1
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Zhang J, Lei J, Liu X, Zhang N, Wu L, Li Y. LC-MS simultaneous profiling of acyl-CoA and acyl-carnitine in dynamic metabolic status. Anal Chim Acta 2024; 1329:343235. [PMID: 39396298 DOI: 10.1016/j.aca.2024.343235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 09/08/2024] [Accepted: 09/09/2024] [Indexed: 10/15/2024]
Affiliation(s)
- Jiangang Zhang
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Juan Lei
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Xudong Liu
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Nan Zhang
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Lei Wu
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Yongsheng Li
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China.
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2
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Liao Y, Chen Q, Liu L, Huang H, Sun J, Bai X, Jin C, Li H, Sun F, Xiao X, Zhang Y, Li J, Han W, Fu S. Amino acid is a major carbon source for hepatic lipogenesis. Cell Metab 2024; 36:2437-2448.e8. [PMID: 39461344 DOI: 10.1016/j.cmet.2024.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 04/24/2024] [Accepted: 10/02/2024] [Indexed: 10/29/2024]
Abstract
Increased de novo lipogenesis is a hallmark of metabolic dysfunction-associated steatotic liver disease (MASLD) in obesity, but the macronutrient carbon source for over half of hepatic fatty acid synthesis remains undetermined. Here, we discover that dietary protein, rather than carbohydrates or fat, is the primary nutritional risk factor for MASLD in humans. Consistently, ex vivo tracing studies identify amino acids as a major carbon supplier for the tricarboxylic acid (TCA) cycle and lipogenesis in isolated mouse hepatocytes. In vivo, dietary amino acids are twice as efficient as glucose in fueling hepatic fatty acid synthesis. The onset of obesity further drives amino acids into fatty acid synthesis through reductive carboxylation, while genetic and chemical interventions that divert amino acid carbon away from lipogenesis alleviate hepatic steatosis. Finally, low-protein diets (LPDs) not only prevent body weight gain in obese mice but also reduce hepatic lipid accumulation and liver damage. Together, this study uncovers the significant role of amino acids in hepatic lipogenesis and suggests a previously unappreciated nutritional intervention target for MASLD.
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Affiliation(s)
- Yilie Liao
- Zhongshan Institute for Drug Discovery (ZIDD), Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, Guangdong 528400, China; School of Life Sciences, Tsinghua University, Beijing 100084, China; Center for Neurometabolism and Regenerative Medicine, Bioland Laboratories, Guangzhou, Guangdong 510530, China; Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore.
| | - Qishan Chen
- Guangzhou National Laboratory, Guangzhou, Guangdong 510005, China
| | - Lei Liu
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haipeng Huang
- School of Life Sciences, Tsinghua University, Beijing 100084, China; Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing 100871, China
| | - Jingyun Sun
- Center for Neurometabolism and Regenerative Medicine, Bioland Laboratories, Guangzhou, Guangdong 510530, China
| | - Xiaojie Bai
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chenchen Jin
- Guangzhou National Laboratory, Guangzhou, Guangdong 510005, China
| | - Honghao Li
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fangfang Sun
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xia Xiao
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yahong Zhang
- Guangzhou National Laboratory, Guangzhou, Guangdong 510005, China
| | - Jia Li
- Zhongshan Institute for Drug Discovery (ZIDD), Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, Guangdong 528400, China; Shanghai Institute of Materia Medica (SIMM), Chinese Academy of Sciences, Shanghai 201203, China
| | - Weiping Han
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A(∗)STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Singapore.
| | - Suneng Fu
- Guangzhou National Laboratory, Guangzhou, Guangdong 510005, China.
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3
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Ren Y, Ye P, Zhang L, Zhao J, Liu J, Lei J, Wang L. Three-dimensional porous wood monolithic columns for efficient purification of spike glycoprotein of SARS-CoV-2. Int J Biol Macromol 2023; 248:125713. [PMID: 37437676 DOI: 10.1016/j.ijbiomac.2023.125713] [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: 02/24/2023] [Revised: 05/26/2023] [Accepted: 07/04/2023] [Indexed: 07/14/2023]
Abstract
Considerable research has been devoted to finding a cost-effective chromatographic matrix with efficient adsorption and high throughput. Wood exhibits complex micro-network structures that make it a powerful contender for a novel environment-friendly chromatographic matrix material. We demonstrate a novel strategy to manufacture a wood monolithic column, which chemically modified the wood and imported diethyl aminoethyl, diethylamine, and amino groups. This wood monolithic column can maintain fully monolithic column performances and highly selective to spike glycoprotein of SARS-CoV-2 by ion exchange force. The wood monolithic column was evaluated by static adsorption, dynamic adsorption, and frontal analysis. The results showed that the static adsorption capacity of the wood monolithic column with 2-diethylaminoethylchloride hydrochloride for bovine serum albumin was 14.72 mg/g, and the adsorption process was chemisorption. In addition, it retained 80 % adsorption capacity after 110 repeated adsorption-elution cycles.
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Affiliation(s)
- Yuting Ren
- Beijing Key Laboratory of Lignocellulosic Chemistry, College of Material Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Peng Ye
- Beijing Key Laboratory of Lignocellulosic Chemistry, College of Material Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Limei Zhang
- Beijing Key Laboratory of Lignocellulosic Chemistry, College of Material Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jingyang Zhao
- Beijing Key Laboratory of Lignocellulosic Chemistry, College of Material Science and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jing Liu
- Beijing Key Laboratory of Lignocellulosic Chemistry, College of Material Science and Technology, Beijing Forestry University, Beijing 100083, China; MOE Engineering Research Center of Forestry Biomass Materials and Bioenergy, Beijing Forestry University, Beijing 100083, China
| | - Jiandu Lei
- Beijing Key Laboratory of Lignocellulosic Chemistry, College of Material Science and Technology, Beijing Forestry University, Beijing 100083, China; MOE Engineering Research Center of Forestry Biomass Materials and Bioenergy, Beijing Forestry University, Beijing 100083, China.
| | - Luying Wang
- Beijing Key Laboratory of Lignocellulosic Chemistry, College of Material Science and Technology, Beijing Forestry University, Beijing 100083, China; MOE Engineering Research Center of Forestry Biomass Materials and Bioenergy, Beijing Forestry University, Beijing 100083, China
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4
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Kim J, Jung I, Cheong YE, Kim KH. Evaluation and optimization of quantitative analysis of cofactors from yeast by liquid chromatography/mass spectrometry. Anal Chim Acta 2022; 1211:339890. [DOI: 10.1016/j.aca.2022.339890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/17/2022] [Accepted: 04/28/2022] [Indexed: 11/01/2022]
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5
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Wang X, Luo X. Precursor Quantitation Methods for Next Generation Food Production. Front Bioeng Biotechnol 2022; 10:849177. [PMID: 35360389 PMCID: PMC8960114 DOI: 10.3389/fbioe.2022.849177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/22/2022] [Indexed: 11/21/2022] Open
Abstract
Food is essential for human survival. Nowadays, traditional agriculture faces challenges in balancing the need of sustainable environmental development and the rising food demand caused by an increasing population. In addition, in the emerging of consumers' awareness of health related issues bring a growing trend towards novel nature-based food additives. Synthetic biology, using engineered microbial cell factories for production of various molecules, shows great advantages for generating food alternatives and additives, which not only relieve the pressure laid on tradition agriculture, but also create a new stage in healthy and sustainable food supplement. The biosynthesis of food components (protein, fats, carbohydrates or vitamins) in engineered microbial cells often involves cellular central metabolic pathways, where common precursors are processed into different proteins and products. Quantitation of the precursors provides information of the metabolic flux and intracellular metabolic state, giving guidance for precise pathway engineering. In this review, we summarized the quantitation methods for most cellular biosynthetic precursors, including energy molecules and co-factors involved in redox-reactions. It will also be useful for studies worked on pathway engineering of other microbial-derived metabolites. Finally, advantages and limitations of each method are discussed.
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Affiliation(s)
- Xinran Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiaozhou Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen Institute of Advanced Technology, Shenzhen, China
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6
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Zhang XJ, She ZG, Wang J, Sun D, Shen LJ, Xiang H, Cheng X, Ji YX, Huang YP, Li PL, Yang X, Cheng Y, Ma JP, Wang HP, Hu Y, Hu F, Tian S, Tian H, Zhang P, Zhao GN, Wang L, Hu ML, Yang Q, Zhu LH, Cai J, Yang J, Zhang X, Ma X, Xu Q, Touyz RM, Liu PP, Loomba R, Wang Y, Li H. Multiple omics study identifies an interspecies conserved driver for nonalcoholic steatohepatitis. Sci Transl Med 2021; 13:eabg8117. [PMID: 34910546 DOI: 10.1126/scitranslmed.abg8117] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Xiao-Jing Zhang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China.,Institute of Model Animal of Wuhan University, Wuhan 430071, China.,School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Zhi-Gang She
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China.,Institute of Model Animal of Wuhan University, Wuhan 430071, China
| | - Junyong Wang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China.,Institute of Model Animal of Wuhan University, Wuhan 430071, China
| | - Dating Sun
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China.,Institute of Model Animal of Wuhan University, Wuhan 430071, China
| | - Li-Jun Shen
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China.,Institute of Model Animal of Wuhan University, Wuhan 430071, China
| | - Hui Xiang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China.,Institute of Model Animal of Wuhan University, Wuhan 430071, China
| | - Xu Cheng
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China.,Institute of Model Animal of Wuhan University, Wuhan 430071, China
| | - Yan-Xiao Ji
- Institute of Model Animal of Wuhan University, Wuhan 430071, China.,School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Yong-Ping Huang
- Institute of Model Animal of Wuhan University, Wuhan 430071, China.,College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Peng-Long Li
- Institute of Model Animal of Wuhan University, Wuhan 430071, China.,School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Xia Yang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China.,Institute of Model Animal of Wuhan University, Wuhan 430071, China
| | - Yanjie Cheng
- Institute of Model Animal of Wuhan University, Wuhan 430071, China.,Medical Science Research Center, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Jun-Peng Ma
- Institute of Model Animal of Wuhan University, Wuhan 430071, China.,School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Hai-Ping Wang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China.,Institute of Model Animal of Wuhan University, Wuhan 430071, China
| | - Yufeng Hu
- Institute of Model Animal of Wuhan University, Wuhan 430071, China.,Medical Science Research Center, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Fengjiao Hu
- Institute of Model Animal of Wuhan University, Wuhan 430071, China.,Medical Science Research Center, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Song Tian
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China.,Institute of Model Animal of Wuhan University, Wuhan 430071, China
| | - Han Tian
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China.,Institute of Model Animal of Wuhan University, Wuhan 430071, China
| | - Peng Zhang
- Institute of Model Animal of Wuhan University, Wuhan 430071, China.,School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China
| | - Guang-Nian Zhao
- Institute of Model Animal of Wuhan University, Wuhan 430071, China.,Medical Science Research Center, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Lin Wang
- Department of Hepatic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Man-Li Hu
- Institute of Model Animal of Wuhan University, Wuhan 430071, China.,Medical Science Research Center, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Qin Yang
- Institute of Model Animal of Wuhan University, Wuhan 430071, China.,Medical Science Research Center, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Li-Hua Zhu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China.,Institute of Model Animal of Wuhan University, Wuhan 430071, China
| | - Jingjing Cai
- Department of Cardiology, The Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Juan Yang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China.,Institute of Model Animal of Wuhan University, Wuhan 430071, China
| | - Xin Zhang
- Institute of Model Animal of Wuhan University, Wuhan 430071, China
| | - Xinliang Ma
- Department of Emergency Medicine, Thomas Jefferson University, Philadelphia, PA 19004, USA
| | - Qingbo Xu
- Centre for Clinic Pharmacology, The William Harvey Research Institute, Queen Mary University of London, London SE5 9NU, UK
| | - Rhian M Touyz
- British Heart Foundation Chair in Cardiovascular Medicine, and Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Peter P Liu
- Division of Cardiology, Department of Medicine, University of Ottawa Heart Institute, Ottawa, Ontario K1Y 4W7, Canada
| | - Rohit Loomba
- NAFLD Research Center, Division of Gastroenterology and Epidemiology, University of California, San Diego, San Diego, CA 92093, USA
| | - Yibin Wang
- Department of Anesthesiology, Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Hongliang Li
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan 430060, China.,Institute of Model Animal of Wuhan University, Wuhan 430071, China.,School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China.,Medical Science Research Center, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
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7
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Baidoo EEK, Wang G, Joshua CJ, Benites VT, Keasling JD. Liquid Chromatography and Mass Spectrometry Analysis of Isoprenoid Intermediates in Escherichia coli. Methods Mol Biol 2019; 1859:209-224. [PMID: 30421231 DOI: 10.1007/978-1-4939-8757-3_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Isoprenoids are a highly diverse group of natural products with broad application as high value chemicals and advanced biofuels. They are synthesized using two primary building blocks, namely, isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) that are generated via the mevalonate (MVA) or deoxy-D-xylulose-5-phosphate (DXP) pathways. Isoprenoid biosynthetic pathways are prevalent in eukaryotes, archaea, and bacteria. Measurement of isoprenoid intermediates via standard liquid chromatography-mass spectrometry (LC-MS) protocols is generally challenging because of the hydrophilicity and complex physicochemical properties of the molecules. In addition, there is currently no reliable analytical method that can simultaneously measure metabolic intermediates from MVA and DXP pathways, including the prenyl diphosphates. Therefore, we describe a robust hydrophilic interaction liquid chromatography time-of-flight mass spectrometry (HILIC-TOF-MS) method for analyzing isoprenoid intermediates from metabolically engineered Escherichia coli strains.
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Affiliation(s)
- Edward E K Baidoo
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Joint BioEnergy Institute, Emeryville, CA, USA.
| | - George Wang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Chijioke J Joshua
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Veronica Teixeira Benites
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Emeryville, CA, USA
| | - Jay D Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Emeryville, CA, USA
- Department of Chemical Engineering, University of California, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
- Center for Synthetic Biochemistry, Institute of Synthetic Biology Research, Shenzhen Institutes of Advanced Technologies, Shenzhen, Guangdong, China
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8
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Fu X, Deja S, Kucejova B, Duarte JAG, McDonald JG, Burgess SC. Targeted Determination of Tissue Energy Status by LC-MS/MS. Anal Chem 2019; 91:5881-5887. [PMID: 30938977 PMCID: PMC6506803 DOI: 10.1021/acs.analchem.9b00217] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
![]()
Intracellular
nucleotides and acyl-CoAs are metabolites that are
central to the regulation of energy metabolism. They set the cellular
energy charge and redox state, act as allosteric regulators, modulate
signaling and transcription factors, and thermodynamically activate
substrates for oxidation or biosynthesis. Unfortunately, no method
exists to simultaneously quantify these biomolecules in tissue extracts.
A simple method was developed using ion-pairing reversed-phase high-performance
liquid chromatography–electrospray-ionization tandem mass spectrometry
(HPLC-ESI-MS/MS) to simultaneously quantify adenine nucleotides (AMP,
ADP, and ATP), pyridine dinucleotides (NAD+ and NADH),
and short-chain acyl-CoAs (acetyl, malonyl, succinyl, and propionyl).
Quantitative analysis of these molecules in mouse liver was achieved
using stable-isotope-labeled internal standards. The method was extensively
validated by determining the linearity, accuracy, repeatability, and
assay stability. Biological responsiveness was confirmed in assays
of liver tissue with variable durations of ischemia, which had substantial
effects on tissue energy charge and redox state. We conclude that
the method provides a simple, fast, and reliable approach to the simultaneous
analysis of nucleotides and short-chain acyl-CoAs.
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9
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Speziale R, Montesano C, De Leonibus ML, Bonelli F, Fezzardi P, Beconi MG, Monteagudo E, Elbaum D, Orsatti L. Determination of acetyl coenzyme A in human whole blood by ultra-performance liquid chromatography-mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2018. [PMID: 29524693 DOI: 10.1016/j.jchromb.2018.02.039] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Acetyl coenzyme A is involved in several key metabolic pathways. Its concentration can vary considerably in response to physiological or pathological conditions making it a potentially valuable biomarker. However, little information about the measurement and concentration of acetyl CoA in human whole blood is found in the literature. The aim of this study was the development of an accurate method for the determination of acetyl CoA in human whole blood by LC-MS/MS. The method, involving extraction from whole blood by a rapid protein precipitation procedure was thoroughly validated: limit of quantitation was 3.91 ng mL-1. Accuracy and precision were calculated at five concentrations and were within ±15%. The average endogenous level of acetyl CoA in human whole blood was determined in 17 healthy individuals to be 220.9 ng mL-1 (ranging from 124.0 to 308.0 ng mL-1). This represents, to our knowledge, the first report of acetyl CoA levels in human whole blood, and the first practical and reliable method for its determination.
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Affiliation(s)
- Roberto Speziale
- IRBM Science Park, Via Pontina km 30,600, 00040 Pomezia, Roma, Italy.
| | - Camilla Montesano
- IRBM Science Park, Via Pontina km 30,600, 00040 Pomezia, Roma, Italy.
| | | | - Fabio Bonelli
- IRBM Science Park, Via Pontina km 30,600, 00040 Pomezia, Roma, Italy.
| | - Paola Fezzardi
- IRBM Science Park, Via Pontina km 30,600, 00040 Pomezia, Roma, Italy.
| | - Maria G Beconi
- Retrophin Inc (RTRX), 3721 Valley Centre Drive, San Diego, CA 90213, USA.
| | - Edith Monteagudo
- IRBM Science Park, Via Pontina km 30,600, 00040 Pomezia, Roma, Italy.
| | - Daniel Elbaum
- Retrophin Inc (RTRX), 3721 Valley Centre Drive, San Diego, CA 90213, USA.
| | - Laura Orsatti
- IRBM Science Park, Via Pontina km 30,600, 00040 Pomezia, Roma, Italy.
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10
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Schriewer A, Cadenas C, Hayen H. Hydrophilic interaction liquid chromatography tandem mass spectrometry analysis of malonyl-coenzyme A in breast cancer cell cultures applying online solid-phase extraction. J Sep Sci 2017; 40:4303-4310. [PMID: 28877409 DOI: 10.1002/jssc.201700617] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/29/2017] [Accepted: 08/29/2017] [Indexed: 11/09/2022]
Abstract
Cofactors such as coenzyme A and its derivatives acetyl-coenzyme A and malonyl-coenzyme A are involved in many metabolic pathways. Due to trace level concentrations in biological samples and the high reactivity of cofactors, a fast, sensitive, and selective method for quantification is mandatory. In this study, online solid-phase extraction was coupled successfully to hydrophilic interaction liquid chromatography with tandem mass spectrometry for isolation of analytes in complex matrix and quantification by external calibration. Online solid-phase extraction was carried out by application of a weak anion-exchange column, whereas hydrophilic interaction liquid chromatography separation was performed on an amide modified stationary phase. Sample preparation of the extracts before the analysis was reduced to a centrifugation and dilution step. Moreover, the applied online solid-phase extraction significantly reduced matrix effects and increased the signal-to-noise ratio. The limit of detection and the limit of quantification were in the lower nanomolar range. Finally, the applicability of this method was demonstrated on MCF-7 breast cancer cell cultures, a commonly used model system, where acetyl-coenzyme A and malonyl-coenzyme A were determined using standard addition procedure in concentrations of 1.98 μM and 41 nM, respectively.
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Affiliation(s)
- Alexander Schriewer
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Cristina Cadenas
- Leibniz-Research Centre for Working Environment and Human Factors, University of Dortmund, Dortmund, Germany
| | - Heiko Hayen
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
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11
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Riera-Borrull M, Rodríguez-Gallego E, Hernández-Aguilera A, Luciano F, Ras R, Cuyàs E, Camps J, Segura-Carretero A, Menendez JA, Joven J, Fernández-Arroyo S. Exploring the Process of Energy Generation in Pathophysiology by Targeted Metabolomics: Performance of a Simple and Quantitative Method. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:168-177. [PMID: 26383735 DOI: 10.1007/s13361-015-1262-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/23/2015] [Accepted: 08/27/2015] [Indexed: 06/05/2023]
Abstract
Abnormalities in mitochondrial metabolism and regulation of energy balance contribute to human diseases. The consequences of high fat and other nutrient intake, and the resulting acquired mitochondrial dysfunction, are essential to fully understand common disorders, including obesity, cancer, and atherosclerosis. To simultaneously and noninvasively measure and quantify indirect markers of mitochondrial function, we have developed a method based on gas chromatography coupled to quadrupole-time of flight mass spectrometry and an electron ionization interface, and validated the system using plasma from patients with peripheral artery disease, human cancer cells, and mouse tissues. This approach was used to increase sensibility in the measurement of a wide dynamic range and chemical diversity of multiple intermediate metabolites used in energy metabolism. We demonstrate that our targeted metabolomics method allows for quick and accurate identification and quantification of molecules, including the measurement of small yet significant biological changes in experimental samples. The apparently low process variability required for its performance in plasma, cell lysates, and tissues allowed a rapid identification of correlations between interconnected pathways. Our results suggest that delineating the process of energy generation by targeted metabolomics can be a valid surrogate for predicting mitochondrial dysfunction in biological samples. Importantly, when used in plasma, targeted metabolomics should be viewed as a robust and noninvasive source of biomarkers in specific pathophysiological scenarios.
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Affiliation(s)
- Marta Riera-Borrull
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, IISPV, Universitat Rovira i Virgili, Reus, Spain
- Campus of International Excellence Southern Catalonia, Tarragona, Spain
| | - Esther Rodríguez-Gallego
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, IISPV, Universitat Rovira i Virgili, Reus, Spain
- Campus of International Excellence Southern Catalonia, Tarragona, Spain
| | - Anna Hernández-Aguilera
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, IISPV, Universitat Rovira i Virgili, Reus, Spain
- Campus of International Excellence Southern Catalonia, Tarragona, Spain
| | - Fedra Luciano
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, IISPV, Universitat Rovira i Virgili, Reus, Spain
- Campus of International Excellence Southern Catalonia, Tarragona, Spain
| | - Rosa Ras
- Center for Omics Sciences, Reus, Spain
| | - Elisabet Cuyàs
- Metabolism and Cancer Group, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Girona, Spain
- Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Jordi Camps
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, IISPV, Universitat Rovira i Virgili, Reus, Spain
- Campus of International Excellence Southern Catalonia, Tarragona, Spain
| | - Antonio Segura-Carretero
- Department of Analytical Chemistry, University of Granada, Granada, Spain
- Research and Development of Functional Food Centre (CIDAF), Granada, Spain
| | - Javier A Menendez
- Metabolism and Cancer Group, Translational Research Laboratory, Catalan Institute of Oncology (ICO), Girona, Spain
- Girona Biomedical Research Institute (IDIBGI), Girona, Spain
| | - Jorge Joven
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, IISPV, Universitat Rovira i Virgili, Reus, Spain.
- Campus of International Excellence Southern Catalonia, Tarragona, Spain.
| | - Salvador Fernández-Arroyo
- Unitat de Recerca Biomèdica, Hospital Universitari de Sant Joan, IISPV, Universitat Rovira i Virgili, Reus, Spain.
- Campus of International Excellence Southern Catalonia, Tarragona, Spain.
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12
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Hopcroft PJ, Fisher DI. Development of a Medium-Throughput Targeted LCMS Assay to Detect Endogenous Cellular Levels of Malonyl-CoA to Screen Fatty Acid Synthase Inhibitors. ACTA ACUST UNITED AC 2015; 21:111-6. [PMID: 26586251 DOI: 10.1177/1087057115617894] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 10/26/2015] [Indexed: 01/24/2023]
Abstract
The fatty acid synthase (FAS) enzyme in mammalian cells is a large multidomain protein responsible for de novo synthesis of fatty acids. The steps catalyzed by FAS involve the condensation of acetyl-CoA and malonyl-CoA moieties in the presence of NADPH until palmitate is formed. Inhibition of FAS causes an accumulation of intracellular malonyl-CoA, as this metabolite is essentially committed to fatty acid synthesis once formed. Detection of intracellular metabolites for screening can be problematic due to a lack of appropriate tools, but here we describe a targeted liquid chromatography-mass spectroscopy (LCMS) method to directly measure endogenous levels of malonyl-CoA to drive a drug development structure-activity relationship (SAR) screening cascade. Our process involves preparation of samples at 96-well scale, normalization postpermeabilization via use of a whole-well imaging platform, and the LCMS detection methodology. The assay is amenable to multiplexing cellular endpoints, has a typical Z' of >0.6, and has high reproducibility of EC50 values.
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13
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Surrogate matrix: opportunities and challenges for tissue sample analysis. Bioanalysis 2015; 7:2419-2433. [DOI: 10.4155/bio.15.161] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Often there is limited availability of matching tissue matrix and/or the analyte may occur endogenously in the target tissue. Surrogate matrix provides an option for quantitation of drug, metabolite(s) and biomarker(s) in these circumstances. However, the use of a surrogate matrix also presents challenges. This paper summarizes and discusses the challenges of selecting a proper surrogate, validating the suitability of the surrogate and establishing a surrogate tissue method using the fit-for-purpose approach. This paper also systematically reviews the current practices for evaluating key parameters of a surrogate tissue assay, including sensitivity, specificity, selectivity, interference, precision, accuracy, recovery, matrix effects and stability. Considerations and suggestions are provided for dealing with such challenges during method establishment and tissue sample analysis.
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14
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Kuo YM, Henry RA, Huang L, Chen X, Stargell LA, Andrews AJ. Utilizing targeted mass spectrometry to demonstrate Asf1-dependent increases in residue specificity for Rtt109-Vps75 mediated histone acetylation. PLoS One 2015; 10:e0118516. [PMID: 25781956 PMCID: PMC4364511 DOI: 10.1371/journal.pone.0118516] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 01/17/2015] [Indexed: 11/19/2022] Open
Abstract
In Saccharomyces cerevisiae, Rtt109, a lysine acetyltransferase (KAT), associates with a histone chaperone, either Vps75 or Asf1. It has been proposed that these chaperones alter the selectivity of Rtt109 or which residues it preferentially acetylates. In the present study, we utilized a label-free quantitative mass spectrometry-based method to determine the steady-state kinetic parameters of acetylation catalyzed by Rtt109-Vps75 on H3 monomer, H3/H4 tetramer, and H3/H4-Asf1 complex. These results show that among these histone conformations, only H3K9 and H3K23 are significantly acetylated under steady-state conditions and that Asf1 promotes H3/H4 acetylation by Rtt109-Vps75. Asf1 equally increases the Rtt109-Vps75 specificity for both of these residues with a maximum stoichiometry of 1:1 (Asf1 to H3/H4), but does not alter the selectivity between these two residues. These data suggest that the H3/H4-Asf1 complex is a substrate for Rtt109-Vps75 without altering selectivity between residues. The deletion of either Rtt109 or Asf1 in vivo results in the same reduction of H3K9 acetylation, suggesting that Asf1 is required for efficient H3K9 acetylation both in vitro and in vivo. Furthermore, we found that the acetylation preference of Rtt109-Vps75 could be directed to H3K56 when those histones already possess modifications, such as those found on histones purified from chicken erythrocytes. Taken together, Vps75 and Asf1 both enhance Rtt109 acetylation for H3/H4, although via different mechanisms, but have little impact on the residue selectivity. Importantly, these results provide evidence that histone chaperones can work together via interactions with either the enzyme or the substrate to more efficiently acetylate histones.
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Affiliation(s)
- Yin-Ming Kuo
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - Ryan A. Henry
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
| | - Liangqun Huang
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Xu Chen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Laurie A. Stargell
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Andrew J. Andrews
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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15
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Acetyl-L-carnitine increases mitochondrial protein acetylation in the aged rat heart. Mech Ageing Dev 2015; 145:39-50. [PMID: 25660059 DOI: 10.1016/j.mad.2015.01.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 11/24/2014] [Accepted: 01/27/2015] [Indexed: 12/30/2022]
Abstract
Previously we showed that in vivo treatment of elderly Fisher 344 rats with acetylcarnitine abolished the age-associated defect in respiratory chain complex III in interfibrillar mitochondria and improved the functional recovery of the ischemic/reperfused heart. Herein, we explored mitochondrial protein acetylation as a possible mechanism for acetylcarnitine's effect. In vivo treatment of elderly rats with acetylcarnitine restored cardiac acetylcarnitine content and increased mitochondrial protein lysine acetylation and increased the number of lysine-acetylated proteins in cardiac subsarcolemmal and interfibrillar mitochondria. Enzymes of the tricarboxylic acid cycle, mitochondrial β-oxidation, and ATP synthase of the respiratory chain showed the greatest acetylation. Acetylation of isocitrate dehydrogenase, long-chain acyl-CoA dehydrogenase, complex V, and aspartate aminotransferase was accompanied by decreased catalytic activity. Several proteins were found to be acetylated only after treatment with acetylcarnitine, suggesting that exogenous acetylcarnitine served as the acetyl-donor. Two-dimensional fluorescence difference gel electrophoresis analysis revealed that acetylcarnitine treatment also induced changes in mitochondrial protein amount; a two-fold or greater increase/decrease in abundance was observed for thirty one proteins. Collectively, our data provide evidence for the first time that in the aged rat heart in vivo administration of acetylcarnitine provides acetyl groups for protein acetylation and affects the amount of mitochondrial proteins.
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16
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Purves RW, Ambrose SJ, Clark SM, Stout JM, Page JE. Separation of isomeric short-chain acyl-CoAs in plant matrices using ultra-performance liquid chromatography coupled with tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 980:1-7. [PMID: 25553535 DOI: 10.1016/j.jchromb.2014.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 11/26/2014] [Accepted: 12/08/2014] [Indexed: 10/24/2022]
Abstract
Acyl coenzyme A (acyl-CoA) thioesters are important intermediates in cellular metabolism and being able to distinguish among them is critical to fully understanding metabolic pathways in plants. Although significant advances have been made in the identification and quantification of acyl-CoAs using liquid chromatography tandem mass spectrometry (LC-MS/MS), separation of isomeric species such as isobutyryl- and n-butyrl-CoA has remained elusive. Here we report an ultra-performance liquid chromatography (UPLC)-MS/MS method for quantifying short-chain acyl-CoAs including isomeric species n-butyryl-CoA and isobutyryl-CoA as well as n-valeryl-CoA and isovaleryl-CoA. The method was applied to the analysis of extracts of hop (Humulus lupulus) and provided strong evidence for the existence of an additional structural isomer of valeryl-CoA, 2-methylbutyryl-CoA, as well as an unexpected isomer of hexanoyl-CoA. The results showed differences in the acyl-CoA composition among varieties of Humulus lupulus, both in glandular trichomes and cone tissues. When compared with the analysis of hemp (Cannabis sativa) extracts, the contribution of isobutyryl-CoAs in hop was greater as would be expected based on the downstream polyketide products. Surprisingly, branched chain valeryl-CoAs (isovaleryl-CoA and 2-methylbutyryl-CoA) were the dominant form of valeryl-CoAs in both hop and hemp. The capability to separate these isomeric forms will help to understand biochemical pathways leading to specialized metabolites in plants.
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Affiliation(s)
- Randy W Purves
- Plant Sciences Department, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, Canada S7N 5A8; National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, Canada S7N 0W9.
| | - Stephen J Ambrose
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, Canada S7N 0W9
| | - Shawn M Clark
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, Canada S7N 0W9; Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK, Canada S7N 5E2
| | - Jake M Stout
- Department of Biological Sciences, University of Manitoba, 50 Sifton Road, Winnipeg, MB, Canada R3T 2N2
| | - Jonathan E Page
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK, Canada S7N 0W9; Department of Biology, University of Saskatchewan, 112 Science Place, Saskatoon, SK, Canada S7N 5E2; Department of Botany, The University of British Columbia, #3529-6270 University Boulevard, Vancouver, BC, Canada V6T 1Z4
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17
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Vaitheesvaran B, Hartil K, Navare A, Zheng, ÓBroin P, Golden A, Guha, Lee WN, Kurland I, Bruce JE. Role of the tumor suppressor IQGAP2 in metabolic homeostasis: Possible link between diabetes and cancer. Metabolomics 2014; 10:920-937. [PMID: 25254002 PMCID: PMC4169985 DOI: 10.1007/s11306-014-0639-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Deficiency of IQGAP2, a scaffolding protein expressed primarily in liver leads to rearrangements of hepatic protein compartmentalization and altered regulation of enzyme functions predisposing development of hepatocellular carcinoma and diabetes. Employing a systems approach with proteomics, metabolomics and fluxes characterizations, we examined the effects of IQGAP2 deficient proteomic changes on cellular metabolism and the overall metabolic phenotype. Iqgap2-/- mice demonstrated metabolic inflexibility, fasting hyperglycemia and obesity. Such phenotypic characteristics were associated with aberrant hepatic regulations of glycolysis/gluconeogenesis, glycogenolysis, lipid homeostasis and futile cycling corroborated with corresponding proteomic changes in cytosolic and mitochondrial compartments. IQGAP2 deficiency also led to truncated TCA-cycle, increased anaplerosis, increased supply of acetyl-CoA for de novo lipogenesis, and increased mitochondrial methyl-donor metabolism necessary for nucleotides synthesis. Our results suggest that changes in metabolic networks in IQGAP2 deficiency create a hepatic environment of a 'pre-diabetic' phenotype and a predisposition to non-alcoholic fatty liver disease (NAFLD) which has been linked to the development of hepatocellular carcinoma.
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Affiliation(s)
- B. Vaitheesvaran
- Department of Medicine, Diabetes Center, Stable Isotope and Metabolomics Core Facility, Albert Einstein College of Medicine, Bronx, New York, 10461
| | - K. Hartil
- Department of Medicine, Diabetes Center, Stable Isotope and Metabolomics Core Facility, Albert Einstein College of Medicine, Bronx, New York, 10461
| | - A. Navare
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109
| | - Zheng
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109
| | - P. ÓBroin
- Department of Medicine, Diabetes Center, Stable Isotope and Metabolomics Core Facility, Albert Einstein College of Medicine, Bronx, New York, 10461
- Department of Genetics., Division of Computational Genetics, Albert Einstein College of Medicine, Bronx, NewYork, 10461
| | - A. Golden
- Department of Genetics., Division of Computational Genetics, Albert Einstein College of Medicine, Bronx, NewYork, 10461
| | - Guha
- Department of Radiation Oncology, Albert Einstein College of Medicine, Bronx, New York, 10461
| | - WN. Lee
- Department of Pediatrics, Division of Endocrinology and Metabolism, University of California, Los Angeles, California 90502
| | - I.J Kurland
- Department of Medicine, Diabetes Center, Stable Isotope and Metabolomics Core Facility, Albert Einstein College of Medicine, Bronx, New York, 10461
| | - J. E. Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109
- Corresponding author: James E. Bruce. Department of Genome Sciences, University of Washington, Seattle, Washington, 98109., , Phone: 206-543-0220, Fax: 206-616-0008
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18
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Identifying Sources of Hepatic Lipogenic Acetyl-CoA Using Stable Isotope Tracers and NMR. ACTA ACUST UNITED AC 2014. [DOI: 10.1155/2014/109252] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The role of hepatic de novo lipogenesis (DNL) in promoting fatty liver disease and hypertriglyceridemia during excessive nutrient intake is becoming firmly established. Certain nutrients such as fructose promote hepatic DNL activity and this has been at least partly attributed to their efficient conversion to the acetyl-CoA precursors of DNL. However, tracer studies indicate a paradoxically low level of fructose incorporation into lipids, which begs the question of what the actual lipogenic acetyl-CoA sources are under these and other conditions. Here, we describe novel approaches for measuring substrate contributions to lipogenic hepatic acetyl-CoA using 13C-tracers and 13C-NMR analysis of lipids and acetyl-CoA probes. We review and address aspects of hepatic intermediary fluxes and acetyl-CoA compartmentation that can confound the relationship between 13C-precursor substrate and lipogenic 13C-acetyl-CoA enrichments and demonstrate novel methodologies that can provide realistic estimates of 13C-enriched substrate contributions to DNL. The most striking realization is that the principal substrate contributors to lipogenic acetyl-CoA have yet to be identified, but they are probably not the so-called “lipogenic substrates” such as fructose. The proposed methods may improve our insight into the nutrient sources of DNL under various feeding and disease states.
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19
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Ruiz-Angel M, García-Alvarez-Coque M, Berthod A, Carda-Broch S. Are analysts doing method validation in liquid chromatography? J Chromatogr A 2014; 1353:2-9. [DOI: 10.1016/j.chroma.2014.05.052] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 05/16/2014] [Accepted: 05/19/2014] [Indexed: 01/05/2023]
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20
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Li Q, Zhang S, Berthiaume JM, Simons B, Zhang GF. Novel approach in LC-MS/MS using MRM to generate a full profile of acyl-CoAs: discovery of acyl-dephospho-CoAs. J Lipid Res 2013; 55:592-602. [PMID: 24367045 DOI: 10.1194/jlr.d045112] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
A metabolomic approach to selectively profile all acyl-CoAs was developed using a programmed multiple reaction monitoring (MRM) method in LC-MS/MS and was employed in the analysis of various rat organs. The programmed MRM method possessed 300 mass ion transitions with the mass difference of 507 between precursor ion (Q1) and product ion (Q3), and the precursor ion started from m/z 768 and progressively increased one mass unit at each step. Acyl-dephospho-CoAs resulting from the dephosphorylation of acyl-CoAs were identified by accurate MS and fragmentation. Acyl-dephospho-CoAs were also quantitatively scanned by the MRM method with the mass difference of 427 between Q1 and Q3 mass ions. Acyl-CoAs and dephospho-CoAs were assayed with limits of detection ranging from 2 to 133 nM. The accuracy of the method was demonstrated by assaying a range of concentrations of spiked acyl-CoAs with the results of 80-114%. The distribution of acyl-CoAs reflects the metabolic status of each organ. The physiological role of dephosphorylation of acyl-CoAs remains to be further characterized. The methodology described herein provides a novel strategy in metabolomic studies to quantitatively and qualitatively profile all potential acyl-CoAs and acyl-dephospho-CoAs.
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Affiliation(s)
- Qingling Li
- Department of Nutrition, Case Western Reserve University, Cleveland, OH 44106
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21
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Siegel D, Permentier H, Reijngoud DJ, Bischoff R. Chemical and technical challenges in the analysis of central carbon metabolites by liquid-chromatography mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 966:21-33. [PMID: 24326023 DOI: 10.1016/j.jchromb.2013.11.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 11/10/2013] [Accepted: 11/12/2013] [Indexed: 11/18/2022]
Abstract
This review deals with chemical and technical challenges in the analysis of small-molecule metabolites involved in central carbon and energy metabolism via liquid-chromatography mass-spectrometry (LC-MS). The covered analytes belong to the prominent pathways in biochemical carbon oxidation such as glycolysis or the tricarboxylic acid cycle and, for the most part, share unfavorable properties such as a high polarity, chemical instability or metal-affinity. The topic is introduced by selected examples on successful applications of metabolomics in the clinic. In the core part of the paper, the structural features of important analyte classes such as nucleotides, coenzyme A thioesters or carboxylic acids are linked to "problematic hotspots" along the analytical chain (sample preparation and-storage, separation and detection). We discuss these hotspots from a chemical point of view, covering issues such as analyte degradation or interactions with metals and other matrix components. Based on this understanding we propose solutions wherever available. A major notion derived from these considerations is that comprehensive carbon metabolomics inevitably requires multiple, complementary analytical approaches covering different chemical classes of metabolites.
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Affiliation(s)
- David Siegel
- University of Groningen, Department of Pharmacy, Analytical Biochemistry, Antonius-Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Hjalmar Permentier
- University of Groningen, Department of Pharmacy, Mass Spectrometry Core Facility, Antonius-Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Dirk-Jan Reijngoud
- University Medical Center Groningen, Department of Pediatrics, Center for Liver, Digestive and Metabolic Diseases, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Rainer Bischoff
- University of Groningen, Department of Pharmacy, Analytical Biochemistry, Antonius-Deusinglaan 1, 9713 AV Groningen, The Netherlands.
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22
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Henry RA, Kuo YM, Andrews AJ. Differences in specificity and selectivity between CBP and p300 acetylation of histone H3 and H3/H4. Biochemistry 2013; 52:5746-59. [PMID: 23862699 PMCID: PMC3756530 DOI: 10.1021/bi400684q] [Citation(s) in RCA: 118] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
![]()
Although
p300 and CBP lysine acetyltransferases are often treated
interchangeably, the inability of one enzyme to compensate for the
loss of the other suggests unique roles for each. As these deficiencies
coincide with aberrant levels of histone acetylation, we hypothesized
that the key difference between p300 and CBP activity is differences
in their specificity/selectivity for lysines within the histones.
Utilizing a label-free, quantitative mass spectrometry based technique,
we determined the kinetic parameters of both CBP and p300 at each
lysine of H3 and H4, under conditions we would expect to encounter
in the cell (either limiting acetyl-CoA or histone). Our results show
that while p300 and CBP acetylate many common residues on H3 and H4,
they do in fact possess very different specificities, and these specificities
are dependent on whether histone or acetyl-CoA is limiting. Steady-state
experiments with limiting H3 demonstrate that both CBP and p300 acetylate
H3K14, H3K18, H3K23, with p300 having specificities up to 1010-fold higher than CBP. Utilizing tetramer as a substrate, both enzymes
also acetylate H4K5, H4K8, H4K12, and H4K16. With limiting tetramer,
CBP displays higher specificities, especially at H3K18, where CBP
specificity is 1032-fold higher than p300. With limiting
acetyl-CoA, p300 has the highest specificity at H4K16, where specificity
is 1018-fold higher than CBP. This discovery of unique
specificity for targets of CBP- vs p300-mediated acetylation of histone
lysine residues presents a new model for understanding their respective
biological roles and possibly an opportunity for selective therapeutic
intervention.
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Affiliation(s)
- Ryan A Henry
- Department of Cancer Biology, Fox Chase Cancer Center, Philadelphia, Pennsylvania, United States
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23
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Identification of a novel malonyl-CoA IC(50) for CPT-I: implications for predicting in vivo fatty acid oxidation rates. Biochem J 2013; 448:13-20. [PMID: 22928974 DOI: 10.1042/bj20121110] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Published values regarding the sensitivity (IC(50)) of CPT-I (carnitine palmitoyltransferase I) to M-CoA (malonyl-CoA) inhibition in isolated mitochondria are inconsistent with predicted in vivo rates of fatty acid oxidation. Therefore we have re-examined M-CoA inhibition kinetics under various P-CoA (palmitoyl-CoA) concentrations in both isolated mitochondria and PMFs (permeabilized muscle fibres). PMFs have an 18-fold higher IC(50) (0.61 compared with 0.034 μM) in the presence of 25 μM P-CoA and a 13-fold higher IC(50) (6.3 compared with 0.49 μM) in the presence of 150 μM P-CoA compared with isolated mitochondria. M-CoA inhibition kinetics determined in PMFs predicts that CPT-I activity is inhibited by 33% in resting muscle compared with >95% in isolated mitochondria. Additionally, the ability of M-CoA to inhibit CPT-I appears to be dependent on P-CoA concentration, as the relative inhibitory capacity of M-CoA is decreased with increasing P-CoA concentrations. Altogether, the use of PMFs appears to provide an M-CoA IC(50) that better reflects the predicted in vivo rates of fatty acid oxidation. These findings also demonstrate that the ratio of [P-CoA]/[M-CoA] is critical for regulating CPT-I activity and may partially rectify the in vivo disconnect between M-CoA content and CPT-I flux within the context of exercise and Type 2 diabetes.
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Stanislaus A, Guo K, Li L. Development of an isotope labeling ultra-high performance liquid chromatography mass spectrometric method for quantification of acylglycines in human urine. Anal Chim Acta 2012; 750:161-72. [DOI: 10.1016/j.aca.2012.05.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 05/05/2012] [Accepted: 05/06/2012] [Indexed: 12/31/2022]
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25
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Vaitheesvaran B, Yang L, Hartil K, Glaser S, Yazulla S, Bruce JE, Kurland IJ. Peripheral effects of FAAH deficiency on fuel and energy homeostasis: role of dysregulated lysine acetylation. PLoS One 2012; 7:e33717. [PMID: 22442717 PMCID: PMC3307749 DOI: 10.1371/journal.pone.0033717] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 02/16/2012] [Indexed: 12/01/2022] Open
Abstract
Background FAAH (fatty acid amide hydrolase), primarily expressed in the liver, hydrolyzes the endocannabinoids fatty acid ethanolamides (FAA). Human FAAH gene mutations are associated with increased body weight and obesity. In our present study, using targeted metabolite and lipid profiling, and new global acetylome profiling methodologies, we examined the role of the liver on fuel and energy homeostasis in whole body FAAH−/− mice. Methodology/Principal Findings FAAH−/− mice exhibit altered energy homeostasis demonstrated by decreased oxygen consumption (Indirect calorimetry). FAAH−/− mice are hyperinsulinemic and have adipose, skeletal and hepatic insulin resistance as indicated by stable isotope phenotyping (SIPHEN). Fed state skeletal muscle and liver triglyceride levels was increased 2–3 fold, while glycogen was decreased 42% and 57% respectively. Hepatic cholesterol synthesis was decreased 22% in FAAH−/− mice. Dysregulated hepatic FAAH−/− lysine acetylation was consistent with their metabolite profiling. Fasted to fed increases in hepatic FAAH−/− acetyl-CoA (85%, p<0.01) corresponded to similar increases in citrate levels (45%). Altered FAAH−/− mitochondrial malate dehydrogenase (MDH2) acetylation, which can affect the malate aspartate shuttle, was consistent with our observation of a 25% decrease in fed malate and aspartate levels. Decreased fasted but not fed dihydroxyacetone-P and glycerol-3-P levels in FAAH−/− mice was consistent with a compensating contribution from decreased acetylation of fed FAAH−/− aldolase B. Fed FAAH−/− alcohol dehydrogenase (ADH) acetylation was also decreased. Conclusions/Significance Whole body FAAH deletion contributes to a pre-diabetic phenotype by mechanisms resulting in impairment of hepatic glucose and lipid metabolism. FAAH−/− mice had altered hepatic lysine acetylation, the pattern sharing similarities with acetylation changes reported with chronic alcohol treatment. Dysregulated hepatic lysine acetylation seen with impaired FAA hydrolysis could support the liver's role in fostering the pre-diabetic state, and may reflect part of the mechanism underlying the hepatic effects of endocannabinoids in alcoholic liver disease mouse models.
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Affiliation(s)
- Bhavapriya Vaitheesvaran
- Department of Medicine, Stable Isotope and Metabolomics Core Facility, Albert Einstein College of Medicine Diabetes Center, Bronx, New York, United States of America
| | - Li Yang
- Department of Chemistry, Washington State University, Pullman, Washington, United States of America
| | - Kirsten Hartil
- Department of Medicine, Stable Isotope and Metabolomics Core Facility, Albert Einstein College of Medicine Diabetes Center, Bronx, New York, United States of America
| | - Sherrye Glaser
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York, United States of America
| | - Stephen Yazulla
- Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York, United States of America
| | - James E. Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Irwin J. Kurland
- Department of Medicine, Stable Isotope and Metabolomics Core Facility, Albert Einstein College of Medicine Diabetes Center, Bronx, New York, United States of America
- * E-mail:
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