16:0 fatty acids into extra- and intra-mitochondrial acyl-CoA pools. We found that pupal mitochondria preferentially import and oxidise C12:0-CoAs (accumulated as C12:0-carnitines in L3 stage) over C16:0-CoAs. Preferential oxidation of medium-chain acyl-CoAs limits mitochondrial utilization of long-chain acyl-CoAs (C16-C18), leading to pupal-specific accumulation of long-chain acyl-carnitines mediated by enhanced CPT1-6A activity. HFD skewed C16:0-CoAs towards catabolism over anabolism in pupa, thereby adversely affecting overall development. Our developed platform emphasizes the importance of integrating biological knowledge in the design of pathway-oriented platforms to derive maximal physiological insights from analysis of complex biological systems.
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Affiliation(s)
- Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tianxing Zhou
- LipidALL Technologies Company Limited, Changzhou 213022, China
| | - Jie Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shaohua Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Gek Huey Chua
- LipidALL Technologies Company Limited, Changzhou 213022, China
| | - Bowen Li
- LipidALL Technologies Company Limited, Changzhou 213022, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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7
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Miniewska K, Godzien J, Mojsak P, Maliszewska K, Kretowski A, Ciborowski M. Mass spectrometry-based determination of lipids and small molecules composing adipose tissue with a focus on brown adipose tissue. J Pharm Biomed Anal 2020; 191:113623. [PMID: 32966938 DOI: 10.1016/j.jpba.2020.113623] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 12/11/2022]
Abstract
Adipose tissue has been the subject of research for a very long time. Many studies perform a comprehensive analysis of different types of adipose tissue with an emphasis on brown adipose tissue. Mass spectrometry-based approaches are particularly useful in the exploration not only of the metabolic composition of adipose tissue but also its function. In the presented review, a complex and critical overview of publications devoted to the analysis of adipose tissue by means of mass spectrometry was performed. Detailed investigation of analytical aspects related to either untargeted or targeted analysis of adipose tissue was performed, leading to the formation of a collection of hints at the available analytical methods. Moreover, a profound analysis of the metabolic composition of brown adipose tissue was performed. Brown adipose tissue metabolome was characterized on structural and functional levels, providing information about its exact metabolic composition but also connecting these molecules and placing them into biochemical pathways. All our work resulted in a very broad picture of the analysis of adipose tissue, starting from the analytical aspects and finishing on the current knowledge about its composition.
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Affiliation(s)
- Katarzyna Miniewska
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Joanna Godzien
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Patrycja Mojsak
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Katarzyna Maliszewska
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Adam Kretowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland; Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Michal Ciborowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland.
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8
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Wang HYJ, Hsu FF. Revelation of Acyl Double Bond Positions on Fatty Acyl Coenzyme A Esters by MALDI/TOF Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1047-1057. [PMID: 32167298 DOI: 10.1021/jasms.9b00139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fatty acyl coenzyme A esters (FA-CoAs) are important crossroad intermediates in lipid catabolism and anabolism, and the structures are complicated. Several mass spectrometric approaches have been previously described to elucidate their structures. However, a direct mass spectrometric approach toward a complete identification of the molecule, including the location of unsaturated bond(s) in the fatty acid chain has not been reported. In this study, we applied a simple MALDI/TOF mass spectrometric method to a near-complete characterization of long-chain FA-CoAs, including the location(s) of the double bond in the fatty acyl chain, and the common structural features that recognize FA-CoAs. Negative ion mass spectra of saturated, monounsaturated, and polyunsaturated FA-CoAs were acquired with a MALDI/TOF mass spectrometer using 2,5-dihydroxybenzoic acid as the matrix and ionized with a laser fluence two folds of the threshold to induce the in-source fragmentation (ISF) of the analytes. The resulting ISF spectra contained fragment ions arising from specific cleavages of the C-C bond immediate adjacent to the acyl double-bond. This structural feature affords locating the double-bond position(s) of the fatty acyl substituent. Thereby, positional isomer such as 18:3(n - 3) and 18:3(n - 6) FA-CoA can be differentiated without applying tandem mass spectrometry.
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Affiliation(s)
- Hay-Yan J Wang
- Department of Biological Sciences, National Sun Yat-Sen University, Kaohsiung 80424, Taiwan
| | - Fong-Fu Hsu
- Mass Spectrometry Resource, Division of Endocrinology, Diabetes, Metabolism, and Lipid Research, Washington University School of Medicine Box 8127, 660 S Euclid Ave., St. Louis, Missouri 63110, United States
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9
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Teclemariam ET, Pergande MR, Cologna SM. Considerations for mass spectrometry-based multi-omic analysis of clinical samples. Expert Rev Proteomics 2020; 17:99-107. [PMID: 31996049 DOI: 10.1080/14789450.2020.1724540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Introduction: The role of mass spectrometry in biomolecule analysis has become paramount over the last several decades ranging in the analysis across model systems and human specimens. Accordingly, the presence of mass spectrometers in clinical laboratories has also expanded alongside the number of researchers investigating the protein, lipid, and metabolite composition of an array of biospecimens. With this increase in the number of omic investigations, it is important to consider the entire experimental strategy from sample collection and storage, data collection and analysis.Areas covered: In this short review, we outline considerations for working with clinical (e.g. human) specimens including blood, urine, and cerebrospinal fluid, with emphasis on sample handling, profiling composition, targeted measurements and relevance to disease. Discussions of integrated genomic or transcriptomic datasets are not included. A brief commentary is also provided regarding new technologies with clinical relevance.Expert opinion: The role of mass spectrometry to investigate clinically related specimens is on the rise and the ability to integrate multiple omics datasets from mass spectrometry measurements will be crucial to further understanding human health and disease.
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Affiliation(s)
- Esei T Teclemariam
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Melissa R Pergande
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA.,Laboratory of Integrated Neuroscience, University of Illinois at Chicago, Chicago, IL, USA
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10
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King AM, Trengove RD, Mullin LG, Rainville PD, Isaac G, Plumb RS, Gethings LA, Wilson ID. Rapid profiling method for the analysis of lipids in human plasma using ion mobility enabled-reversed phase-ultra high performance liquid chromatography/mass spectrometry. J Chromatogr A 2020; 1611:460597. [DOI: 10.1016/j.chroma.2019.460597] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 09/19/2019] [Accepted: 10/03/2019] [Indexed: 12/22/2022]
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11
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Tian Y, Zhang L, Li Y, Gao J, Yu H, Guo Y, Jia L. Variant analysis of PEX11B gene from a family with peroxisome biogenesis disorder 14B by whole exome sequencing. Mol Genet Genomic Med 2019; 8. [PMID: 31724321 PMCID: PMC6978261 DOI: 10.1002/mgg3.1042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 08/30/2019] [Accepted: 10/22/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Peroxisome biogenesis disorder 14B (PBD14B) is an autosomal recessive peroxisome biogenesis disorder characterized clinically by mild intellectual disability, congenital cataracts, progressive hearing loss, and polyneuropathy peroxisome biogenesis disorders are genetically heterogeneous group of disorders caused by biallelic mutations in peroxin (PEX) genes. METHODOLOGY/LABORATORY EXAMINATION DNA of the family was extracted and sequenced by whole exome sequencing. The results were validated with Sanger sequencing analyzed with Bioinformatics software. RESULTS Sequencing result showed that the patient has carried a homozygous variant of c.277C>T of the PEX11B gene. The patient's brother has carried a homozygous variant of c.277C>T of the PEX11B gene and their variants of c.277C>T of the PEX11B gene were inherited, respectively, from his mother and father. DISCUSSION AND CONCLUSION The homozygous variant of c.277C>T of the PEX11B gene probably underlie the disease in this child and her brother.
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Affiliation(s)
- Yuan Tian
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Linlin Zhang
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Li
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jinshuang Gao
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haiyang Yu
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yaqing Guo
- Department of Clinical Laboratory, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Liting Jia
- Screening Center, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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12
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Metherel AH, Lacombe RS, Aristizabal Henao JJ, Morin-Rivron D, Kitson AP, Hopperton KE, Chalil D, Masoodi M, Stark KD, Bazinet RP. Two weeks of docosahexaenoic acid (DHA) supplementation increases synthesis-secretion kinetics of n-3 polyunsaturated fatty acids compared to 8 weeks of DHA supplementation. J Nutr Biochem 2018; 60:24-34. [DOI: 10.1016/j.jnutbio.2018.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 06/25/2018] [Accepted: 07/02/2018] [Indexed: 11/26/2022]
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13
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Wang S, Wang Z, Zhou L, Shi X, Xu G. Comprehensive Analysis of Short-, Medium-, and Long-Chain Acyl-Coenzyme A by Online Two-Dimensional Liquid Chromatography/Mass Spectrometry. Anal Chem 2017; 89:12902-12908. [PMID: 29098853 DOI: 10.1021/acs.analchem.7b03659] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Acyl-coenzyme A (CoA) is a pivotal metabolic intermediate in numerous biological processes. However, comprehensive analysis of acyl-CoAs is still challenging as the properties of acyl-CoAs greatly vary with different carbon chains. Here, we designed a two-dimensional liquid chromatography method coupled with high-resolution mass spectrometry (2D LC/HRMS) to cover all short-, medium-, and long-chain acyl-CoAs within one analytical run. Complex acyl-CoAs were separated into two fractions according to their acyl chains by the first dimensional prefractionation. Then, two fractions containing short-chain acyl-CoAs or medium- and long-chain acyl-CoAs were further separated by the two parallel columns in the second dimension. Nineteen representative standards were chosen to optimize the analytical conditions of the 2D LC/HRMS method. Resolution and sensitivity were demonstrated to be improved greatly, and lowly abundant acyl-CoAs and acyl-CoA isomers could be detected and distinguished. By using the 2D LC/HRMS method, 90 acyl-CoAs (including 21 acyl-dephospho-CoAs) were identified from liver extracts, which indicated that our method was one of the most powerful approaches for obtaining comprehensive profiling of acyl-CoAs so far. The method was further employed in the metabolomics study of malignant glioma cells with an isocitrate dehydrogenase 1 (IDH1) mutation to explore their metabolic differences. A total of 46 acyl-CoAs (including 2 acyl-dephospho-CoAs) were detected, and 12 of them were dysregulated in glioma cells with the IDH1 mutation. These results demonstrated the practicability and the superiority of the established method. Therefore, the 2D LC/HRMS method provides a robust and reproducible approach to the comprehensive analysis of acyl-CoAs in tissues, cells, and other biological samples.
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Affiliation(s)
- Shuangyuan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Zhichao Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Lina Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
| | - Xianzhe Shi
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023, China
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