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Meijer NWF, Zwakenberg S, Gerrits J, Westland D, Ardisasmita AI, Fuchs SA, Verhoeven-Duif NM, Jans JJM, Zwartkruis FJT. Direct Infusion Mass Spectrometry to Rapidly Map Metabolic Flux of Substrates Labeled with Stable Isotopes. Metabolites 2024; 14:246. [PMID: 38786724 PMCID: PMC11122925 DOI: 10.3390/metabo14050246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/16/2024] [Accepted: 04/20/2024] [Indexed: 05/25/2024] Open
Abstract
Direct infusion-high-resolution mass spectrometry (DI-HRMS) allows for rapid profiling of complex mixtures of metabolites in blood, cerebrospinal fluid, tissue samples and cultured cells. Here, we present a DI-HRMS method suitable for the rapid determination of metabolic fluxes of isotopically labeled substrates in cultured cells and organoids. We adapted an automated annotation pipeline by selecting labeled adducts that best represent the majority of 13C and/or 15N-labeled glycolytic and tricarboxylic acid cycle intermediates as well as a number of their derivatives. Furthermore, valine, leucine and several of their degradation products were included. We show that DI-HRMS can determine anticipated and unanticipated alterations in metabolic fluxes along these pathways that result from the genetic alteration of single metabolic enzymes, including pyruvate dehydrogenase (PDHA1) and glutaminase (GLS). In addition, it can precisely pinpoint metabolic adaptations to the loss of methylmalonyl-CoA mutase in patient-derived liver organoids. Our results highlight the power of DI-HRMS in combination with stable isotopically labeled compounds as an efficient screening method for fluxomics.
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Affiliation(s)
- Nils W. F. Meijer
- Department of Genetics, Section Metabolic Diagnostics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, The Netherlands; (N.W.F.M.); (N.M.V.-D.)
| | - Susan Zwakenberg
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands (D.W.); (F.J.T.Z.)
| | - Johan Gerrits
- Department of Genetics, Section Metabolic Diagnostics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, The Netherlands; (N.W.F.M.); (N.M.V.-D.)
| | - Denise Westland
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands (D.W.); (F.J.T.Z.)
| | - Arif I. Ardisasmita
- Department of Genetics, Section Metabolic Diagnostics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, The Netherlands; (N.W.F.M.); (N.M.V.-D.)
| | - Sabine A. Fuchs
- Department of Genetics, Section Metabolic Diagnostics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, The Netherlands; (N.W.F.M.); (N.M.V.-D.)
| | - Nanda M. Verhoeven-Duif
- Department of Genetics, Section Metabolic Diagnostics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, The Netherlands; (N.W.F.M.); (N.M.V.-D.)
| | - Judith J. M. Jans
- Department of Genetics, Section Metabolic Diagnostics, University Medical Center Utrecht, Lundlaan 6, 3584 EA Utrecht, The Netherlands; (N.W.F.M.); (N.M.V.-D.)
| | - Fried J. T. Zwartkruis
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands (D.W.); (F.J.T.Z.)
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Krause N, Wegner A. N-acetyl-aspartate metabolism at the interface of cancer, immunity, and neurodegeneration. Curr Opin Biotechnol 2024; 85:103051. [PMID: 38103520 DOI: 10.1016/j.copbio.2023.103051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/15/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023]
Abstract
N-acetyl-L-aspartic acid (NAA) is a prominent amino acid derivative primarily associated with vertebrate brain metabolism. This review delineates the critical role of NAA across various cell types and its significance in pathophysiological contexts, including Canavan disease and cancer metabolism. Although traditionally linked with myelination and aspartoacylase-driven carbon donation, its significance as a carbon source for myelination remains debated. Evidence suggests that intact NAA might substantially impact cellular signaling, particularly processes such as histone acetylation. Beyond the brain, NAA metabolism's relevance is evident in diverse tissues, such as adipocytes, immune cells, and notably, cancer cells. In several cancer types, there is an observed upregulation of NAA synthesis accompanied by a simultaneous downregulation of its degradation. This pattern highlights the potential signaling role of intact NAA in disease.
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Affiliation(s)
- Nils Krause
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Andre Wegner
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.
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3
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Zheng N, Liu X, Yang Y, Liu Y, Yan F, Zeng Y, Cheng Y, Wu D, Chen C, Wang X. Regulatory roles of NAT10 in airway epithelial cell function and metabolism in pathological conditions. Cell Biol Toxicol 2023; 39:1237-1256. [PMID: 35877022 DOI: 10.1007/s10565-022-09743-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/20/2022] [Indexed: 12/01/2022]
Abstract
N-acetyltransferase 10 (NAT10), a nuclear acetyltransferase and a member of the GNAT family, plays critical roles in RNA stability and translation processes as well as cell proliferation. Little is known about regulatory effects of NAT10 in lung epithelial cell proliferation. We firstly investigated NTA10 mRNA expression in alveolar epithelial types I and II, basal, ciliated, club, and goblet/mucous epithelia from heathy and patients with chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, lung adenocarcinoma, para-tumor tissue, and systemic sclerosis, respectively. We selected A549 cells for representative of alveolar epithelia or H1299 and H460 cells as airway epithelia with different genetic backgrounds and studied dynamic responses of NAT10-down-regulated epithelia to high temperature, lipopolysaccharide, cigarette smoking extract (CSE), drugs, radiation, and phosphoinositide 3-kinase (PI3K) inhibitors at various doses. We also compared transcriptomic profiles between alveolar and airway epithelia, between cells with or without NAT10 down-regulation, between early and late stages, and between challenges. The present study demonstrated that NAT10 expression increased in human lung epithelia and varied among epithelial types, challenges, and diseases. Knockdown of NAT10 altered epithelial mitochondrial functions, dynamic responses to LPS, CSE, or PI3K inhibitors, and transcriptomic phenomes. NAT10 regulates biological phenomes, and behaviors are more complex and are dependent upon multiple signal pathways. Thus, NAT10-associated signal pathways can be a new alternative for understanding the disease and developing new biomarkers and targets.
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Affiliation(s)
- Nannan Zheng
- Department of Respiratory Medicine, The First Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Xuanqi Liu
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Ying Yang
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Yifei Liu
- Center of Molecular Diagnosis and Therapy, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Furong Yan
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
- Center of Molecular Diagnosis and Therapy, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China
| | - Yiming Zeng
- Center of Molecular Diagnosis and Therapy, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
| | - Yunfeng Cheng
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China
| | - Duojiao Wu
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China.
| | - Chengshui Chen
- Department of Respiratory Medicine, The First Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, China.
- Quzhou Hospital of Wenzhou Medical University, Quzhou, Zhejiang Province, China.
| | - Xiangdong Wang
- Jinshan Hospital Centre for Tumor Diagnosis and Therapy, Department of Oncology, Fudan University Shanghai Medical College, Shanghai, China.
- Center of Molecular Diagnosis and Therapy, The Second Hospital of Fujian Medical University, Quanzhou, Fujian Province, China.
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4
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Zill NA, Du Y, Marinkovich S, Gu D, Seidel J, Zhang W. Bioactive Natural Product Discovery via Deuterium Adduct Bioactivity Screening. ACS Chem Biol 2023; 18:1192-1199. [PMID: 37125845 DOI: 10.1021/acschembio.3c00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The discovery of bioactive natural products lies at the forefront of human medicine. The continued discovery of these molecules is imperative in the fight against infection and disease. While natural products have historically dominated the drug market, discovery in recent years has slowed significantly, partly due to limitations in current discovery methodologies. This work demonstrates a new workflow, deuterium adduct bioactivity screening (DABS), which pairs untargeted isotope labeling with whole cell binding assays for bioactive natural product discovery. DABS was validated and led to the discovery of a new isoprenyl guanidine alkaloid, zillamycin, which showed anti-cancer and anti-microbial activities. DABS thus represents a new workflow to accelerate discovery of natural products with a wide range of bioactive potentials.
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Affiliation(s)
- Nicholas A Zill
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Yongle Du
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
| | - Samantha Marinkovich
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Di Gu
- Department of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Jeremy Seidel
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California 94720, United States
- Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong 999077, China
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5
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Yu D, Zhou L, Liu X, Xu G. Stable isotope-resolved metabolomics based on mass spectrometry: Methods and their applications. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
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6
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Zhang R, Chen B, Zhang H, Tu L, Luan T. Stable isotope-based metabolic flux analysis: A robust tool for revealing toxicity pathways of emerging contaminants. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2022.116909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Butin N, Bergès C, Portais JC, Bellvert F. An optimization method for untargeted MS-based isotopic tracing investigations of metabolism. Metabolomics 2022; 18:41. [PMID: 35713733 PMCID: PMC9205802 DOI: 10.1007/s11306-022-01897-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 05/17/2022] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Stable isotope tracer studies are increasingly applied to explore metabolism from the detailed analysis of tracer incorporation into metabolites. Untargeted LC/MS approaches have recently emerged and provide potent methods for expanding the dimension and complexity of the metabolic networks that can be investigated. A number of software tools have been developed to process the highly complex MS data collected in such studies; however, a method to optimize the extraction of valuable isotopic data is lacking. OBJECTIVES To develop and validate a method to optimize automated data processing for untargeted MS-based isotopic tracing investigations of metabolism. METHODS The method is based on the application of a suitable reference material to rationally perform parameter optimization throughout the complete data processing workflow. It was applied in the context of 13C-labelling experiments and with two different software, namely geoRge and X13CMS. It was illustrated with the study of a E. coli mutant impaired for central metabolism. RESULTS The optimization methodology provided significant gain in the number and quality of extracted isotopic data, independently of the software considered. Pascal triangle samples are well suited for such purpose since they allow both the identification of analytical issues and optimization of data processing at the same time. CONCLUSION The proposed method maximizes the biological value of untargeted MS-based isotopic tracing investigations by revealing the full metabolic information that is encoded in the labelling patterns of metabolites.
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Affiliation(s)
- Noémie Butin
- RESTORE, CNRS ERL5311, EFS, ENVT, Inserm U1031, UPS, Université de Toulouse, Toulouse, France
- Toulouse Biotechnology Institute, TBI-INSA de Toulouse INSA/ CNRS 5504-UMR INSA/INRA 792, 5504, Toulouse, France
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, 31077, Toulouse, France
| | - Cécilia Bergès
- Toulouse Biotechnology Institute, TBI-INSA de Toulouse INSA/ CNRS 5504-UMR INSA/INRA 792, 5504, Toulouse, France
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, 31077, Toulouse, France
| | - Jean-Charles Portais
- RESTORE, CNRS ERL5311, EFS, ENVT, Inserm U1031, UPS, Université de Toulouse, Toulouse, France
- Toulouse Biotechnology Institute, TBI-INSA de Toulouse INSA/ CNRS 5504-UMR INSA/INRA 792, 5504, Toulouse, France
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, 31077, Toulouse, France
| | - Floriant Bellvert
- Toulouse Biotechnology Institute, TBI-INSA de Toulouse INSA/ CNRS 5504-UMR INSA/INRA 792, 5504, Toulouse, France.
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, 31077, Toulouse, France.
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8
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He W, Henne A, Lauterbach M, Geißmar E, Nikolka F, Kho C, Heinz A, Dostert C, Grusdat M, Cordes T, Härm J, Goldmann O, Ewen A, Verschueren C, Blay-Cadanet J, Geffers R, Garritsen H, Kneiling M, Holm CK, Metallo CM, Medina E, Abdullah Z, Latz E, Brenner D, Hiller K. Mesaconate is synthesized from itaconate and exerts immunomodulatory effects in macrophages. Nat Metab 2022; 4:524-533. [PMID: 35655024 PMCID: PMC9744384 DOI: 10.1038/s42255-022-00565-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 03/25/2022] [Indexed: 01/04/2023]
Abstract
Since its discovery in inflammatory macrophages, itaconate has attracted much attention due to its antimicrobial and immunomodulatory activity1-3. However, instead of investigating itaconate itself, most studies used derivatized forms of itaconate and thus the role of non-derivatized itaconate needs to be scrutinized. Mesaconate, a metabolite structurally very close to itaconate, has never been implicated in mammalian cells. Here we show that mesaconate is synthesized in inflammatory macrophages from itaconate. We find that both, non-derivatized itaconate and mesaconate dampen the glycolytic activity to a similar extent, whereas only itaconate is able to repress tricarboxylic acid cycle activity and cellular respiration. In contrast to itaconate, mesaconate does not inhibit succinate dehydrogenase. Despite their distinct impact on metabolism, both metabolites exert similar immunomodulatory effects in pro-inflammatory macrophages, specifically a reduction of interleukin (IL)-6 and IL-12 secretion and an increase of CXCL10 production in a manner that is independent of NRF2 and ATF3. We show that a treatment with neither mesaconate nor itaconate impairs IL-1β secretion and inflammasome activation. In summary, our results identify mesaconate as an immunomodulatory metabolite in macrophages, which interferes to a lesser extent with cellular metabolism than itaconate.
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Affiliation(s)
- Wei He
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Antonia Henne
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Mario Lauterbach
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Eike Geißmar
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Fabian Nikolka
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Celia Kho
- Institute of Experimental Immunology, University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Alexander Heinz
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Catherine Dostert
- Experimental and Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Immunology and Genetics, Luxembourg Centre for System Biomedicine (LCSB), University of Luxembourg, Belval, Luxembourg
| | - Melanie Grusdat
- Experimental and Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Immunology and Genetics, Luxembourg Centre for System Biomedicine (LCSB), University of Luxembourg, Belval, Luxembourg
| | - Thekla Cordes
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Janika Härm
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
- Experimental and Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Immunology and Genetics, Luxembourg Centre for System Biomedicine (LCSB), University of Luxembourg, Belval, Luxembourg
| | - Oliver Goldmann
- Infection Immunology Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Anouk Ewen
- Experimental and Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Immunology and Genetics, Luxembourg Centre for System Biomedicine (LCSB), University of Luxembourg, Belval, Luxembourg
| | - Charlène Verschueren
- Experimental and Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Immunology and Genetics, Luxembourg Centre for System Biomedicine (LCSB), University of Luxembourg, Belval, Luxembourg
| | | | - Robert Geffers
- Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Hendrikus Garritsen
- Institute of Transfusion Medicine, Klinikum Braunschweig, Braunschweig, Germany
- Fraunhofer Institute for Surface Engineering and Thin Films IST, Braunschweig, Germany
| | - Manfred Kneiling
- Department of Dermatology, Eberhard Karls University, Tübingen, Germany
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University, Tübingen, Germany
| | | | - Christian M Metallo
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Eva Medina
- Infection Immunology Research Group, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Zeinab Abdullah
- Institute of Experimental Immunology, University Hospital Bonn, University of Bonn, Bonn, Germany
- Department of Immunology, Tehran University of Medical Sciences, Tehran, Iran
| | - Eicke Latz
- Institute of Innate Immunity, University Hospital Bonn, University of Bonn, Bonn, Germany
- German Center for Neurodegenerative Diseases, Bonn, Germany
- Department of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA, USA
- Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Trondheim, Norway
| | - Dirk Brenner
- Experimental and Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Immunology and Genetics, Luxembourg Centre for System Biomedicine (LCSB), University of Luxembourg, Belval, Luxembourg
- Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, Odense, Denmark
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.
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Isaacs-Ten A, Moreno-Gonzalez M, Bone C, Martens A, Bernuzzi F, Ludwig T, Hellmich C, Hiller K, Rushworth SA, Beraza N. Metabolic Regulation of Macrophages by SIRT1 Determines Activation During Cholestatic Liver Disease in Mice. Cell Mol Gastroenterol Hepatol 2021; 13:1019-1039. [PMID: 34952202 PMCID: PMC8873616 DOI: 10.1016/j.jcmgh.2021.12.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 12/13/2021] [Accepted: 12/13/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Inflammation is the hallmark of chronic liver disease. Metabolism is a key determinant to regulate the activation of immune cells. Here, we define the role of sirtuin 1 (SIRT1), a main metabolic regulator, in controlling the activation of macrophages during cholestatic liver disease and in response to endotoxin. METHODS We have used mice overexpressing SIRT1, which we treated with intraperitoneal lipopolysaccharides or induced cholestasis by bile duct ligation. Bone marrow-derived macrophages were used for mechanistic in vitro studies. Finally, PEPC-Boy mice were used for adoptive transfer experiments to elucidate the impact of SIRT1-overexpressing macrophages in contributing to cholestatic liver disease. RESULTS We found that SIRT1 overexpression promotes increased liver inflammation and liver injury after lipopolysaccharide/GalN and bile duct ligation; this was associated with an increased activation of the inflammasome in macrophages. Mechanistically, SIRT1 overexpression associated with the activation of the mammalian target of rapamycin (mTOR) pathway that led to increased activation of macrophages, which showed metabolic rewiring with increased glycolysis and broken tricarboxylic acid cycle in response to endotoxin in vitro. Activation of the SIRT1/mTOR axis in macrophages associated with the activation of the inflammasome and the attenuation of autophagy. Ultimately, in an in vivo model of cholestatic disease, the transplantation of SIRT1-overexpressing myeloid cells contributed to liver injury and fibrosis. CONCLUSIONS Our study provides novel mechanistic insights into the regulation of macrophages during cholestatic disease and the response to endotoxin, in which the SIRT1/mTOR crosstalk regulates macrophage activation controlling the inflammasome, autophagy and metabolic rewiring.
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Affiliation(s)
- Anna Isaacs-Ten
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Mar Moreno-Gonzalez
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Caitlin Bone
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Andre Martens
- Department of Bioinfomatics and Biochemistry, Braunschweig Integrated Center of Systems Biology, Braunschweig, Germany
| | - Federico Bernuzzi
- Food Innovation and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Tobias Ludwig
- Department of Bioinfomatics and Biochemistry, Braunschweig Integrated Center of Systems Biology, Braunschweig, Germany
| | - Charlotte Hellmich
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, United Kingdom; Department of Haematology, Norfolk and Norwich University Hospitals NHS Trust, Norwich, United Kingdom
| | - Karsten Hiller
- Department of Bioinfomatics and Biochemistry, Braunschweig Integrated Center of Systems Biology, Braunschweig, Germany; Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stuart A Rushworth
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, United Kingdom.
| | - Naiara Beraza
- Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom; Food Innovation and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich, United Kingdom.
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Abstract
Mitochondria are considered to be the powerhouse of the cell. Normal functioning of the mitochondria is not only essential for cellular energy production but also for several immunomodulatory processes. Macrophages operate in metabolic niches and rely on rapid adaptation to specific metabolic conditions such as hypoxia, nutrient limitations, or reactive oxygen species to neutralize pathogens. In this regard, the fast reprogramming of mitochondrial metabolism is indispensable to provide the cells with the necessary energy and intermediates to efficiently mount the inflammatory response. Moreover, mitochondria act as a physical scaffold for several proteins involved in immune signaling cascades and their dysfunction is immediately associated with a dampened immune response. In this review, we put special focus on mitochondrial function in macrophages and highlight how mitochondrial metabolism is involved in macrophage activation.
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Affiliation(s)
- Mohamed Zakaria Nassef
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Brunswick, Germany
| | - Jasmin E Hanke
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Brunswick, Germany
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Brunswick, Germany
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11
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Audano M, Pedretti S, Ligorio S, Giavarini F, Caruso D, Mitro N. Investigating metabolism by mass spectrometry: From steady state to dynamic view. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4658. [PMID: 33084147 DOI: 10.1002/jms.4658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
Metabolism is the set of life-sustaining reactions in organisms. These biochemical reactions are organized in metabolic pathways, in which one metabolite is converted through a series of steps catalyzed by enzymes in another chemical compound. Metabolic reactions are categorized as catabolic, the breaking down of metabolites to produce energy, and/or anabolic, the synthesis of compounds that consume energy. The balance between catabolism of the preferential fuel substrate and anabolism defines the overall metabolism of a cell or tissue. Metabolomics is a powerful tool to gain new insights contributing to the identification of complex molecular mechanisms in the field of biomedical research, both basic and translational. The enormous potential of this kind of analyses consists of two key aspects: (i) the possibility of performing so-called targeted and untargeted experiments through which it is feasible to verify or formulate a hypothesis, respectively, and (ii) the opportunity to run either steady-state analyses to have snapshots of the metabolome at a given time under different experimental conditions or dynamic analyses through the use of labeled tracers. In this review, we will highlight the most important practical (e.g., different sample extraction approaches) and conceptual steps to consider for metabolomic analysis, describing also the main application contexts in which it is used. In addition, we will provide some insights into the most innovative approaches and progress in the field of data analysis and processing, highlighting how this part is essential for the proper extrapolation and interpretation of data.
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Affiliation(s)
- Matteo Audano
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| | - Silvia Pedretti
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| | - Simona Ligorio
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| | - Flavio Giavarini
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| | - Donatella Caruso
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
| | - Nico Mitro
- DiSFeB, Dipartimento di Scienze Farmacologiche e Biomolecolari, Università degli Studi di Milano, Milan, 20133, Italy
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12
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Dudek CA, Reuse C, Fuchs R, Hendriks J, Starck V, Hiller K. MIAMI--a tool for non-targeted detection of metabolic flux changes for mode of action identification. Bioinformatics 2020; 36:3925-3926. [PMID: 32324861 PMCID: PMC7320603 DOI: 10.1093/bioinformatics/btaa251] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 02/13/2020] [Accepted: 04/16/2020] [Indexed: 12/02/2022] Open
Abstract
Summary Mass isotopolome analysis for mode of action identification (MIAMI) combines the strengths of targeted and non-targeted approaches to detect metabolic flux changes in gas chromatography/mass spectrometry datasets. Based on stable isotope labeling experiments, MIAMI determines a mass isotopomer distribution-based (MID) similarity network and incorporates the data into metabolic reference networks. By identifying MID variations of all labeled compounds between different conditions, targets of metabolic changes can be detected. Availability and implementation We implemented the data processing in C++17 with Qt5 back-end using MetaboliteDetector and NTFD libraries. The data visualization is implemented as web application. Executable binaries and visualization are freely available for Linux operating systems, the source code is licensed under General Public License version 3.
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Affiliation(s)
- Christian-Alexander Dudek
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig 38106, Germany
| | - Carsten Reuse
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig 38106, Germany
| | - Regine Fuchs
- BASF Metabolome Solutions GmbH, Berlin 10589, Germany
| | | | - Veronique Starck
- BASF Metabolome Solutions GmbH, Berlin 10589, Germany.,BASF SE, Lampertheim 68623, Germany
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, Technische Universität Braunschweig, Braunschweig 38106, Germany.,Department of Immunometabolism, Helmholtz Center for Infection Research, Braunschweig 38124, Germany
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13
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Moffett JR, Puthillathu N, Vengilote R, Jaworski DM, Namboodiri AM. Acetate Revisited: A Key Biomolecule at the Nexus of Metabolism, Epigenetics, and Oncogenesis - Part 2: Acetate and ACSS2 in Health and Disease. Front Physiol 2020; 11:580171. [PMID: 33304273 PMCID: PMC7693462 DOI: 10.3389/fphys.2020.580171] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/19/2020] [Indexed: 12/19/2022] Open
Abstract
Acetate, the shortest chain fatty acid, has been implicated in providing health benefits whether it is derived from the diet or is generated from microbial fermentation of fiber in the gut. These health benefits range widely from improved cardiac function to enhanced red blood cell generation and memory formation. Understanding how acetate could influence so many disparate biological functions is now an area of intensive research. Protein acetylation is one of the most common post-translational modifications and increased systemic acetate strongly drives protein acetylation. By virtue of acetylation impacting the activity of virtually every class of protein, acetate driven alterations in signaling and gene transcription have been associated with several common human diseases, including cancer. In part 2 of this review, we will focus on some of the roles that acetate plays in health and human disease. The acetate-activating enzyme acyl-CoA short-chain synthetase family member 2 (ACSS2) will be a major part of that focus due to its role in targeted protein acetylation reactions that can regulate central metabolism and stress responses. ACSS2 is the only known enzyme that can recycle acetate derived from deacetylation reactions in the cytoplasm and nucleus of cells, including both protein and metabolite deacetylation reactions. As such, ACSS2 can recycle acetate derived from histone deacetylase reactions as well as protein deacetylation reactions mediated by sirtuins, among many others. Notably, ACSS2 can activate acetate released from acetylated metabolites including N-acetylaspartate (NAA), the most concentrated acetylated metabolite in the human brain. NAA has been associated with the metabolic reprograming of cancer cells, where ACSS2 also plays a role. Here, we discuss the context-specific roles that acetate can play in health and disease.
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Affiliation(s)
- John R. Moffett
- Department of Anatomy, Physiology and Genetics, and Neuroscience Program, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Narayanan Puthillathu
- Department of Anatomy, Physiology and Genetics, and Neuroscience Program, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Ranjini Vengilote
- Department of Anatomy, Physiology and Genetics, and Neuroscience Program, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Diane M. Jaworski
- Department of Neurological Sciences, University of Vermont College of Medicine, Burlington, VT, United States
| | - Aryan M. Namboodiri
- Department of Anatomy, Physiology and Genetics, and Neuroscience Program, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
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14
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Challenges in Analysis of Hydrophilic Metabolites Using Chromatography Coupled with Mass Spectrometry. JOURNAL OF ANALYSIS AND TESTING 2020. [DOI: 10.1007/s41664-020-00126-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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15
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Dudek CA, Schlicker L, Hiller K. Non-Targeted Mass Isotopolome Analysis Using Stable Isotope Patterns to Identify Metabolic Changes. Methods Mol Biol 2020; 2088:17-32. [PMID: 31893368 DOI: 10.1007/978-1-0716-0159-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Gas chromatography coupled with mass spectrometry can provide an extensive overview of the metabolic state of a biological system. Analysis of raw mass spectrometry data requires powerful data processing software to generate interpretable results. Here we describe a data processing workflow to generate metabolite levels, mass isotopomer distribution, similarity and variability analysis of metabolites in a nontargeted manner, using stable isotope labeling. Using our data analysis software, no bioinformatic or programming background is needed to generate results from raw mass spectrometry data.
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Affiliation(s)
- Christian-Alexander Dudek
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Lisa Schlicker
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.
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16
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Volpari T, De Santis F, Bracken AP, Pupa SM, Buschbeck M, Wegner A, Di Cosimo S, Lisanti MP, Dotti G, Massaia M, Pruneri G, Anichini A, Fortunato O, De Braud F, Del Vecchio M, Di Nicola M. Anticancer innovative therapy: Highlights from the ninth annual meeting. Cytokine Growth Factor Rev 2019; 51:1-9. [PMID: 31862236 DOI: 10.1016/j.cytogfr.2019.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The Ninth Annual Conference of "Anticancer Innovative Therapy", organized by Fondazione IRCCS Istituto Nazionale dei Tumori di Milano (Fondazione IRCCS INT) and hosted by Hotel Michelangelo, was held in Milan on 25 January 2019. Cutting-edge science was presented in two main scientific sessions: i) pre-clinical evidences and new targets, and ii) clinical translation. The Keynote lecture entitled "Cancer stem cells (CSCs): metabolic strategies for their identification and eradication" presented by M. Lisanti, was one of the highlights of the conference. One key concept of the meeting was how the continuous advances in our knowledge about molecular mechanisms in various fields of research (cancer metabolism reprogramming, epigenetic regulation, transformation/invasiveness, and immunology, among others) are driving cancer research towards more effective personalized antineoplastic strategies. Specifically, recent preclinical data on the following topics were discussed: 1. Polycomb group proteins in cancer; 2. A d16HER2 splice variant is a flag of HER2 addiction across HER2-positive cancers; 3. Studying chromatin as a nexus between translational and basic research; 4. Metabolomic analysis in cancer patients; 5. CDK4-6 cyclin inhibitors: clinical activity and future perspectives as immunotherapy adjuvant; and 6. Cancer stem cells (CSCs): metabolic strategies for their identification and eradication. In terms of clinical translation, several novel approaches were presented: 1. Developing CAR-T cell therapies: an update of preclinical and clinical development at University of North Carolina; 2. Vγ9Vδ2 T-cell activation and immune suppression in multiple myeloma; 3. Predictive biomarkers for real-world immunotherapy: the cancer immunogram model in the clinical arena; and 4. Mechanisms of resistance to immune checkpoint blockade in solid tumors. Overall, the pre-clinical and clinical findings presented could pave the way to identify novel actionable therapeutic targets to significantly enhance the care of persons with cancer.
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Affiliation(s)
- T Volpari
- Immunotherapy and Innovative Therapeutics Unit, Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - F De Santis
- Immunotherapy and Innovative Therapeutics Unit, Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - A P Bracken
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - S M Pupa
- Molecular Targeting Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - M Buschbeck
- Josep Carreras Leukemia Research Institute (IJC), Campus ICO-Germans Trias I Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - A Wegner
- Technische Universiät Braunschweig, Department of Bioinfomatics and Biochemistry and Braunschweig Integrated Center of Systems Biology (BRICS), Rebenring 56, 38106, Braunschweig, Germany
| | - S Di Cosimo
- Department of Applied Research and Technological Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - M P Lisanti
- Translational Medicine, Biomedical Research Centre, School of Environment and Life Sciences, University of Salford, Greater Manchester, United Kingdom
| | - G Dotti
- Lineberger Comprehensive Cancer Center and Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, United States
| | - M Massaia
- Laboratorio di Immunologia dei Tumori del Sangue, Centro Interdipartimentale di Ricerca in Biologia Molecolare, Università degli Studi di Torino, Turin, Italy; SC Ematologia, AO S. Croce e Carle, Cuneo, Italy
| | - G Pruneri
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS - Istituto Nazionale dei Tumori, Milan, Italy
| | - A Anichini
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - O Fortunato
- Tumor Genomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - F De Braud
- Medical Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - M Del Vecchio
- Immunotherapy and Innovative Therapeutics Unit, Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Unit of Melanoma Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - M Di Nicola
- Immunotherapy and Innovative Therapeutics Unit, Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; Medical Oncology Unit, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
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17
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Lyu Y, Wu J, Shi Y. Metabolic and physiological perturbations of Escherichia coli W3100 by bacterial small RNA RyhB. Biochimie 2019; 162:144-155. [PMID: 31002843 DOI: 10.1016/j.biochi.2019.04.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 04/12/2019] [Indexed: 11/17/2022]
Abstract
RyhB is a key regulator of iron level in Escherichia coli (E. coli), which assists in conserving iron for life-sustaining cellular functions when cytoplasmic levels of the ferrous form of iron is limited. RyhB affects glucose metabolism. Seventy percent of the genes that are regulated by RyhB are related to metabolism. We demonstrated for the first time that the activity of the pentose phosphate pathway increased upon ryhB activation using a13C stable isotope-based technique called METAFoR (Metabolic flux ratio analysis). U-13C glucose-based studies showed that the reversible exchange activity of serine and glycine was enhanced by flux redistribution, which further favors NADPH formation. In addition, Entner-Doudoroff (ED) pathway activity was inhibited in the ryhB-defective cells. Quantitative physiology-based experiments highlighted a significant increase in the levels of reactive oxygen species (ROS) in ryhB-induced W3100 E. coli cells in batch culture. A simultaneous decrease in NADH/NAD+ and NADPH/NADP+ ratios outlined the potentially direct roles of NADH and NADPH in antagonizing the excess ROS formed after ryhB activation. Our observations offer a new perspective regarding the roles of RyhB and highlight that this small RNA can significantly affect cell metabolism in addition to its role as a regulator of gene expression.
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Affiliation(s)
- Yu Lyu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Jihui Wu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, People's Republic of China.
| | - Yunyu Shi
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, People's Republic of China.
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18
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Schwaiger-Haber M, Hermann G, El Abiead Y, Rampler E, Wernisch S, Sas K, Pennathur S, Koellensperger G. Proposing a validation scheme for 13C metabolite tracer studies in high-resolution mass spectrometry. Anal Bioanal Chem 2019; 411:3103-3113. [PMID: 30972471 PMCID: PMC6526147 DOI: 10.1007/s00216-019-01773-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/25/2019] [Accepted: 03/08/2019] [Indexed: 12/31/2022]
Abstract
13C metabolite tracer and metabolic flux analyses require upfront experimental planning and validation tools. Here, we present a validation scheme including a comparison of different LC methods that allow for customization of analytical strategies for tracer studies with regard to the targeted metabolites. As the measurement of significant changes in labeling patterns depends on the spectral accuracy, we investigate this aspect comprehensively for high-resolution orbitrap mass spectrometry combined with reversed-phase chromatography, hydrophilic interaction liquid chromatography, or anion-exchange chromatography. Moreover, we propose a quality control protocol based on (1) a metabolite containing selenium to assess the instrument performance and on (2) in vivo synthesized isotopically enriched Pichia pastoris to validate the accuracy of carbon isotopologue distributions (CIDs), in this case considering each isotopologue of a targeted metabolite panel. Finally, validation involved a thorough assessment of procedural blanks and matrix interferences. We compared the analytical figures of merit regarding CID determination for over 40 metabolites between the three methods. Excellent precisions of less than 1% and trueness bias as small as 0.01-1% were found for the majority of compounds, whereas the CID determination of a small fraction was affected by contaminants. For most compounds, changes of labeling pattern as low as 1% could be measured. Graphical abstract.
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Affiliation(s)
- Michaela Schwaiger-Haber
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090, Vienna, Austria.,Division of Nephrology, Department of Internal Medicine, University of Michigan, 1000 Wall St., Ann Arbor, MI, 48105, USA
| | - Gerrit Hermann
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090, Vienna, Austria.,ISOtopic solutions, Waehringer Str. 38, 1090, Vienna, Austria
| | - Yasin El Abiead
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090, Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090, Vienna, Austria.,Chemistry Meets Microbiology, Althanstraße 14, 1090, Vienna, Austria
| | - Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090, Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090, Vienna, Austria.,Chemistry Meets Microbiology, Althanstraße 14, 1090, Vienna, Austria
| | - Stefanie Wernisch
- Division of Nephrology, Department of Internal Medicine, University of Michigan, 1000 Wall St., Ann Arbor, MI, 48105, USA
| | - Kelli Sas
- Division of Nephrology, Department of Internal Medicine, University of Michigan, 1000 Wall St., Ann Arbor, MI, 48105, USA
| | - Subramaniam Pennathur
- Division of Nephrology, Department of Internal Medicine, University of Michigan, 1000 Wall St., Ann Arbor, MI, 48105, USA.,Department of Molecular and Integrative Physiology, University of Michigan, 1000 Wall St, Ann Arbor, MI, 48105, USA
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090, Vienna, Austria. .,Vienna Metabolomics Center (VIME), University of Vienna, Althanstraße 14, 1090, Vienna, Austria. .,Chemistry Meets Microbiology, Althanstraße 14, 1090, Vienna, Austria.
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19
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Zeng J, Wang Z, Huang X, Eckstein SS, Lin X, Piao H, Weigert C, Yin P, Lehmann R, Xu G. Comprehensive Profiling by Non-targeted Stable Isotope Tracing Capillary Electrophoresis-Mass Spectrometry: A New Tool Complementing Metabolomic Analyses of Polar Metabolites. Chemistry 2019; 25:5427-5432. [PMID: 30810245 DOI: 10.1002/chem.201900539] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Indexed: 01/25/2023]
Abstract
Mass spectrometry (MS) driven metabolomics is a frequently used tool in various areas of life sciences; however, the analysis of polar metabolites is less commonly included. In general, metabolomic analyses lead to the detection of the total amount of all covered metabolites. This is currently a major limitation with respect to metabolites showing high turnover rates, but no changes in their concentration. Such metabolites and pathways could be crucial metabolic nodes (e.g., potential drug targets in cancer metabolism). A stable-isotope tracing capillary electrophoresis-mass spectrometry (CE-MS) metabolomic approach was developed to cover both polar metabolites and isotopologues in a non-targeted way. An in-house developed software enables high throughput processing of complex multidimensional data. The practicability is demonstrated analyzing [U-13 C]-glucose exposed prostate cancer and non-cancer cells. This CE-MS-driven analytical strategy complements polar metabolite profiles through isotopologue labeling patterns, thereby improving not only the metabolomic coverage, but also the understanding of metabolism.
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Affiliation(s)
- Jun Zeng
- 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
| | - Xin Huang
- Department of Computer Science & Engineering, Dalian University of Technology, Dalian, 116024, China
| | - Sabine S Eckstein
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, 72076, Tübingen, Germany.,Core Facility German Center for Diabetes Research (DZD), Clinical Chemistry Laboratory, Institute for Diabetes Research and Metabolic Diseases, University Hospital Tübingen, 72076, Tübingen, Germany.,German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Xiaohui Lin
- Department of Computer Science & Engineering, Dalian University of Technology, Dalian, 116024, China
| | - Hailong Piao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Cora Weigert
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, 72076, Tübingen, Germany.,Core Facility German Center for Diabetes Research (DZD), Clinical Chemistry Laboratory, Institute for Diabetes Research and Metabolic Diseases, University Hospital Tübingen, 72076, Tübingen, Germany.,German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Peiyuan Yin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Rainer Lehmann
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tübingen, 72076, Tübingen, Germany.,Core Facility German Center for Diabetes Research (DZD), Clinical Chemistry Laboratory, Institute for Diabetes Research and Metabolic Diseases, University Hospital Tübingen, 72076, Tübingen, Germany.,German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
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20
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Puchalska P, Huang X, Martin SE, Han X, Patti GJ, Crawford PA. Isotope Tracing Untargeted Metabolomics Reveals Macrophage Polarization-State-Specific Metabolic Coordination across Intracellular Compartments. iScience 2018; 9:298-313. [PMID: 30448730 PMCID: PMC6240706 DOI: 10.1016/j.isci.2018.10.029] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 08/21/2018] [Accepted: 10/29/2018] [Indexed: 12/18/2022] Open
Abstract
We apply stable isotope tracing, mass-spectrometry-based untargeted metabolomics, to reveal the biochemical space labeled by 13C-substrates in bone-marrow-derived macrophages. At the pathway level, classically (lipopolysaccharide [LPS]-polarized, M1) and alternatively (interleukin [IL]-4-polarized, M2) polarized macrophages were 13C-labeled with surprising concordance. Total pools of uridine diphosphate N-acetylglucosamine (UDP-GlcNAc), an intermediate in the hexosamine biosynthetic pathway, were equally abundant in LPS- and IL-4-polarized macrophages. Informatic scrutiny of 13C-isotopologues revealed that LPS-polarized macrophages leverage the pentose phosphate pathway to generate UDP-GlcNAc, whereas IL-4-polarized macrophages rely on intact glucose and mitochondrial metabolism of glucose carbon. Labeling from [13C]glucose is competed by unlabeled fatty acids and acetoacetate, underscoring the broad roles for substrate metabolism beyond energy conversion. Finally, the LPS-polarized macrophage metabolite itaconate is imported into IL-4-polarized macrophages, in which it reprograms [13C]glucose metabolism. Thus, use of fully unsupervised isotope tracing metabolomics in macrophages reveals polarization-state-specific metabolic pathway connectivity, substrate competition, and metabolite allocation among cellular compartments.
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Affiliation(s)
- Patrycja Puchalska
- Division of Molecular Medicine, Department of Medicine, University of Minnesota, 401 East River Parkway, MMC 194, Minneapolis, MN 55455, USA; Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827, USA
| | - Xiaojing Huang
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827, USA; Department of Chemistry, Washington University, St. Louis, MO 63110, USA; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Shannon E Martin
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827, USA; Pathobiology Graduate Program, Brown University, Providence, RI 02912, USA
| | - Xianlin Han
- Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827, USA; Barshop Institute for Longevity and Aging Studies, Department of Medicine, Division of Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Gary J Patti
- Department of Chemistry, Washington University, St. Louis, MO 63110, USA
| | - Peter A Crawford
- Division of Molecular Medicine, Department of Medicine, University of Minnesota, 401 East River Parkway, MMC 194, Minneapolis, MN 55455, USA; Center for Metabolic Origins of Disease, Sanford Burnham Prebys Medical Discovery Institute, Orlando, FL 32827, USA; Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.
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21
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Huber K, Hofer DC, Trefely S, Pelzmann HJ, Madreiter-Sokolowski C, Duta-Mare M, Schlager S, Trausinger G, Stryeck S, Graier WF, Kolb D, Magnes C, Snyder NW, Prokesch A, Kratky D, Madl T, Wellen KE, Bogner-Strauss JG. N-acetylaspartate pathway is nutrient responsive and coordinates lipid and energy metabolism in brown adipocytes. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1866:337-348. [PMID: 30595160 PMCID: PMC6390944 DOI: 10.1016/j.bbamcr.2018.08.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 08/27/2018] [Indexed: 12/22/2022]
Abstract
The discovery of significant amounts of metabolically active brown adipose tissue (BAT) in adult humans renders it a promising target for anti-obesity therapies by inducing weight loss through increased energy expenditure. The components of the N-acetylaspartate (NAA) pathway are highly abundant in BAT. Aspartate N-acetyltransferase (Asp-NAT, encoded by Nat8l) synthesizes NAA from acetyl-CoA and aspartate and increases energy expenditure in brown adipocytes. However, the exact mechanism how the NAA pathway contributes to accelerated mobilization and oxidation of lipids and the physiological regulation of the NAA pathway remained elusive. Here, we demonstrate that the expression of NAA pathway genes corresponds to nutrient availability and specifically responds to changes in exogenous glucose. NAA is preferentially produced from glucose-derived acetyl-CoA and aspartate and its concentration increases during adipogenesis. Overexpression of Nat8l drains glucose-derived acetyl-CoA into the NAA pool at the expense of cellular lipids and certain amino acids. Mechanistically, we elucidated that a combined activation of neutral and lysosomal (acid) lipolysis is responsible for the increased lipid degradation. Specifically, translocation of the transcription factor EB to the nucleus activates the biosynthesis of autophagosomes and lysosomes. Lipid degradation within lysosomes accompanied by adipose triglyceride lipase-mediated lipolysis delivers fatty acids for the support of elevated mitochondrial respiration. Together, our data suggest a crucial role of the NAA pathway in energy metabolism and metabolic adaptation in BAT.
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Affiliation(s)
- Katharina Huber
- Institute of Biochemistry, Graz University of Technology, Graz, Austria; Department of Cancer Biology, University of Pennsylvania, Philadelphia, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, USA
| | - Dina C Hofer
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Sophie Trefely
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, USA; AJ Drexel Autism Institute, Drexel University, Philadelphia, USA
| | - Helmut J Pelzmann
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Corina Madreiter-Sokolowski
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Madalina Duta-Mare
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Stefanie Schlager
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Gert Trausinger
- HEALTH Institute for Biomedicine and Health Sciences, Joanneum Research, Graz, Austria
| | - Sarah Stryeck
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Wolfgang F Graier
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Dagmar Kolb
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Christoph Magnes
- HEALTH Institute for Biomedicine and Health Sciences, Joanneum Research, Graz, Austria
| | | | - Andreas Prokesch
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Dagmar Kratky
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Kathryn E Wellen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, USA
| | - Juliane G Bogner-Strauss
- Institute of Biochemistry, Graz University of Technology, Graz, Austria; BioTechMed-Graz, Graz, Austria.
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22
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Bogner-Strauss JG. N-Acetylaspartate Metabolism Outside the Brain: Lipogenesis, Histone Acetylation, and Cancer. Front Endocrinol (Lausanne) 2017; 8:240. [PMID: 28979238 PMCID: PMC5611401 DOI: 10.3389/fendo.2017.00240] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 08/30/2017] [Indexed: 01/18/2023] Open
Abstract
N-acetylaspartate (NAA) is a highly abundant brain metabolite. Aberrant NAA concentrations have been detected in many pathological conditions and although the function of NAA has been extensively investigated in the brain it is still controversial. Only recently, a role of NAA has been reported outside the brain. In brown adipocytes, which show high expression of the NAA-producing and the NAA-cleaving enzyme, the metabolism of NAA has been implicated in lipid synthesis and histone acetylation. Increased expression of N-acetyltransferase 8-like (Nat8l, the gene encoding the NAA synthesizing enzyme) induces de novo lipogenesis and the brown adipocyte phenotype. Accordingly silencing of aspartoacylase, the NAA-cleaving enzyme, reduced brown adipocyte differentiation mechanistically by decreasing histone acetylation and gene transcription. Notably, the expression of Nat8l and the amount of NAA were also shown to be increased in several tumors and inversely correlate with patients' survival. Additionally, Nat8l silencing reduced cell proliferation in tumor and non-tumor cells, while NAA supplementation could rescue it. However, the mechanism behind has not yet been clarified. It remains to be addressed whether NAA per se and/or its catabolism to acetate and aspartate, metabolites that have both been implicated in tumor growth, are valuable targets for future therapies.
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Affiliation(s)
- Juliane G. Bogner-Strauss
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
- BioTechMed-Graz, Graz, Austria
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23
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Azizan KA, Ressom HW, Mendoza ER, Baharum SN. 13C based proteinogenic amino acid (PAA) and metabolic flux ratio analysis of Lactococcus lactis reveals changes in pentose phosphate (PP) pathway in response to agitation and temperature related stresses. PeerJ 2017; 5:e3451. [PMID: 28695065 PMCID: PMC5501154 DOI: 10.7717/peerj.3451] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/19/2017] [Indexed: 11/20/2022] Open
Abstract
Lactococcus lactis subsp. cremoris MG1363 is an important starter culture for dairy fermentation. During industrial fermentations, L. lactis is constantly exposed to stresses that affect the growth and performance of the bacterium. Although the response of L. lactis to several stresses has been described, the adaptation mechanisms at the level of in vivo fluxes have seldom been described. To gain insights into cellular metabolism, 13C metabolic flux analysis and gas chromatography mass spectrometry (GC-MS) were used to measure the flux ratios of active pathways in the central metabolism of L. lactis when subjected to three conditions varying in temperature (30°C, 37°C) and agitation (with and without agitation at 150 rpm). Collectively, the concentrations of proteinogenic amino acids (PAAs) and free fatty acids (FAAs) were compared, and Pearson correlation analysis (r) was calculated to measure the pairwise relationship between PAAs. Branched chain and aromatic amino acids, threonine, serine, lysine and histidine were correlated strongly, suggesting changes in flux regulation in glycolysis, the pentose phosphate (PP) pathway, malic enzyme and anaplerotic reaction catalysed by pyruvate carboxylase (pycA). Flux ratio analysis revealed that glucose was mainly converted by glycolysis, highlighting the stability of L. lactis’ central carbon metabolism despite different conditions. Higher flux ratios through oxaloacetate (OAA) from pyruvate (PYR) reaction in all conditions suggested the activation of pyruvate carboxylate (pycA) in L. lactis, in response to acid stress during exponential phase. Subsequently, more significant flux ratio differences were seen through the oxidative and non-oxidative pentose phosphate (PP) pathways, malic enzyme, and serine and C1 metabolism, suggesting NADPH requirements in response to environmental stimuli. These reactions could play an important role in optimization strategies for metabolic engineering in L. lactis. Overall, the integration of systematic analysis of amino acids and flux ratio analysis provides a systems-level understanding of how L. lactis regulates central metabolism under various conditions.
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Affiliation(s)
- Kamalrul Azlan Azizan
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor, Malaysia
| | - Habtom W Ressom
- Departments of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, D.C., United States of America
| | - Eduardo R Mendoza
- Institute of Mathematics, University of the Philippines Diliman, Quezon City, Metro Manila, Philippines.,Membrane Biochemistry Group, Max Planck Institute of Biochemistry, Planegg, Germany
| | - Syarul Nataqain Baharum
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor, Malaysia
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24
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Appu AP, Moffett JR, Arun P, Moran S, Nambiar V, Krishnan JKS, Puthillathu N, Namboodiri AMA. Increasing N-acetylaspartate in the Brain during Postnatal Myelination Does Not Cause the CNS Pathologies of Canavan Disease. Front Mol Neurosci 2017; 10:161. [PMID: 28626388 PMCID: PMC5454052 DOI: 10.3389/fnmol.2017.00161] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 05/09/2017] [Indexed: 01/03/2023] Open
Abstract
Canavan disease is caused by mutations in the gene encoding aspartoacylase (ASPA), a deacetylase that catabolizes N-acetylaspartate (NAA). The precise involvement of elevated NAA in the pathogenesis of Canavan disease is an ongoing debate. In the present study, we tested the effects of elevated NAA in the brain during postnatal development. Mice were administered high doses of the hydrophobic methyl ester of NAA (M-NAA) twice daily starting on day 7 after birth. This treatment increased NAA levels in the brain to those observed in the brains of Nur7 mice, an established model of Canavan disease. We evaluated various serological parameters, oxidative stress, inflammatory and neurodegeneration markers and the results showed that there were no pathological alterations in any measure with increased brain NAA levels. We examined oxidative stress markers, malondialdehyde content (indicator of lipid peroxidation), expression of NADPH oxidase and nuclear translocation of the stress-responsive transcription factor nuclear factor (erythroid-derived 2)-like 2 (NRF-2) in brain. We also examined additional pathological markers by immunohistochemistry and the expression of activated caspase-3 and interleukin-6 by Western blot. None of the markers were increased in the brains of M-NAA treated mice, and no vacuoles were observed in any brain region. These results show that ASPA expression prevents the pathologies associated with excessive NAA concentrations in the brain during postnatal myelination. We hypothesize that the pathogenesis of Canavan disease involves not only disrupted NAA metabolism, but also excessive NAA related signaling processes in oligodendrocytes that have not been fully determined and we discuss some of the potential mechanisms.
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Affiliation(s)
- Abhilash P. Appu
- Department of Anatomy, Physiology and Genetics and Neuroscience Program, Uniformed Services University of the Health SciencesBethesda, MD, United States
| | - John R. Moffett
- Department of Anatomy, Physiology and Genetics and Neuroscience Program, Uniformed Services University of the Health SciencesBethesda, MD, United States
| | - Peethambaran Arun
- Department of Anatomy, Physiology and Genetics and Neuroscience Program, Uniformed Services University of the Health SciencesBethesda, MD, United States
| | - Sean Moran
- Department of Anatomy, Physiology and Genetics and Neuroscience Program, Uniformed Services University of the Health SciencesBethesda, MD, United States
| | - Vikram Nambiar
- Department of Anatomy, Physiology and Genetics and Neuroscience Program, Uniformed Services University of the Health SciencesBethesda, MD, United States
| | - Jishnu K. S. Krishnan
- Department of Anatomy, Physiology and Genetics and Neuroscience Program, Uniformed Services University of the Health SciencesBethesda, MD, United States
| | - Narayanan Puthillathu
- Department of Anatomy, Physiology and Genetics and Neuroscience Program, Uniformed Services University of the Health SciencesBethesda, MD, United States
| | - Aryan M. A. Namboodiri
- Department of Anatomy, Physiology and Genetics and Neuroscience Program, Uniformed Services University of the Health SciencesBethesda, MD, United States
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25
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Quantitative metabolic flux analysis reveals an unconventional pathway of fatty acid synthesis in cancer cells deficient for the mitochondrial citrate transport protein. Metab Eng 2016; 43:198-207. [PMID: 27856334 DOI: 10.1016/j.ymben.2016.11.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/13/2016] [Accepted: 11/07/2016] [Indexed: 11/23/2022]
Abstract
The mitochondrial citrate transport protein (CTP), encoded by SLC25A1, accommodates bidirectional trafficking of citrate between the mitochondria and cytosol, supporting lipid biosynthesis and redox homeostasis. Genetic CTP deficiency causes a fatal neurodevelopmental syndrome associated with the accumulation of L- and D-2-hydroxyglutaric acid, and elevated CTP expression is associated with poor prognosis in several types of cancer, emphasizing the importance of this transporter in multiple human pathologies. Here we describe the metabolic consequences of CTP deficiency in cancer cells. As expected from the phenotype of CTP-deficient humans, somatic CTP loss in cancer cells induces broad dysregulation of mitochondrial metabolism, resulting in accumulation of lactate and of the L- and D- enantiomers of 2-hydroxyglutarate (2HG) and depletion of TCA cycle intermediates. It also eliminates mitochondrial import of citrate from the cytosol. To quantify the impact of CTP deficiency on metabolic flux, cells were cultured with a set of 13C-glucose and 13C-glutamine tracers with resulting data integrated by metabolic flux analysis (MFA). CTP-deficient cells displayed a major restructuring of central carbon metabolism, including suppression of pyruvate dehydrogenase (PDH) and induction of glucose-dependent anaplerosis through pyruvate carboxylase (PC). We also observed an unusual lipogenic pathway in which carbon from glucose supplies mitochondrial production of alpha-ketoglutarate (AKG), which is then trafficked to the cytosol and used to supply reductive carboxylation by isocitrate dehydrogenase 1 (IDH1). The resulting citrate is cleaved to produce lipogenic acetyl-CoA, thereby completing a novel pathway of glucose-dependent reductive carboxylation. In CTP deficient cells, IDH1 inhibition suppresses lipogenesis from either glucose or glutamine, implicating IDH1 as a required component of fatty acid synthesis in states of CTP deficiency.
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26
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Leippe D, Sobol M, Vidugiris G, Cali JJ, Vidugiriene J. Bioluminescent Assays for Glucose and Glutamine Metabolism: High-Throughput Screening for Changes in Extracellular and Intracellular Metabolites. SLAS DISCOVERY 2016; 22:366-377. [DOI: 10.1177/1087057116675612] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cancer cell metabolism is a complex, dynamic network of regulated pathways. Interrogation of this network would benefit from rapid, sensitive techniques that are adaptable to high-throughput formats, facilitating novel compound screening. This requires assays that have minimal sample preparation and are adaptable to lower-volume 384-well formats and automation. Here we describe bioluminescent glucose, lactate, glutamine, and glutamate detection assays that are well suited for high-throughput analysis of two major metabolic pathways in cancer cells: glycolysis and glutaminolysis. The sensitivity (1–5 pmol/sample), broad linear range (0.1–100 µM), and wide dynamic range (>100-fold) are advantageous for measuring both extracellular and intracellular metabolites. Importantly, the assays incorporate rapid inactivation of endogenous enzymes, eliminating deproteinization steps required by other methods. Using ovarian cancer cell lines as a model system, the assays were used to monitor changes in glucose and glutamine consumption and lactate and glutamate secretion over time. Homogeneous formats of the lactate and glutamate assays were robust (Z′ = 0.6–0.9) and could be multiplexed with a real-time viability assay to generate internally controlled data. Screening a small-compound library with these assays resulted in the identification of both inhibitors and activators of lactate and glutamate production.
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Affiliation(s)
- Donna Leippe
- Research and Development, Promega Corporation, Madison, WI, USA
| | - Mary Sobol
- Research and Development, Promega Corporation, Madison, WI, USA
| | | | - James J. Cali
- Research and Development, Promega Corporation, Madison, WI, USA
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27
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Weindl D, Wegner A, Hiller K. MIA: non-targeted mass isotopolome analysis. Bioinformatics 2016; 32:2875-6. [PMID: 27273671 PMCID: PMC5018370 DOI: 10.1093/bioinformatics/btw317] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/06/2016] [Accepted: 05/15/2016] [Indexed: 01/22/2023] Open
Abstract
UNLABELLED MIA detects and visualizes isotopic enrichment in gas chromatography electron ionization mass spectrometry (GC-EI-MS) datasets in a non-targeted manner. It provides an easy-to-use graphical user interface that allows for visual mass isotopomer distribution analysis across multiple datasets. MIA helps to reveal changes in metabolic fluxes, visualizes metabolic proximity of isotopically enriched compounds and shows the fate of the applied stable isotope labeled tracer. AVAILABILITY AND IMPLEMENTATION Linux and Windows binaries, documentation, and sample data are freely available for download at http://massisotopolomeanalyzer.lu MIA is a stand-alone application implemented in C ++ and based on Qt5, NTFD and the MetaboliteDetector framework. CONTACT karsten.hiller@uni.lu.
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Affiliation(s)
- Daniel Weindl
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Andre Wegner
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Karsten Hiller
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
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