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Furukawa F, Aoyagi A, Sano K, Sameshima K, Goto M, Tseng YC, Ikeda D, Lin CC, Uchida K, Okumura SI, Yasumoto K, Jimbo M, Hwang PP. Gluconeogenesis in the extraembryonic yolk syncytial layer of the zebrafish embryo. PNAS NEXUS 2024; 3:pgae125. [PMID: 38585339 PMCID: PMC10997050 DOI: 10.1093/pnasnexus/pgae125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 03/11/2024] [Indexed: 04/09/2024]
Abstract
Yolk-consuming (lecithotrophic) embryos of oviparous animals, such as those of fish, need to make do with the maternally derived yolk. However, in many cases, yolk possesses little carbohydrates and sugars, including glucose, the essential monosaccharide. Interestingly, increases in the glucose content were found in embryos of some teleost fishes; however, the origin of this glucose has been unknown. Unveiling new metabolic strategies in fish embryos has a potential for better aquaculture technologies. In the present study, using zebrafish, we assessed how these embryos obtain the glucose. We employed stable isotope (13C)-labeled substrates and injected them to the zebrafish embryos. Our liquid chromatography-mass spectrometry-based isotope tracking revealed that among all tested substrate, glutamate was most actively metabolized to produce glucose in the zebrafish embryos. Expression analysis for gluconeogenic genes found that many of these were expressed in the yolk syncytial layer (YSL), an extraembryonic tissue found in teleost fishes. Generation 0 (G0) knockout of pck2, a gene encoding the key enzyme for gluconeogenesis from Krebs cycle intermediates, reduced gluconeogenesis from glutamate, suggesting that this gene is responsible for gluconeogenesis from glutamate in the zebrafish embryos. These results showed that teleost YSL undergoes gluconeogenesis, likely contributing to the glucose supplementation to the embryos with limited glucose source. Since many other animal lineages lack YSL, further comparative analysis will be interesting.
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Affiliation(s)
- Fumiya Furukawa
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Sec. 2, Nankang, Taipei 11529, Taiwan ROC
| | - Akihiro Aoyagi
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Kaori Sano
- Department of Chemistry, Faculty of Science, Josai University, 1-1 Keyakidai, Sakado, Saitama 350-0295, Japan
| | - Keita Sameshima
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Miku Goto
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Yung-Che Tseng
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Sec. 2, Nankang, Taipei 11529, Taiwan ROC
| | - Daisuke Ikeda
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Ching-Chun Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Sec. 2, Nankang, Taipei 11529, Taiwan ROC
| | - Katsuhisa Uchida
- Department of Marine Biology and Environmental Sciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen Kibanadai-Nishi, Miyazaki 889-2192, Japan
| | - Sei-ichi Okumura
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Ko Yasumoto
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Mitsuru Jimbo
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitazato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Pung-Pung Hwang
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Sec. 2, Nankang, Taipei 11529, Taiwan ROC
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McKay RT. Metabolomics and NMR. Handb Exp Pharmacol 2023; 277:73-116. [PMID: 36355220 DOI: 10.1007/164_2022_616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The purpose of this manuscript will be to convince the reader to dive deeper into NMR spectroscopy and prevent the technique from being just another "black-box" in the lab. We will try to concisely highlight interesting topics and supply additional references for further exploration at each stage. The advantages of delving into the technique will be shown. The secondary objective, i.e., avoiding common problems before starting, will hopefully then become clear. Lastly, we will emphasize the spectrometer information needed for manuscript reporting to allow reproduction of results and confirm findings.
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Affiliation(s)
- Ryan T McKay
- Department Chemistry, College of Natural and Applied Sciences, University of Alberta, Edmonton, AB, Canada.
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3
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Eylem CC, Reçber T, Waris M, Kır S, Nemutlu E. State-of-the-art GC-MS approaches for probing central carbon metabolism. Microchem J 2022. [DOI: 10.1016/j.microc.2021.106892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Varshavi D, Varshavi D, McCarthy N, Veselkov K, Keun HC, Everett JR. Metabonomics study of the effects of single copy mutant KRAS in the presence or absence of WT allele using human HCT116 isogenic cell lines. Metabolomics 2021; 17:104. [PMID: 34822010 PMCID: PMC8616861 DOI: 10.1007/s11306-021-01852-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/31/2021] [Indexed: 12/02/2022]
Abstract
INTRODUCTION KRAS was one of the earliest human oncogenes to be described and is one of the most commonly mutated genes in different human cancers, including colorectal cancer. Despite KRAS mutants being known driver mutations, KRAS has proved difficult to target therapeutically, necessitating a comprehensive understanding of the molecular mechanisms underlying KRAS-driven cellular transformation. OBJECTIVES To investigate the metabolic signatures associated with single copy mutant KRAS in isogenic human colorectal cancer cells and to determine what metabolic pathways are affected. METHODS Using NMR-based metabonomics, we compared wildtype (WT)-KRAS and mutant KRAS effects on cancer cell metabolism using metabolic profiling of the parental KRAS G13D/+ HCT116 cell line and its isogenic, derivative cell lines KRAS +/- and KRAS G13D/-. RESULTS Mutation in the KRAS oncogene leads to a general metabolic remodelling to sustain growth and counter stress, including alterations in the metabolism of amino acids and enhanced glutathione biosynthesis. Additionally, we show that KRASG13D/+ and KRASG13D/- cells have a distinct metabolic profile characterized by dysregulation of TCA cycle, up-regulation of glycolysis and glutathione metabolism pathway as well as increased glutamine uptake and acetate utilization. CONCLUSIONS Our study showed the effect of a single point mutation in one KRAS allele and KRAS allele loss in an isogenic genetic background, hence avoiding confounding genetic factors. Metabolic differences among different KRAS mutations might play a role in their different responses to anticancer treatments and hence could be exploited as novel metabolic vulnerabilities to develop more effective therapies against oncogenic KRAS.
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Affiliation(s)
- Dorna Varshavi
- Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, ME4 4TB, Kent, UK
- Department of Biological Sciences, University of Alberta, 116 Street & 85 Ave, Edmonton, AB, T6G 2R3, Canada
| | - Dorsa Varshavi
- Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, ME4 4TB, Kent, UK
- Department of Biological Sciences, University of Alberta, 116 Street & 85 Ave, Edmonton, AB, T6G 2R3, Canada
| | - Nicola McCarthy
- Horizon Discovery Ltd., Cambridge Research Park, 8100 Beach Dr, Waterbeach, Cambridge, CB25 9TL, UK
- Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Kirill Veselkov
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College, London, SW7 2AZ, UK
| | - Hector C Keun
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 ONN, UK
| | - Jeremy R Everett
- Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, ME4 4TB, Kent, UK.
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Eylem CC, Baysal İ, Erikci A, Yabanoglu-Ciftci S, Zhang S, Kır S, Terzic A, Dzeja P, Nemutlu E. Gas chromatography-mass spectrometry based 18O stable isotope labeling of Krebs cycle intermediates. Anal Chim Acta 2021; 1154:338325. [PMID: 33736808 DOI: 10.1016/j.aca.2021.338325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/07/2021] [Accepted: 02/11/2021] [Indexed: 11/16/2022]
Abstract
New technologies permit determining metabolomic profiles of human diseases by fingerprinting metabolites levels. However, to fully understand metabolomic phenotypes, metabolite levels and turnover rates are necessary to know. Krebs cycle is the major hub of energy metabolism and cell signaling. Traditionally, 13C stable isotope labeled substrates were used to track the carbon turnover rates in Krebs cycle metabolites. In this study, for the first time we introduce H2[18O] based stable isotope marker that permit tracking oxygen exchange rates in separate segments of Krebs cycle. The chromatographic and non-chromatographic parameters were systematically tested on the effect of labeling ratio of Krebs cycle mediators to increase selectivity and sensitivity of the method. We have developed a rapid, precise, and robust GC-MS method for determining the percentage of 18O incorporation to Krebs cycle metabolites. The developed method was applied to track the cancer-induced shift in the Krebs cycle dynamics of Caco-2 cells as compared to the control FHC cells revealing Warburg effects in Caco-2 cells. We demonstrate that unique information could be obtained using this newly developed 18O-labeling analytical technology by following the oxygen exchange rates of Krebs cycle metabolites. Thus, 18O-labeling of Krebs cycle metabolites expands the arsenal of techniques for monitoring the dynamics of cellular metabolism. Moreover, the developed method will allow to apply the 18O-labeling technique to numerous other metabolic pathways where oxygen exchange with water takes place.
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Affiliation(s)
- Cemil Can Eylem
- Hacettepe University, Faculty of Pharmacy, Department of Analytical Chemistry, Ankara, Turkey.
| | - İpek Baysal
- Hacettepe University, Hacettepe University, Vocational School of Health Services, Ankara, Turkey.
| | - Acelya Erikci
- Lokman Hekim University, Faculty of Pharmacy, Department of Biochemistry, Ankara, Turkey.
| | | | - Song Zhang
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Sedef Kır
- Hacettepe University, Faculty of Pharmacy, Department of Analytical Chemistry, Ankara, Turkey.
| | - Andre Terzic
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Petras Dzeja
- Department of Cardiovascular Medicine, Mayo Clinic, Rochester, MN, USA.
| | - Emirhan Nemutlu
- Hacettepe University, Faculty of Pharmacy, Department of Analytical Chemistry, Ankara, Turkey.
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Maniam S, Maniam S. Cancer Cell Metabolites: Updates on Current Tracing Methods. Chembiochem 2020; 21:3476-3488. [PMID: 32639076 DOI: 10.1002/cbic.202000290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/07/2020] [Indexed: 12/15/2022]
Abstract
Cancer is the second leading cause of death-1 in 6 deaths globally is due to cancer. Cancer metabolism is a complex and one of the most actively researched area in cancer biology. Metabolic reprogramming in cancer cells entails activities that involve several enzymes and metabolites to convert nutrient into building blocks that alter energy metabolism to fuel rapid cell division. Metabolic dependencies in cancer generate signature metabolites that have key regulatory roles in tumorigenesis. In this minireview, we highlight recent advances in the popular methods ingrained in biochemistry research such as stable and flux isotope analysis, as well as radioisotope labeling, which are valuable in elucidating cancer metabolites. These methods together with analytical tools such as chromatography, nuclear magnetic resonance spectroscopy and mass spectrometry have helped to bring about exploratory work in understanding the role of important as well as obscure metabolites in cancer cells. Information obtained from these analyses significantly contribute in the diagnosis and prognosis of tumors leading to potential therapeutic targets for cancer therapy.
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Affiliation(s)
- Subashani Maniam
- School of Applied Science, RMIT University, 240 La Trobe Street, Melbourne, VIC 3001, Australia
| | - Sandra Maniam
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
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Fan XX, Pan HD, Li Y, Guo RJ, Leung ELH, Liu L. Novel therapeutic strategy for cancer and autoimmune conditions: Modulating cell metabolism and redox capacity. Pharmacol Ther 2018; 191:148-161. [PMID: 29953901 DOI: 10.1016/j.pharmthera.2018.06.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Dysregulation of cell metabolism and redox balance is implicated in the pathogenesis and progression of cancer and autoimmune diseases. Because the cell proliferation and apoptotic regulatory pathways are interconnected with metabolic and redox signalling pathways, the current mono-target treatment is ineffective, and multi-drug resistance remains common. Complex diseases are often implicated in a network-based context of pathology; therefore, a new holistic intervention approach is required to block multi-crosstalk in such complicated circumstances. The use of therapeutic agents isolated from herbs to holistically modulate metabolism and redox state has been shown to relieve carcinoma growth and the inflammatory response in autoimmune disorders. Multiple clinically applied or novel herbal chemicals with metabolic and redox modulatory capacity as well as low toxicity have recently been identified. Moreover, new metabolic targets and mechanisms of drug action have been discovered, leading to the exploration of new pathways for drug repositioning, clinical biomarker spectra, clinical treatment strategies and drug development. Taken together with multiple supporting examples, the modulation of cell metabolism and the redox capacity using herbal chemicals is emerging as a new, alternative strategy for the holistic treatment of cancer and autoimmune disorders. In the future, the development of new diagnostic tools based on the detection of metabolic and redox biomarkers, reformulation of optimized herbal compositions using artificial intelligence, and the combination of herbs with mono-targeting drugs will reveal new potential for clinical application.
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Affiliation(s)
- Xing-Xing Fan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, SAR, China
| | - Hu-Dan Pan
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, SAR, China
| | - Ying Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, SAR, China
| | - Rui-Jin Guo
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, SAR, China
| | - Elaine Lai-Han Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, SAR, China; Department of Respiratory and Critical Care Medicine, Taihe Hospital, Hubei University of Medicine, Hubei, China; Department of Thoracic Surgery, Guangzhou Institute of Respiratory Health and State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Liang Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, SAR, China.
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8
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Sinnaeve D, Dinclaux M, Cahoreau E, Millard P, Portais JC, Létisse F, Lippens G. Improved Isotopic Profiling by Pure Shift Heteronuclear 2D J-Resolved NMR Spectroscopy. Anal Chem 2018; 90:4025-4031. [DOI: 10.1021/acs.analchem.7b05206] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Davy Sinnaeve
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, B-9000, Belgium
| | - Mickael Dinclaux
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, 31077, France
| | - Edern Cahoreau
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, 31077, France
| | - Pierre Millard
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, 31077, France
| | | | - Fabien Létisse
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, 31077, France
| | - Guy Lippens
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, 31077, France
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9
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Monocarboxylate transporter 1 (MCT1), a tool to stratify acute myeloid leukemia (AML) patients and a vehicle to kill cancer cells. Oncotarget 2017; 8:82803-82823. [PMID: 29137304 PMCID: PMC5669930 DOI: 10.18632/oncotarget.20294] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/27/2017] [Indexed: 12/12/2022] Open
Abstract
Dysregulation of glucose/lactate dynamics plays a role in cancer progression, and MCTs are key elements in metabolic remodeling. VEGF is a relevant growth factor in the maintenance of bone marrow microenvironment and it is also important in hematological diseases. Our aim was to investigate the role of VEGF in the metabolic adaptation of Acute myeloid leukemia (AML) cells by evaluating the metabolic profiles and cell features according to the AML lineage and testing lactate as a metabolic coin. Our in vitro results showed that AML promyelocytic (HL60) and monocytic (THP1) (but not erythroid- HEL) lineages are well adapted to VEGF and lactate rich environment. Their metabolic adaptation relies on high rates of glycolysis to generate intermediates for PPP to support cell proliferation, and on the consumption of glycolysis-generated lactate to supply biomass and energy production. VEGF orchestrates this metabolic network by regulating MCT1 expression. Bromopyruvic acid (BPA) was proven to be an effective cytotoxic in AML, possibly transported by MCT1. Our study reinforces that targeting metabolism can be a good strategy to fight cancer. MCT1 expression at the time of diagnosis can assist on the identification of AML patients that will benefit from BPA therapy. Additionally, MCT1 can be used in targeted delivery of conventional cytotoxic drugs.
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Burgeiro A, Fuhrmann A, Cherian S, Espinoza D, Jarak I, Carvalho RA, Loureiro M, Patrício M, Antunes M, Carvalho E. Glucose uptake and lipid metabolism are impaired in epicardial adipose tissue from heart failure patients with or without diabetes. Am J Physiol Endocrinol Metab 2016; 310:E550-64. [PMID: 26814014 PMCID: PMC4824138 DOI: 10.1152/ajpendo.00384.2015] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 01/20/2016] [Indexed: 01/25/2023]
Abstract
Type 2 diabetes mellitus is a complex metabolic disease, and cardiovascular disease is a leading complication of diabetes. Epicardial adipose tissue surrounding the heart displays biochemical, thermogenic, and cardioprotective properties. However, the metabolic cross-talk between epicardial fat and the myocardium is largely unknown. This study sought to understand epicardial adipose tissue metabolism from heart failure patients with or without diabetes. We aimed to unravel possible differences in glucose and lipid metabolism between human epicardial and subcutaneous adipocytes and elucidate the potential underlying mechanisms involved in heart failure. Insulin-stimulated [(14)C]glucose uptake and isoproterenol-stimulated lipolysis were measured in isolated epicardial and subcutaneous adipocytes. The expression of genes involved in glucose and lipid metabolism was analyzed by reverse transcription-polymerase chain reaction in adipocytes. In addition, epicardial and subcutaneous fatty acid composition was analyzed by high-resolution proton nuclear magnetic resonance spectroscopy. The difference between basal and insulin conditions in glucose uptake was significantly decreased (P= 0.006) in epicardial compared with subcutaneous adipocytes. Moreover, a significant (P< 0.001) decrease in the isoproterenol-stimulated lipolysis was also observed when the two fat depots were compared, and it was strongly correlated with lipolysis, lipid storage, and inflammation-related gene expression. Moreover, the fatty acid composition of these tissues was significantly altered by diabetes. These results emphasize potential metabolic differences between both fat depots in the presence of heart failure and highlight epicardial fat as a possible therapeutic target in situ in the cardiac microenvironment.
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Affiliation(s)
- Ana Burgeiro
- Center of Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Amelia Fuhrmann
- Center of Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Sam Cherian
- Faculty of Integrative Sciences and Technology, Quest International University Perak, Perak, Malaysia
| | - Daniel Espinoza
- Center of Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Ivana Jarak
- Center of Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Rui A Carvalho
- Center of Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal;
| | - Marisa Loureiro
- Laboratory of Biostatistics and Medical Informatics, IBILI - Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Miguel Patrício
- Laboratory of Biostatistics and Medical Informatics, IBILI - Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Manuel Antunes
- Cardiothroracic Surgery Unit at the University Hospital of Coimbra, Coimbra, Portugal
| | - Eugénia Carvalho
- Center of Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal; Portuguese Diabetes Association, Lisbon, Portugal; Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas; and Arkansas Children's Hospital Research Institute, Little Rock, Arkansas
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11
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Fan TWM, Lane AN. Applications of NMR spectroscopy to systems biochemistry. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 92-93:18-53. [PMID: 26952191 PMCID: PMC4850081 DOI: 10.1016/j.pnmrs.2016.01.005] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/26/2016] [Accepted: 01/28/2016] [Indexed: 05/05/2023]
Abstract
The past decades of advancements in NMR have made it a very powerful tool for metabolic research. Despite its limitations in sensitivity relative to mass spectrometric techniques, NMR has a number of unparalleled advantages for metabolic studies, most notably the rigor and versatility in structure elucidation, isotope-filtered selection of molecules, and analysis of positional isotopomer distributions in complex mixtures afforded by multinuclear and multidimensional experiments. In addition, NMR has the capacity for spatially selective in vivo imaging and dynamical analysis of metabolism in tissues of living organisms. In conjunction with the use of stable isotope tracers, NMR is a method of choice for exploring the dynamics and compartmentation of metabolic pathways and networks, for which our current understanding is grossly insufficient. In this review, we describe how various direct and isotope-edited 1D and 2D NMR methods can be employed to profile metabolites and their isotopomer distributions by stable isotope-resolved metabolomic (SIRM) analysis. We also highlight the importance of sample preparation methods including rapid cryoquenching, efficient extraction, and chemoselective derivatization to facilitate robust and reproducible NMR-based metabolomic analysis. We further illustrate how NMR has been applied in vitro, ex vivo, or in vivo in various stable isotope tracer-based metabolic studies, to gain systematic and novel metabolic insights in different biological systems, including human subjects. The pathway and network knowledge generated from NMR- and MS-based tracing of isotopically enriched substrates will be invaluable for directing functional analysis of other 'omics data to achieve understanding of regulation of biochemical systems, as demonstrated in a case study. Future developments in NMR technologies and reagents to enhance both detection sensitivity and resolution should further empower NMR in systems biochemical research.
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Affiliation(s)
- Teresa W-M Fan
- Department of Toxicology and Cancer Biology, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536, United States.
| | - Andrew N Lane
- Department of Toxicology and Cancer Biology, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536, United States.
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