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Wilkinson DJ, Crossland H, Atherton PJ. Metabolomic and proteomic applications to exercise biomedicine. TRANSLATIONAL EXERCISE BIOMEDICINE 2024; 1:9-22. [PMID: 38660119 PMCID: PMC11036890 DOI: 10.1515/teb-2024-2006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/07/2024] [Indexed: 04/26/2024]
Abstract
Objectives 'OMICs encapsulates study of scaled data acquisition, at the levels of DNA, RNA, protein, and metabolite species. The broad objectives of OMICs in biomedical exercise research are multifarious, but commonly relate to biomarker development and understanding features of exercise adaptation in health, ageing and metabolic diseases. Methods This field is one of exponential technical (i.e., depth of feature coverage) and scientific (i.e., in health, metabolic conditions and ageing, multi-OMICs) progress adopting targeted and untargeted approaches. Results Key findings in exercise biomedicine have led to the identification of OMIC features linking to heritability or adaptive responses to exercise e.g., the forging of GWAS/proteome/metabolome links to cardiovascular fitness and metabolic health adaptations. The recent addition of stable isotope tracing to proteomics ('dynamic proteomics') and metabolomics ('fluxomics') represents the next phase of state-of-the-art in 'OMICS. Conclusions These methods overcome limitations associated with point-in-time 'OMICs and can be achieved using substrate-specific tracers or deuterium oxide (D2O), depending on the question; these methods could help identify how individual protein turnover and metabolite flux may explain exercise responses. We contend application of these methods will shed new light in translational exercise biomedicine.
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Affiliation(s)
- Daniel J. Wilkinson
- Centre of Metabolism, Ageing & Physiology (CoMAP), Medical Research Council/Versus Arthritis UK Centre of Excellence for Musculoskeletal Ageing Research (CMAR), School of Medicine, University of Nottingham, Royal Derby Hospital, Derby, UK
| | - Hannah Crossland
- Centre of Metabolism, Ageing & Physiology (CoMAP), Medical Research Council/Versus Arthritis UK Centre of Excellence for Musculoskeletal Ageing Research (CMAR), School of Medicine, University of Nottingham, Royal Derby Hospital, Derby, UK
| | - Philip J. Atherton
- Centre of Metabolism, Ageing & Physiology (CoMAP), Medical Research Council/Versus Arthritis UK Centre of Excellence for Musculoskeletal Ageing Research (CMAR), School of Medicine, University of Nottingham, Royal Derby Hospital, Derby, UK
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Hernandez-Resendiz S, Prakash A, Loo SJ, Semenzato M, Chinda K, Crespo-Avilan GE, Dam LC, Lu S, Scorrano L, Hausenloy DJ. Targeting mitochondrial shape: at the heart of cardioprotection. Basic Res Cardiol 2023; 118:49. [PMID: 37955687 PMCID: PMC10643419 DOI: 10.1007/s00395-023-01019-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/14/2023]
Abstract
There remains an unmet need to identify novel therapeutic strategies capable of protecting the myocardium against the detrimental effects of acute ischemia-reperfusion injury (IRI), to reduce myocardial infarct (MI) size and prevent the onset of heart failure (HF) following acute myocardial infarction (AMI). In this regard, perturbations in mitochondrial morphology with an imbalance in mitochondrial fusion and fission can disrupt mitochondrial metabolism, calcium homeostasis, and reactive oxygen species production, factors which are all known to be critical determinants of cardiomyocyte death following acute myocardial IRI. As such, therapeutic approaches directed at preserving the morphology and functionality of mitochondria may provide an important strategy for cardioprotection. In this article, we provide an overview of the alterations in mitochondrial morphology which occur in response to acute myocardial IRI, and highlight the emerging therapeutic strategies for targeting mitochondrial shape to preserve mitochondrial function which have the future therapeutic potential to improve health outcomes in patients presenting with AMI.
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Affiliation(s)
- Sauri Hernandez-Resendiz
- Duke-NUS Medical School, Cardiovascular and Metabolic Disorders Programme, Singapore, Singapore
- National Heart Centre Singapore, National Heart Research Institute Singapore, Singapore, Singapore
| | - Aishwarya Prakash
- Duke-NUS Medical School, Cardiovascular and Metabolic Disorders Programme, Singapore, Singapore
- National Heart Centre Singapore, National Heart Research Institute Singapore, Singapore, Singapore
| | - Sze Jie Loo
- Duke-NUS Medical School, Cardiovascular and Metabolic Disorders Programme, Singapore, Singapore
- National Heart Centre Singapore, National Heart Research Institute Singapore, Singapore, Singapore
| | | | - Kroekkiat Chinda
- Department of Physiology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Gustavo E Crespo-Avilan
- Duke-NUS Medical School, Cardiovascular and Metabolic Disorders Programme, Singapore, Singapore
- National Heart Centre Singapore, National Heart Research Institute Singapore, Singapore, Singapore
| | - Linh Chi Dam
- Duke-NUS Medical School, Cardiovascular and Metabolic Disorders Programme, Singapore, Singapore
- National Heart Centre Singapore, National Heart Research Institute Singapore, Singapore, Singapore
| | - Shengjie Lu
- Duke-NUS Medical School, Cardiovascular and Metabolic Disorders Programme, Singapore, Singapore
- National Heart Centre Singapore, National Heart Research Institute Singapore, Singapore, Singapore
| | - Luca Scorrano
- Veneto Institute of Molecular Medicine, Padova, Italy
- Department of Biology, University of Padova, Padova, Italy
| | - Derek J Hausenloy
- Duke-NUS Medical School, Cardiovascular and Metabolic Disorders Programme, Singapore, Singapore.
- National Heart Centre Singapore, National Heart Research Institute Singapore, Singapore, Singapore.
- National University Singapore, Yong Loo Lin School of Medicine, Singapore, Singapore.
- University College London, The Hatter Cardiovascular Institute, London, UK.
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Aghayev M, Arias-Alvarado A, Ilchenko S, Lepp J, Scott I, Chen YR, Zhang GF, Tsai TH, Kasumov T. A high-fat diet increases hepatic mitochondrial turnover through restricted acetylation in a NAFLD mouse model. Am J Physiol Endocrinol Metab 2023; 325:E83-E98. [PMID: 37224468 PMCID: PMC10312330 DOI: 10.1152/ajpendo.00310.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/26/2023]
Abstract
Lysine acetylation of proteins has emerged as a key posttranslational modification (PTM) that regulates mitochondrial metabolism. Acetylation may regulate energy metabolism by inhibiting and affecting the stability of metabolic enzymes and oxidative phosphorylation (OxPhos) subunits. Although protein turnover can be easily measured, due to the low abundance of modified proteins, it has been difficult to evaluate the effect of acetylation on the stability of proteins in vivo. We applied 2H2O-metabolic labeling coupled with immunoaffinity and high-resolution mass spectrometry method to measure the stability of acetylated proteins in mouse liver based on their turnover rates. As a proof-of-concept, we assessed the consequence of high-fat diet (HFD)-induced altered acetylation in protein turnover in LDL receptor-deficient (LDLR-/-) mice susceptible to diet-induced nonalcoholic fatty liver disease (NAFLD). HFD feeding for 12 wk led to steatosis, the early stage of NAFLD. A significant reduction in acetylation of hepatic proteins was observed in NAFLD mice, based on immunoblot analysis and label-free quantification with mass spectrometry. Compared with control mice on a normal diet, NAFLD mice had overall increased turnover rates of hepatic proteins, including mitochondrial metabolic enzymes (0.159 ± 0.079 vs. 0.132 ± 0.068 day-1), suggesting their reduced stability. Also, acetylated proteins had slower turnover rates (increased stability) than native proteins in both groups (0.096 ± 0.056 vs. 0.170 ± 0.059 day-1 in control, and 0.111 ± 0.050 vs. 0.208 ± 0.074 day-1 in NAFLD). Furthermore, association analysis revealed a relationship between the HFD-induced decrease in acetylation and increased turnover rates for hepatic proteins in NAFLD mice. These changes were associated with increased expressions of the hepatic mitochondrial transcriptional factor (TFAM) and complex II subunit without any changes to other OxPhos proteins, suggesting that enhanced mitochondrial biogenesis prevented restricted acetylation-mediated depletion of mitochondrial proteins. We conclude that decreased acetylation of mitochondrial proteins may contribute to adaptive improved hepatic mitochondrial function in the early stages of NAFLD.NEW & NOTEWORTHY This is the first method to quantify acetylome dynamics in vivo. This method revealed acetylation-mediated altered hepatic mitochondrial protein turnover in response to a high-fat diet in a mouse model of NAFLD.
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Affiliation(s)
- Mirjavid Aghayev
- Department of Pharmaceutical Sciences, College of Pharmacy, Northeast Ohio Medical University, Rootstown, Ohio, United States
| | - Andrea Arias-Alvarado
- Department of Pharmaceutical Sciences, College of Pharmacy, Northeast Ohio Medical University, Rootstown, Ohio, United States
| | - Sergei Ilchenko
- Department of Pharmaceutical Sciences, College of Pharmacy, Northeast Ohio Medical University, Rootstown, Ohio, United States
| | - Josephine Lepp
- Department of Pharmaceutical Sciences, College of Pharmacy, Northeast Ohio Medical University, Rootstown, Ohio, United States
| | - Iain Scott
- Cardiology Division, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
| | - Yeong-Renn Chen
- Department of Integrative Medical Sciences, College of Medicine, Northeast Ohio Medical University, Rootstown, Ohio, United States
| | - Guo-Fang Zhang
- Division of Endocrinology, Metabolism and Nutrition, Duke Molecular Physiology Institute, Duke University, Durham North Carolina, United States
- Department of Medicine, Duke University, Durham North Carolina, United States
| | - Tsung-Heng Tsai
- Department of Mathematical Sciences, Kent State University, Kent, Ohio, United States
| | - Takhar Kasumov
- Department of Pharmaceutical Sciences, College of Pharmacy, Northeast Ohio Medical University, Rootstown, Ohio, United States
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Kim J, Seo S, Kim TY. Metabolic deuterium oxide (D 2O) labeling in quantitative omics studies: A tutorial review. Anal Chim Acta 2023; 1242:340722. [PMID: 36657897 DOI: 10.1016/j.aca.2022.340722] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/25/2022] [Accepted: 12/13/2022] [Indexed: 12/15/2022]
Abstract
Mass spectrometry (MS) is an invaluable tool for sensitive detection and characterization of individual biomolecules in omics studies. MS combined with stable isotope labeling enables the accurate and precise determination of quantitative changes occurring in biological samples. Metabolic isotope labeling, wherein isotopes are introduced into biomolecules through biosynthetic metabolism, is one of the main labeling strategies. Among the precursors employed in metabolic isotope labeling, deuterium oxide (D2O) is cost-effective and easy to implement in any biological systems. This tutorial review aims to explain the basic principle of D2O labeling and its applications in omics research. D2O labeling incorporates D into stable C-H bonds in various biomolecules, including nucleotides, proteins, lipids, and carbohydrates. Typically, D2O labeling is performed at low enrichment of 1%-10% D2O, which causes subtle changes in the isotopic distribution of a biomolecule, instead of the complete separation between labeled and unlabeled samples in a mass spectrum. D2O labeling has been employed in various omics studies to determine the metabolic flux, turnover rate, and relative quantification. Moreover, the advantages and challenges of D2O labeling and its future prospects in quantitative omics are discussed. The economy, versatility, and convenience of D2O labeling will be beneficial for the long-term omics studies for higher organisms.
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Affiliation(s)
- Jonghyun Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - Seungwoo Seo
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - Tae-Young Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea.
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Shi Y, Weng N, Jian W. Measurement of protein in vivo turnover rate with metabolic labeling using LC-MS. Biomed Chromatogr 2023:e5583. [PMID: 36634055 DOI: 10.1002/bmc.5583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
Understanding the protein dynamics of a drug target is important for pharmaceutical research because it provides insight into drug design, target engagement, pharmacodynamics and drug efficacy. Nonradioactive isotope labeling has been the method of choice for protein turnover measurement thanks to the advancement of high-resolution mass spectrometry. While the changes in proteome in cell cultures can be monitored precisely, as the culture media can be completely replaced with 2 H-, 15 N- or 13 C-labeled essential amino acids, quantifying rates of protein synthesis in vivo is more challenging. The amount of isotope tracer that can be administered into the body is relatively small compared with the existing protein, thus requiring more sensitive detection, and the precursor-product labeling relationship is more complicated to interpret. The purpose of this review is to provide an overview of the principles of in vivo protein turnover studies using deuterium water (2 H2 O) with an emphasis on targeted protein analysis by hybrid LC-MS assay platforms. The pursuit of these opportunities will facilitate drug discovery and research in preclinical and clinical stages.
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Affiliation(s)
- Yifan Shi
- Bioanalytical Discovery and Development Sciences, Janssen Research and Development, Spring House, PA, USA
| | - Naidong Weng
- Bioanalytical Discovery and Development Sciences, Janssen Research and Development, Spring House, PA, USA
| | - Wenying Jian
- Bioanalytical Discovery and Development Sciences, Janssen Research and Development, Spring House, PA, USA
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Wood NB, Kelly CM, O’Leary TS, Martin JL, Previs MJ. Cardiac Myosin Filaments are Maintained by Stochastic Protein Replacement. Mol Cell Proteomics 2022; 21:100274. [PMID: 35921914 PMCID: PMC9528119 DOI: 10.1016/j.mcpro.2022.100274] [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: 12/10/2021] [Revised: 07/08/2022] [Accepted: 07/19/2022] [Indexed: 01/18/2023] Open
Abstract
Myosin and myosin-binding protein C are exquisitely organized into giant filamentous macromolecular complexes within cardiac muscle sarcomeres, yet these proteins must be continually replaced to maintain contractile fidelity. The overall hypothesis that myosin filament structure is dynamic and allows for the stochastic replacement of individual components was tested in vivo, using a combination of mass spectrometry- and fluorescence-based proteomic techniques. Adult mice were fed a diet that marked all newly synthesized proteins with a stable isotope-labeled amino acid. The abundance of unlabeled and labeled proteins was quantified by high-resolution mass spectrometry over an 8-week period. The rates of change in the abundance of these proteins were well described by analytical models in which protein synthesis defined stoichiometry and protein degradation was governed by the stochastic selection of individual molecules. To test whether the whole myosin filaments or the individual components were selected for replacement, cardiac muscle was chemically skinned to remove the cellular membrane and myosin filaments were solubilized with ionic solutions. The composition of the filamentous and soluble fractions was quantified by mass spectrometry, and filament depolymerization was visualized by real-time fluorescence microscopy. Myosin molecules were preferentially extracted from ends of the filaments in the presence of the ionic solutions, and there was only a slight bias in the abundance of unlabeled molecules toward the innermost region on the myosin filaments. These data demonstrate for the first time that the newly synthesized myosin and myosin-binding protein C molecules are randomly mixed into preexisting thick filaments in vivo and the rate of mixing may not be equivalent along the length of the thick filament. These data collectively support a new model of cardiac myosin filament structure, with the filaments being dynamic macromolecular assemblies that allow for replacement of their components, rather than rigid bodies.
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Affiliation(s)
- Neil B. Wood
- Department of Molecular Physiology and Biophysics, University of Vermont, Larner College of Medicine, Burlington, Vermont, USA
| | - Colleen M. Kelly
- Department of Molecular Physiology and Biophysics, University of Vermont, Larner College of Medicine, Burlington, Vermont, USA
| | - Thomas S. O’Leary
- Department of Molecular Physiology and Biophysics, University of Vermont, Larner College of Medicine, Burlington, Vermont, USA
| | - Jody L. Martin
- Department of Pharmacology, University of California, Davis, Davis, California, USA
| | - Michael J. Previs
- Department of Molecular Physiology and Biophysics, University of Vermont, Larner College of Medicine, Burlington, Vermont, USA,For correspondence: Michael J. Previs, Department of Molecular Physiology & Biophysics, Larner College of Medicine, University of Vermont, Health Science Research Facility, 149 Beaumont Avenue, Room 108, Burlington, Vermont 05405
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Paggi RA, Albaum SP, Poetsch A, Cerletti M. Proteome Turnover Analysis in Haloferax volcanii by a Heavy Isotope Multilabeling Approach. Methods Mol Biol 2022; 2522:267-286. [PMID: 36125756 DOI: 10.1007/978-1-0716-2445-6_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The cellular protein repertoire is highly dynamic and responsive to internal or external stimuli. Its changes are largely the consequence of the combination of protein synthesis and degradation, referred collectively as protein turnover. Different proteomics techniques have been developed to determine the whole proteome turnover of a cell, but very few have been applied to archaea. In this chapter we describe a heavy isotope multilabeling method that allowed the successful analysis of relative protein synthesis and degradation rates on the proteome scale of the halophilic archaeon Haloferax volcanii. This method combines 15N and 13C isotope metabolic labeling with high-resolution mass spectrometry and data analysis tools (QuPE web-based platform) and could be applied to different archaea.
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Affiliation(s)
- Roberto A Paggi
- Instituto de Investigaciones Biológicas, FCEyN, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina
| | - Stefan P Albaum
- Bioinformatics Resource Facility, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Ansgar Poetsch
- College of Marine Life Sciences, Ocean University of China, Qingdao, China.
- Queen Mary School, Medical College, Nanchang University, Nanchang, China.
- Plant Biochemistry, Ruhr University Bochum, Bochum, Germany.
| | - Micaela Cerletti
- Instituto de Investigaciones Biológicas, FCEyN, Universidad Nacional de Mar del Plata (UNMDP), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Mar del Plata, Argentina.
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Wang X, Liu NM, Zhao YF, Yang F, Zhu ZJ, Song D. Research Progress in the Medical Application of Heavy Water, Especially in the Field of D 2O-Raman Spectroscopy. Int J Med Sci 2022; 19:1357-1363. [PMID: 35928718 PMCID: PMC9346379 DOI: 10.7150/ijms.73150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/07/2022] [Indexed: 11/05/2022] Open
Abstract
Heavy water is an ideal contrast agent for metabolic activity and can be adapted to a wide range of biological systems owing to its non-invasiveness, universal applicability, and cost-effectiveness. As a new type of probe, the heavy isotope of water has been widely used in the study of cell development, metabolism, tissue homeostasis, aging, and tumor heterogeneity. Herein, we review findings supporting the applications of and research on heavy water in monitoring of bacterial metabolism, rapid detection of drug sensitivity, identification of tumor cells, precision medicine, and evaluation of skin barrier function and promote the use of heavy water as a suitable marker for the development of detection and treatment methodologies.
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Affiliation(s)
- Xin Wang
- Department of Breast Surgery, First Hospital of Jilin University, Changchun, Jilin 130021
| | - Nai-Meng Liu
- Department of Breast Surgery, First Hospital of Jilin University, Changchun, Jilin 130021
| | - Ya-Fei Zhao
- Department of Breast Surgery, First Hospital of Jilin University, Changchun, Jilin 130021
| | - Fan Yang
- Department of Breast Surgery, First Hospital of Jilin University, Changchun, Jilin 130021
| | - Zi-Jia Zhu
- Department of Breast Surgery, First Hospital of Jilin University, Changchun, Jilin 130021
| | - Dong Song
- Department of Breast Surgery, First Hospital of Jilin University, Changchun, Jilin 130021
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Gabisonia K, Burjanadze G, Woitek F, Keles A, Seki M, Gorgodze N, Carlucci L, Ilchenko S, Kurishima C, Walsh K, Piontkivska H, Recchia FA, Kasumov T. Proteome dynasmics and bioinformatics reveal major alterations in the turnover rate of functionally related cardiac and plasma proteins in a dog model of congestive heart failure. J Card Fail 2021; 28:588-600. [PMID: 34785403 DOI: 10.1016/j.cardfail.2021.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 11/05/2021] [Accepted: 11/05/2021] [Indexed: 11/26/2022]
Abstract
Protein pool turnover is a critically important cellular homeostatic component, yet it has been little explored in the context of heart failure (HF) pathophysiology. We employed in vivo 2H labeling/ proteome dynamics for non-biased discovery of turnover alterations involving functionally linked cardiac and plasma proteins in canine tachypacing-induced HF, an established preclinical model of dilated cardiomyopathy. Compared to control, dogs with congestive HF displayed bidirectional turnover changes of 28 cardiac proteins, i.e. reduced half-life of several key enzymes involved in glycolysis, homocysteine metabolism and glycogenesis, and increased half-life of proteins involved in proteolysis. Changes in plasma proteins were more modest: only 5 proteins, involved in various functions including proteolysis inhibition, hemoglobin, calcium and ferric-iron binding, displayed increased or decreased turnover rates. In other dogs undergoing cardiac tachypacing, we infused for 2 weeks the myokine Follistatin-like protein 1 (FSTL1), known for its ameliorative effects on HF-induced alterations. Proteome dynamics proved very sensitive in detecting the partial or complete prevention, by FSTL1, of cardiac and plasma protein turnover alterations. In conclusion, our study unveiled, for the first time in a large mammal, numerous HF-related alterations that may serve as the basis for future mechanistic research and/or as conceptually new molecular markers.
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Key Words
- ATIC, 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase /IMP cyclohydrolase
- BNP, brain natriuretic peptide
- CLTC, Clathrin heavy chain
- CRP, Pentraxin
- CYB5R3, NADH-cytochrome b5 reductase
- DPYSL2, Dihydropyrimidinase Like 2
- FDR, false discovery rate
- FSTL1, Follistatin-like protein 1
- GAPDHS, Glyceraldehyde-3-phosphate dehydrogenase
- GYS1, Glycogen synthase
- HF, Heart failure
- HSP90, Heat shock protein 90
- HSP90AB1, Heat shock protein 90 alpha family class B member 1
- HSPA1A, Heat Shock Protein A1
- LC-MS, liquid chromatography-mass spectrometry
- LFQ, Label-free quantification
- LOC479668, Haptoglobin
- LTAH4, Leukotriene A (4) hydrolase
- LV, Left ventricle
- PCA, Principal Component Analysis
- PDHA1, Pyruvate dehydrogenase E1 component subunit alpha
- PDHB, Pyruvate dehydrogenase E1 component subunit beta
- PGM, Phosphoglucomutase 1
- PSMD2, Proteasome 26S subunit, non-ATPase 2
- STIP1, Stress induced phosphoprotein
- TF, Transferrin
- proteome dynamics, bioinformatics, cardiac disease, heart failure, List of abbreviations: ANP, atrial natriuretic peptide
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Affiliation(s)
- Khatia Gabisonia
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa; Fondazione Gabriele Monasterio, Pisa, Italy
| | - Gia Burjanadze
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa; Fondazione Gabriele Monasterio, Pisa, Italy
| | - Felix Woitek
- Heart Center Dresden-University Clinic, Technical University Dresden, Dresden, Germany
| | - Ayse Keles
- Northeast Ohio Medical University, Rootstown, OH, USA
| | - Mitsuru Seki
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Nikoloz Gorgodze
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa; Fondazione Gabriele Monasterio, Pisa, Italy
| | - Lucia Carlucci
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa; Fondazione Gabriele Monasterio, Pisa, Italy
| | - Serguei Ilchenko
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Clara Kurishima
- Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Kenneth Walsh
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Helen Piontkivska
- Department of Biological Sciences and Brain Health Research Institute, Kent State University, Kent, OH, USA
| | - Fabio A Recchia
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa; Fondazione Gabriele Monasterio, Pisa, Italy; Cardiovascular Research Center, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA.
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Hesketh SJ, Stansfield BN, Stead CA, Burniston JG. The application of proteomics in muscle exercise physiology. Expert Rev Proteomics 2021; 17:813-825. [PMID: 33470862 DOI: 10.1080/14789450.2020.1879647] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Exercise offers protection from non-communicable diseases and extends healthspan by offsetting natural physiological declines that occur in older age. Striated muscle is the largest bodily organ; it underpins the capacity for physical work, and the responses of muscle to exercise convey the health benefits of a physically active lifestyle. Proteomic surveys of muscle provide a means to study the protective effects of exercise and this review summaries some key findings from literature listed in PubMed during the last 10 years that have led to new insight in muscle exercise physiology. AREAS COVERED 'Bottom-up' analyses involving liquid-chromatography tandem mass spectrometry (LC-MS/MS) of peptide digests have become the mainstay of proteomic studies and have been applied to muscle mitochondrial fractions. Enrichment techniques for post-translational modifications, including phosphorylation, acetylation and ubiquitination, have evolved and the analysis of site-specific modifications has become a major area of interest in exercise proteomics. Finally, we consider emergent techniques for dynamic analysis of muscle proteomes that offer new insight to protein turnover and the contributions of synthesis and degradation to changes in protein abundance in response to exercise training. EXPERT OPINION Burgeoning methods for dynamic proteome profiling offer new opportunities to study the mechanisms of muscle adaptation.
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Affiliation(s)
- Stuart J Hesketh
- Research Institute for Sport & Exercise Sciences, Liverpool John Moores University , Liverpool, UK
| | - Ben N Stansfield
- Research Institute for Sport & Exercise Sciences, Liverpool John Moores University , Liverpool, UK
| | - Connor A Stead
- Research Institute for Sport & Exercise Sciences, Liverpool John Moores University , Liverpool, UK
| | - Jatin G Burniston
- Research Institute for Sport & Exercise Sciences, Liverpool John Moores University , Liverpool, UK
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11
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Arias-Alvarado A, Aghayev M, Ilchenko S, Rachdaoui N, Lepp J, Tsai TH, Zhang GF, Previs S, Kasumov T. Measuring acetyl-CoA and acetylated histone turnover in vivo: Effect of a high fat diet. Anal Biochem 2020; 615:114067. [PMID: 33340539 DOI: 10.1016/j.ab.2020.114067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/08/2020] [Accepted: 12/13/2020] [Indexed: 11/24/2022]
Abstract
Cellular availability of acetyl-CoA, a central intermediate of metabolism, regulates histone acetylation. The impact of a high-fat diet (HFD) on the turnover rates of acetyl-CoA and acetylated histones is unknown. We developed a method for simultaneous measurement of acetyl-CoA and acetylated histones kinetics using a single 2H2O tracer, and used it to examine effect of HFD-induced perturbations on hepatic histone acetylation in LDLR-/- mice, a mouse model of non-alcoholic fatty liver disease (NAFLD). Mice were given 2H2O in the drinking water and the kinetics of hepatic acetyl-CoA, histones, and acetylated histones were quantified based on their 2H-labeling. Consumption of a high fat Western-diet (WD) for twelve weeks led to decreased acetylation of hepatic histones (p< 0.05), as compared to a control diet. These changes were associated with 1.5-3-fold increased turnover rates of histones without any change in acetyl-CoA flux. Acetylation significantly reduced the stability of histones and the turnover rates of acetylated peptides were correlated with the number of acetyl groups in neighboring lysine sites. We conclude that 2H2O-method can be used to study metabolically controlled histone acetylation and acetylated histone turnover in vivo.
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Affiliation(s)
- Andrea Arias-Alvarado
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, 44272, USA
| | - Mirjavid Aghayev
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, 44272, USA
| | - Serguei Ilchenko
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, 44272, USA
| | - Nadia Rachdaoui
- Department of Animal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Josephine Lepp
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, 44272, USA
| | - Tsung-Heng Tsai
- Department of Mathematical Sciences, Kent State University, Kent, OH, 44242, USA
| | - Guo-Fang Zhang
- Division of Division of Endocrinology, Metabolism and Nutrition, Duke Molecular Physiology Institute, And Department of Medicine, Duke University, Durham, NC, 27701, USA
| | - Stephen Previs
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, NJ, 07033, USA
| | - Takhar Kasumov
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, 44272, USA; Departments of Gastroenterology, Hepatology and Nutrition, Cleveland Clinic Foundation, Cleveland, OH, 44195, USA.
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12
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Daurio NA, Zhou H, Chen Y, Sheth PR, Imbriglio JE, McLaren DG, Tawa P, Rachdaoui N, Previs MJ, Kasumov T, O’Neil J, Previs SF. Examining Targeted Protein Degradation from Physiological and Analytical Perspectives: Enabling Translation between Cells and Subjects. ACS Chem Biol 2020; 15:2623-2635. [PMID: 32930572 DOI: 10.1021/acschembio.0c00380] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The ability to target specific proteins for degradation may open a new door toward developing therapeutics. Although effort in chemistry is essential for advancing this modality, i.e., one needs to generate proteolysis targeting chimeras (bifunctional molecules, also referred to as PROTACS) or "molecular glues" to accelerate protein degradation, we suspect that investigations could also benefit by directing attention toward physiological regulation surrounding protein homeostasis, including the methods that can be used to examine changes in protein kinetics. This perspective will first consider some metabolic scenarios that might be of importance when one aims to change protein abundance by increasing protein degradation. Specifically, could protein turnover impact the apparent outcome? We will then outline how to study protein dynamics by coupling stable isotope tracer methods with mass spectrometry-based detection; since the experimental conditions could have a dramatic effect on protein turnover, special attention is directed toward the application of methods for quantifying protein kinetics using in vitro and in vivo models. Our goal is to present key concepts that should enable mechanistically informed studies which test targeted protein degradation strategies.
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Affiliation(s)
- Natalie A. Daurio
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
| | - Haihong Zhou
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
| | - Ying Chen
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
| | - Payal R. Sheth
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
| | - Jason E. Imbriglio
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
| | - David G. McLaren
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
| | - Paul Tawa
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
| | - Nadia Rachdaoui
- Department of Animal Sciences, Rutgers, the State University of New Jersey, New Brunswick, New Jersey 08901, United States
| | - Michael J. Previs
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, Vermont 05454, United States
| | - Takhar Kasumov
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio 44272, United States
| | - Jennifer O’Neil
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
| | - Stephen F. Previs
- Merck & Co., Inc, 2000 Galloping Hill Rd, Kenilworth, New Jersey 07033, United States
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13
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Abstract
"Omics"-based analyses are widely used in numerous areas of research, advances in instrumentation (both hardware and software) allow investigators to collect a wealth of data and therein characterize metabolic systems. Although analyses generally examine differences in absolute or relative (fold-) changes in concentrations, the ability to extract mechanistic insight would benefit from the use of isotopic tracers. Herein, we discuss important concepts that should be considered when stable isotope tracers are used to capture biochemical flux. Special attention is placed on in vivo systems, however, many of the general ideas have immediate impact on studies in cellular models or isolated-perfused tissues. While it is somewhat trivial to administer labeled precursor molecules and measure the enrichment of downstream products, the ability to make correct interpretations can be challenging. We will outline several critical factors that may influence choices when developing and/or applying a stable isotope tracer method. For example, is there a "best" tracer for a given study? How do I administer a tracer? When do I collect my sample(s)? While these questions may seem straightforward, we will present scenarios that can have dramatic effects on conclusions surrounding apparent rates of metabolic activity.
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Affiliation(s)
- Stephen F Previs
- Department of Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA.
| | - Daniel P Downes
- Department of Chemistry, Merck & Co., Inc., Kenilworth, NJ, USA
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14
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Ilchenko S, Haddad A, Sadana P, Recchia FA, Sadygov RG, Kasumov T. Calculation of the Protein Turnover Rate Using the Number of Incorporated 2H Atoms and Proteomics Analysis of a Single Labeled Sample. Anal Chem 2019; 91:14340-14351. [PMID: 31638786 DOI: 10.1021/acs.analchem.9b02757] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Rate constant estimation with heavy water requires a long-term experiment with data collection at multiple time points (3-4 weeks for mitochondrial proteome dynamics in mice and much longer in other species). When tissue proteins are analyzed, this approach requires euthanizing animals at each time point or multiple tissue biopsies in humans. Although short-term protocols are available, they require knowledge of the maximum number of isotope labels (N) and accurate quantification of observed 2H-enrichment in the peptide. The high-resolution accurate mass spectrometers used for proteome dynamics studies are characterized by a systematic spectral error that compromises these measurements. To circumvent these issues, we developed a simple algorithm for the rate constant calculation based on a single labeled sample and comparable unlabeled (time 0) sample. The algorithm determines N for all proteogenic amino acids from a long-term experiment to calculate the predicted plateau 2H-labeling of peptides for a short-term protocol and estimates the rate constant based on the measured baseline and the predicted plateau 2H-labeling of peptides. The method was validated based on the rate constant estimation in a long-term experiment in mice and dogs. The improved 2 time-point method enables the rate constant calculation with less than 10% relative error compared to the bench-marked multi-point method in mice and dogs and allows us to detect diet-induced subtle changes in ApoAI turnover in mice. In conclusion, we have developed and validated a new algorithm for protein rate constant calculation based on 2-time point measurements that could also be applied to other biomolecules.
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Affiliation(s)
- Serguei Ilchenko
- Northeast Ohio Medical University , Rootstown , Ohio 44272 , United States
| | - Andrew Haddad
- Northeast Ohio Medical University , Rootstown , Ohio 44272 , United States
| | - Prabodh Sadana
- Northeast Ohio Medical University , Rootstown , Ohio 44272 , United States
| | - Fabio A Recchia
- Institute of Life Sciences , Scuola Superiore Sant'Anna, Pisa, Fondazione Gabriele Monasterio , 56100 Pisa , Italy.,Cardiovascular Research Center , Lewis Katz School of Medicine at Temple University , Philadelphia , Pennsylvania 19140 , United States
| | - Rovshan G Sadygov
- University of Texas Medical Branch , Galveston , Texas 77555 , United States
| | - Takhar Kasumov
- Northeast Ohio Medical University , Rootstown , Ohio 44272 , United States
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15
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Angel TE, Naylor BC, Price JC, Evans C, Szapacs M. Improved Sensitivity for Protein Turnover Quantification by Monitoring Immonium Ion Isotopologue Abundance. Anal Chem 2019; 91:9732-9740. [PMID: 31259532 DOI: 10.1021/acs.analchem.9b01329] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe an analytical strategy allowing for the direct quantification of stable isotope label incorporation in newly synthesized proteins following administration of the stable isotope tracer deuterium oxide. We present a demonstration of coupling high-resolution mass spectrometry, metabolic stable isotope labeling, and MS/MS-based isotopologue quantification for the measurement of protein turnover. Stable isotope labeling with deuterium oxide, followed by immonium ion isotopologue quantification, is a more sensitive strategy for determining protein fractional synthesis rates compared to peptide centric mass isotopomer distribution analysis approaches when labeling time and/or stable isotope tracer exposure is limited and, as such, offers a great advantage for human studies.
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Affiliation(s)
- Thomas E Angel
- In-vitro/In-vivo Translation Platform Group , GlaxoSmithKline , 1250 S Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Bradley C Naylor
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84604 , United States
| | - John C Price
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84604 , United States
| | - Christopher Evans
- In-vitro/In-vivo Translation Platform Group , GlaxoSmithKline , 1250 S Collegeville Road , Collegeville , Pennsylvania 19426 , United States
| | - Matthew Szapacs
- In-vitro/In-vivo Translation Platform Group , GlaxoSmithKline , 1250 S Collegeville Road , Collegeville , Pennsylvania 19426 , United States
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16
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Yoshida K, Kita Y, Tokuoka SM, Hamano F, Yamazaki M, Sakimura K, Kano M, Shimizu T. Monoacylglycerol lipase deficiency affects diet-induced obesity, fat absorption, and feeding behavior in CB 1 cannabinoid receptor-deficient mice. FASEB J 2018; 33:2484-2497. [PMID: 30265576 DOI: 10.1096/fj.201801203r] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Excess energy intake causes obesity, which leads to insulin resistance and various other complications of metabolic syndrome, including diabetes, atherosclerosis, dyslipidemia, and nonalcoholic fatty liver disease. Although recent studies have depicted altered lipid metabolism as an underlying feature, the detailed mechanisms are still unclear. Here we describe a possible role in high-fat diet (HFD)-induced obesity for monoacylglycerol lipase (MGL), an enzyme that is also known to hydrolyze the endocannabinoid 2-arachidonoylglycerol in brain. MGL-deficient [MGL-knockout (KO)] mice fed a HFD gained less body weight than wild-type mice and were protected from insulin resistance and hepatic steatosis. Food intake and energy expenditure were not altered in MGL-KO mice, but blood triglyceride levels after oral olive oil gavage were suppressed, indicating a role for MGL in intestinal fat absorption. Experiments with cannabinoid receptor type 1 (CB1)/MGL double-KO mice revealed that these phenotypes may include mechanisms that are independent of CB1-receptor-mediated endocannabinoid functions. We also noted that MGL-KO mice had less preference for HFD over normal chow diet. Oral but not intraperitoneal lipid administration strongly suppressed the appetites of MGL-KO and CB1/MGL double-KO mice, but not of wild-type and CB1-KO mice. Appetite suppression was reversed by vagotomy, suggesting involvement of MGL in the gut-brain axis regulation of appetite. Our results provide mechanistic insights of MGL's role in diet-induced obesity, lipid metabolic disorder, and regulation of appetite.-Yoshida, K., Kita, Y., Tokuoka, S. M., Hamano, F., Yamazaki, M., Sakimura, K., Kano, M., Shimizu, T. Monoacylglycerol lipase deficiency affects diet-induced obesity, fat absorption, and feeding behavior in CB1 cannabinoid receptor-deficient mice.
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Affiliation(s)
- Kenji Yoshida
- Department of Lipidomics, The University of Tokyo, Tokyo, Japan
| | - Yoshihiro Kita
- Department of Lipidomics, The University of Tokyo, Tokyo, Japan.,Life Sciences Core Facility The University of Tokyo, Tokyo, Japan
| | | | - Fumie Hamano
- Department of Lipidomics, The University of Tokyo, Tokyo, Japan.,Life Sciences Core Facility The University of Tokyo, Tokyo, Japan.,Department of Lipid Signaling, National Center for Global Health and Medicine, Tokyo, Japan
| | - Maya Yamazaki
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, Japan.,Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Kenji Sakimura
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Masanobu Kano
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; and.,International Research Center for Neurointelligence (WPI-IRCN), University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, Tokyo, Japan
| | - Takao Shimizu
- Department of Lipidomics, The University of Tokyo, Tokyo, Japan.,Department of Lipid Signaling, National Center for Global Health and Medicine, Tokyo, Japan
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17
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Chen Y, Berejnaia O, Liu J, Wang SP, Daurio NA, Yin W, Mayoral R, Petrov A, Kasumov T, Zhang GF, Previs SF, Kelley DE, McLaren DG. Quantifying ceramide kinetics in vivo using stable isotope tracers and LC-MS/MS. Am J Physiol Endocrinol Metab 2018; 315:E416-E424. [PMID: 29509438 DOI: 10.1152/ajpendo.00457.2017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Numerous studies have implicated dyslipidemia as a key factor in mediating insulin resistance. Ceramides have received special attention since their levels are inversely associated with normal insulin signaling and positively associated with factors that are involved in cardiometabolic disease. Despite the growing literature surrounding ceramide biology, there are limited data regarding the activity of ceramide synthesis and turnover in vivo. Herein, we demonstrate the ability to measure ceramide kinetics by coupling the administration of [2H]water with LC-MS/MS analyses. As a "proof-of-concept" we determined the effect of a diet-induced alteration on ceramide flux; studies also examined the effect of myriocin (a known inhibitor of serine palmitoyltransferase, the first step in sphingosine biosynthesis). Our data suggest that one can estimate ceramide synthesis and draw conclusions regarding the source of fatty acids; we discuss caveats in regards to method development in this area.
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Affiliation(s)
- Ying Chen
- MRL, Merck & Co., Inc., Kenilworth, New Jersey
| | | | - Jinqi Liu
- MRL, Merck & Co., Inc., Kenilworth, New Jersey
| | | | | | - Wu Yin
- MRL, Merck & Co., Inc., Kenilworth, New Jersey
| | | | | | - Takhar Kasumov
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio
| | - Guo-Fang Zhang
- Division of Endocrinology, Metabolism and Nutrition, Duke Molecular Physiology Institute, and Department of Medicine, Duke University , Durham, North Carolina
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18
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Lee K, Haddad A, Osme A, Kim C, Borzou A, Ilchenko S, Allende D, Dasarathy S, McCullough A, Sadygov RG, Kasumov T. Hepatic Mitochondrial Defects in a Nonalcoholic Fatty Liver Disease Mouse Model Are Associated with Increased Degradation of Oxidative Phosphorylation Subunits. Mol Cell Proteomics 2018; 17:2371-2386. [PMID: 30171159 DOI: 10.1074/mcp.ra118.000961] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 08/21/2018] [Indexed: 12/11/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is associated with hepatic mitochondrial dysfunction characterized by reduced ATP synthesis. We applied the 2H2O-metabolic labeling approach to test the hypothesis that the reduced stability of oxidative phosphorylation proteins contributes to mitochondrial dysfunction in a diet-induced mouse model of NAFLD. A high fat diet containing cholesterol (a so-called Western diet (WD)) led to hepatic oxidative stress, steatosis, inflammation and mild fibrosis, all markers of NAFLD, in low density cholesterol (LDL) receptor deficient (LDLR-/-) mice. In addition, compared with controls (LDLR-/- mice on normal diet), livers from NAFLD mice had reduced citrate synthase activity and ATP content, suggesting mitochondrial impairment. Proteome dynamics study revealed that mitochondrial defects are associated with reduced average half-lives of mitochondrial proteins in NAFLD mice (5.41 ± 0.46 versus 5.15 ± 0.49 day, p < 0.05). In particular, the WD reduced stability of oxidative phosphorylation subunits, including cytochrome b-c1 complex subunit 1 (5.9 ± 0.1 versus 3.4 ± 0.8 day), ATP synthase subunit α (6.3 ± 0.4 versus 5.5 ± 0.4 day) and ATP synthase F(0) complex subunit B1 of complex V (8.5 ± 0.6 versus 6.5 ± 0.2 day) (p < 0.05). These changes were associated with impaired complex III and F0F1-ATP synthase activities. Markers of mitophagy were increased, but proteasomal degradation activity were reduced in NAFLD mice liver, suggesting that ATP deficiency because of reduced stability of oxidative phosphorylation complex subunits contributed to inhibition of ubiquitin-proteasome and activation of mitophagy. In conclusion, the 2H2O-metabolic labeling approach shows that increased degradation of hepatic oxidative phosphorylation subunits contributed to mitochondrial impairment in NAFLD mice.
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Affiliation(s)
- Kwangwon Lee
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio 44272
| | - Andrew Haddad
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio 44272
| | - Abdullah Osme
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio 44272
| | - Chunki Kim
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio 44272
| | - Ahmad Borzou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555
| | - Sergei Ilchenko
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio 44272
| | - Daniela Allende
- Department of Pathology, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | | | - Arthur McCullough
- Department of Hepatology, Cleveland Clinic Foundation, Cleveland, Ohio 44195
| | - Rovshan G Sadygov
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555
| | - Takhar Kasumov
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, Ohio 44272; Department of Hepatology, Cleveland Clinic Foundation, Cleveland, Ohio 44195.
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19
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Abstract
Progressive loss of proteostasis is a hallmark of aging that is marked by declines in various components of proteostasis machinery, including: autophagy, ubiquitin-mediated degradation, protein synthesis, and others. While declines in proteostasis have historically been observed as changes in these processes, or as bulk changes in the proteome, recent advances in proteomic methodologies have enabled the comprehensive measurement of turnover directly at the level of individual proteins in vivo. These methods, which utilize a combination of stable-isotope labeling, mass spectrometry, and specialized software analysis, have now been applied to various studies of aging and longevity. Here we review the role of proteostasis in aging and longevity, with a focus on the proteomic methods available to conduct protein turnover in aging models and the insights these studies have provided thus far.
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20
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Wilkinson DJ. Historical and contemporary stable isotope tracer approaches to studying mammalian protein metabolism. MASS SPECTROMETRY REVIEWS 2018; 37:57-80. [PMID: 27182900 PMCID: PMC5763415 DOI: 10.1002/mas.21507] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 04/22/2016] [Indexed: 06/05/2023]
Abstract
Over a century ago, Frederick Soddy provided the first evidence for the existence of isotopes; elements that occupy the same position in the periodic table are essentially chemically identical but differ in mass due to a different number of neutrons within the atomic nucleus. Allied to the discovery of isotopes was the development of some of the first forms of mass spectrometers, driven forward by the Nobel laureates JJ Thomson and FW Aston, enabling the accurate separation, identification, and quantification of the relative abundance of these isotopes. As a result, within a few years, the number of known isotopes both stable and radioactive had greatly increased and there are now over 300 stable or radioisotopes presently known. Unknown at the time, however, was the potential utility of these isotopes within biological disciplines, it was soon discovered that these stable isotopes, particularly those of carbon (13 C), nitrogen (15 N), oxygen (18 O), and hydrogen (2 H) could be chemically introduced into organic compounds, such as fatty acids, amino acids, and sugars, and used to "trace" the metabolic fate of these compounds within biological systems. From this important breakthrough, the age of the isotope tracer was born. Over the following 80 yrs, stable isotopes would become a vital tool in not only the biological sciences, but also areas as diverse as forensics, geology, and art. This progress has been almost exclusively driven through the development of new and innovative mass spectrometry equipment from IRMS to GC-MS to LC-MS, which has allowed for the accurate quantitation of isotopic abundance within samples of complex matrices. This historical review details the development of stable isotope tracers as metabolic tools, with particular reference to their use in monitoring protein metabolism, highlighting the unique array of tools that are now available for the investigation of protein metabolism in vivo at a whole body down to a single protein level. Importantly, it will detail how this development has been closely aligned to the technological development within the area of mass spectrometry. Without the dedicated development provided by these mass spectrometrists over the past century, the use of stable isotope tracers within the field of protein metabolism would not be as widely applied as it is today, this relationship will no doubt continue to flourish in the future and stable isotope tracers will maintain their importance as a tool within the biological sciences for many years to come. © 2016 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc. Mass Spec Rev.
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Affiliation(s)
- Daniel James Wilkinson
- MRC‐ARUK Centre for Musculoskeletal Ageing Research, Clinical, Metabolic and Molecular PhysiologyUniversity of Nottingham, Royal Derby Hospital CentreDerbyUnited Kingdom
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21
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Rachdaoui N, Li L, Willard B, Kasumov T, Previs S, Sarkar D. Turnover of histones and histone variants in postnatal rat brain: effects of alcohol exposure. Clin Epigenetics 2017; 9:117. [PMID: 29075360 PMCID: PMC5654083 DOI: 10.1186/s13148-017-0416-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Accepted: 10/04/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alcohol consumption during pregnancy is a significant public health problem and can result in a continuum of adverse outcomes to the fetus known as fetal alcohol spectrum disorders (FASD). Subjects with FASD show significant neurological deficits, ranging from microencephaly, neurobehavioral, and mental health problems to poor social adjustment and stress tolerance. Neurons are particularly sensitive to alcohol exposure. The neurotoxic action of alcohol, i.e., through ROS production, induces DNA damage and neuronal cell death by apoptosis. In addition, epigenetics, including DNA methylation, histone posttranslational modifications (PTMs), and non-coding RNA, play an important role in the neuropathology of FASD. However, little is known about the temporal dynamics and kinetics of histones and their PTMs in FASD. RESULTS We examined the effects of postnatal alcohol exposure (PAE), an animal model of human third-trimester equivalent, on the kinetics of various histone proteins in two distinct brain regions, the frontal cortex, and the hypothalamus, using in vivo 2H2O-labeling combined with mass spectrometry-based proteomics. We show that histones have long half-lives that are in the order of days. We also show that H3.3 and H2Az histone variants have faster turnovers than canonical histones and that acetylated histones, in general, have a faster turnover than unmodified and methylated histones. Our work is the first to show that PAE induces a differential reduction in turnover rates of histones in both brain regions studied. These alterations in histone turnover were associated with increased DNA damage and decreased cell proliferation in postnatal rat brain. CONCLUSION Alterations in histone turnover might interfere with histone deposition and chromatin stability, resulting in deregulated cell-specific gene expression and therefore contribute to the development of the neurological disorders associated with FASD. Using in vivo 2H2O-labeling and mass spectrometry-based proteomics might help in the understanding of histone turnover following alcohol exposure and could be of great importance in enabling researchers to identify novel targets and/or biomarkers for the prevention and management of fetal alcohol spectrum disorders.
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Affiliation(s)
- Nadia Rachdaoui
- Department of Animal Sciences, Rutgers Endocrine Research Program, Rutgers, the State University of New Jersey, 67 Poultry Farm Lane, New Brunswick, NJ 08901 USA
| | - Ling Li
- Department of Research Core Services, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106 USA
| | - Belinda Willard
- Department of Research Core Services, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106 USA
| | - Takhar Kasumov
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272 USA
| | - Stephen Previs
- Cardiometabolic Disease, Merck & Co., Inc, Kenilworth, NJ USA
| | - Dipak Sarkar
- Department of Animal Sciences, Rutgers Endocrine Research Program, Rutgers, the State University of New Jersey, 67 Poultry Farm Lane, New Brunswick, NJ 08901 USA
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22
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Miyagi M, Kasumov T. Monitoring the synthesis of biomolecules using mass spectrometry. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0378. [PMID: 27644976 PMCID: PMC5031643 DOI: 10.1098/rsta.2015.0378] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/07/2016] [Indexed: 06/01/2023]
Abstract
The controlled and selective synthesis/clearance of biomolecules is critical for most cellular processes. In most high-throughput 'omics' studies, we measure the static quantities of only one class of biomolecules (e.g. DNA, mRNA, proteins or metabolites). It is, however, important to recognize that biological systems are highly dynamic in which biomolecules are continuously renewed and different classes of biomolecules interact and affect each other's production/clearance. Therefore, it is necessary to measure the turnover of diverse classes of biomolecules to understand the dynamic nature of biological systems. Herein, we explain why the kinetic analysis of a diverse range of biomolecules is important and how such an analysis can be done. We argue that heavy water ((2)H2O) could be a universal tracer for monitoring the synthesis of biomolecules on a global scale.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Masaru Miyagi
- Center for Proteomics and Bioinformatics, Department of Nutrition, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Takhar Kasumov
- Mass Spectrometry Laboratory, Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA
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23
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Quijada JV, Schmitt ND, Salisbury JP, Auclair JR, Agar JN. Heavy Sugar and Heavy Water Create Tunable Intact Protein Mass Increases for Quantitative Mass Spectrometry in Any Feed and Organism. Anal Chem 2016; 88:11139-11146. [PMID: 27744677 DOI: 10.1021/acs.analchem.6b03234] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Stable isotope labeling techniques for quantitative top-down proteomics face unique challenges. These include unpredictable mass shifts following isotope labeling, which impedes analysis of unknown proteins and complex mixtures and exponentially greater susceptibility to incomplete isotope incorporation, manifesting as broadening of labeled intact protein peaks. Like popular bottom-up isotope labeling techniques, most top-down labeling methods are restricted to defined media/feed as well as amino acid auxotrophic organisms. We present a labeling method optimized for top-down proteomics that overcomes these challenges. We demonstrated this method through the spiking of 13C-sugar or 2H-water into standard laboratory feedstocks, resulting in tunable intact protein mass increases (TIPMI). After mixing of labeled and unlabeled samples, direct comparison of light and heavy peaks allowed for the relative quantitation of intact proteins in three popular model organisms, including prokaryotic and eukaryotic microorganisms and an animal. This internal standard method proved to be more accurate than label-free quantitation in our hands. Advantages over top-down SILAC include working equally well in nutrient-rich media, conceivably expanding applicability to any organism and all classes of biomolecules, not requiring high-resolving power MS for quantitation and being relatively inexpensive.
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Affiliation(s)
- Jeniffer V Quijada
- Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States.,Barnett Institute of Chemical and Biological Analysis, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Nicholas D Schmitt
- Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States.,Barnett Institute of Chemical and Biological Analysis, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Joseph P Salisbury
- Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States.,Barnett Institute of Chemical and Biological Analysis, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Jared R Auclair
- Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States.,Barnett Institute of Chemical and Biological Analysis, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Jeffrey N Agar
- Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States.,Barnett Institute of Chemical and Biological Analysis, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States.,Department of Pharmaceutical Sciences, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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24
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Abstract
The static levels of proteins are the net results of their production and clearance regulated by the activities of proteins involved in their synthesis, degradation, and transportation. Therefore, the information on the rates of protein synthesis and clearance is needed to understand the underlying dynamic nature of a proteome. In this chapter, the experimental technique, we use in our laboratory for monitoring the synthesis of individual proteins in Caenorhabditis elegans (C. elegans) is described. The technique utilizes a preisotopically labeled amino acid (13C6-Lys) as a precursor for protein synthesis and monitors the kinetics of the precursor incorporation into the newly synthesized proteins. C. elegans is a powerful animal model in various fields of biomedical science such as aging, developmental biology, and neurobiology. The experimental technique would, therefore, be useful for research laboratories using C. elegans as an animal model.
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Affiliation(s)
- M Miyagi
- Center for Proteomics and Bioinformatics, Cleveland, OH, United States; Case Western Reserve University, Cleveland, OH, United States.
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25
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Srivastava A, Kowalski GM, Callahan DL, Meikle PJ, Creek DJ. Strategies for Extending Metabolomics Studies with Stable Isotope Labelling and Fluxomics. Metabolites 2016; 6:metabo6040032. [PMID: 27706078 PMCID: PMC5192438 DOI: 10.3390/metabo6040032] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 09/21/2016] [Accepted: 09/28/2016] [Indexed: 12/13/2022] Open
Abstract
This is a perspective from the peer session on stable isotope labelling and fluxomics at the Australian & New Zealand Metabolomics Conference (ANZMET) held from 30 March to 1 April 2016 at La Trobe University, Melbourne, Australia. This report summarizes the key points raised in the peer session which focused on the advantages of using stable isotopes in modern metabolomics and the challenges in conducting flux analyses. The session highlighted the utility of stable isotope labelling in generating reference standards for metabolite identification, absolute quantification, and in the measurement of the dynamic activity of metabolic pathways. The advantages and disadvantages of different approaches of fluxomics analyses including flux balance analysis, metabolic flux analysis and kinetic flux profiling were also discussed along with the use of stable isotope labelling in in vivo dynamic metabolomics. A number of crucial technical considerations for designing experiments and analyzing data with stable isotope labelling were discussed which included replication, instrumentation, methods of labelling, tracer dilution and data analysis. This report reflects the current viewpoint on the use of stable isotope labelling in metabolomics experiments, identifying it as a great tool with the potential to improve biological interpretation of metabolomics data in a number of ways.
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Affiliation(s)
- Anubhav Srivastava
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Melbourne, Victoria, Australia.
| | - Greg M Kowalski
- Institute for Physical Activity and Nutrition Research, School of Exercise and Nutrition Sciences, Deakin University, Burwood 3125, Victoria, Australia.
| | - Damien L Callahan
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University, Burwood 3125, Victoria, Australia.
| | - Peter J Meikle
- Baker IDI Heart and Diabetes Institute, Melbourne 3004, Victoria, Australia.
| | - Darren J Creek
- Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Melbourne, Victoria, Australia.
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26
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Prevosto C, Usmani MF, McDonald S, Gumienny AM, Key T, Goodman RS, Gaston JSH, Deery MJ, Busch R. Allele-Independent Turnover of Human Leukocyte Antigen (HLA) Class Ia Molecules. PLoS One 2016; 11:e0161011. [PMID: 27529174 PMCID: PMC4987023 DOI: 10.1371/journal.pone.0161011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 07/28/2016] [Indexed: 11/29/2022] Open
Abstract
Major histocompatibility complex class I (MHCI) glycoproteins present cytosolic peptides to CD8+ T cells and regulate NK cell activity. Their heavy chains (HC) are expressed from up to three MHC gene loci (human leukocyte antigen [HLA]-A, -B, and -C in humans), whose extensive polymorphism maps predominantly to the antigen-binding groove, diversifying the bound peptide repertoire. Codominant expression of MHCI alleles is thus functionally critical, but how it is regulated is not fully understood. Here, we have examined the effect of polymorphism on the turnover rates of MHCI molecules in cell lines with functional MHCI peptide loading pathways and in monocyte-derived dendritic cells (MoDCs). Proteins were labeled biosynthetically with heavy water (2H2O), folded MHCI molecules immunoprecipitated, and tryptic digests analysed by mass spectrometry. MHCI-derived peptides were assigned to specific alleles and isotypes, and turnover rates quantified by 2H incorporation, after correcting for cell growth. MHCI turnover half-lives ranged from undetectable to a few hours, depending on cell type, activation state, donor, and MHCI isotype. However, in all settings, the turnover half-lives of alleles of the same isotype were similar. Thus, MHCI protein turnover rates appear to be allele-independent in normal human cells. We propose that this is an important feature enabling the normal function and codominant expression of MHCI alleles.
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Affiliation(s)
- Claudia Prevosto
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - M. Farooq Usmani
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Sarah McDonald
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Tim Key
- Tissue Typing Laboratory, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Reyna S. Goodman
- Tissue Typing Laboratory, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - J. S. Hill Gaston
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Michael J. Deery
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, United Kingdom
| | - Robert Busch
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- Department of Life Sciences, University of Roehampton, London, United Kingdom
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27
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Li L, Bebek G, Previs SF, Smith JD, Sadygov RG, McCullough AJ, Willard B, Kasumov T. Proteome Dynamics Reveals Pro-Inflammatory Remodeling of Plasma Proteome in a Mouse Model of NAFLD. J Proteome Res 2016; 15:3388-404. [PMID: 27439437 DOI: 10.1021/acs.jproteome.6b00601] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is associated with an increased risk of cardiovascular disease. Because the liver is the major source of circulatory proteins, it is not surprising that hepatic disease could lead to alterations in the plasma proteome, which are therein implicated in atherosclerosis. The current study used low-density lipoprotein receptor-deficient (LDLR(-/-)) mice to examine the impact of Western diet (WD)-induced NAFLD on plasma proteome homeostasis. Using a (2)H2O-metabolic labeling method, we found that a WD led to a proinflammatory distribution of circulatory proteins analyzed in apoB-depleted plasma, which was attributed to an increased production. The fractional turnover rates of short-lived proteins that are implicated in stress-response, lipid metabolism, and transport functions were significantly increased with WD (P < 0.05). Pathway analyses revealed that alterations in plasma proteome dynamics were related to the suppression of hepatic PPARα, which was confirmed based on reduced gene and protein expression of PPARα in mice fed a WD. These changes were associated with ∼4-fold increase (P < 0.0001) in the proinflammatory property of apoB-depleted plasma. In conclusion, the proteome dynamics method reveals proinflammatory remodeling of the plasma proteome relevant to liver disease. The approach used herein may provide a useful metric of in vivo liver function and better enable studies of novel therapies surrounding NAFLD and other diseases.
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Affiliation(s)
| | - Gurkan Bebek
- Department of Nutrition, Center for Proteomics and Bioinformatics, Electrical Engineering and Computer Science Department, Case Western Reserve University , Cleveland, Ohio 44195, United States
| | - Stephen F Previs
- School of Medicine, Case Western Reserve University , Cleveland, Ohio 44106, United States
| | | | - Rovshan G Sadygov
- The University of Texas Medical Branch , Galveston, Texas 77555, United States
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28
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Abstract
We describe a stochastic model to compute in vivo protein turnover rate constants from stable-isotope labeling and high-throughput liquid chromatography-mass spectrometry experiments. We show that the often-used one- and two-compartment nonstochastic models allow explicit solutions from the corresponding stochastic differential equations. The resulting stochastic process is a Gaussian processes with Ornstein-Uhlenbeck covariance matrix. We applied the stochastic model to a large-scale data set from (15)N labeling and compared its performance metrics with those of the nonstochastic curve fitting. The comparison showed that for more than 99% of proteins, the stochastic model produced better fits to the experimental data (based on residual sum of squares). The model was used for extracting protein-decay rate constants from mouse brain (slow turnover) and liver (fast turnover) samples. We found that the most affected (compared to two-exponent curve fitting) results were those for liver proteins. The ratio of the median of degradation rate constants of liver proteins to those of brain proteins increased 4-fold in stochastic modeling compared to the two-exponent fitting. Stochastic modeling predicted stronger differences of protein turnover processes between mouse liver and brain than previously estimated. The model is independent of the labeling isotope. To show this, we also applied the model to protein turnover studied in induced heart failure in rats, in which metabolic labeling was achieved by administering heavy water. No changes in the model were necessary for adapting to heavy-water labeling. The approach has been implemented in a freely available R code.
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Affiliation(s)
| | - Stephen F Previs
- Merck Research Laboratories 2015 Galloping Hill Road Kenilworth, New Jersey 07033, United States
| | - Takhar Kasumov
- Department of Gastroenterology & Hepatology, Cleveland Clinic Cleveland, Ohio 44195, United States.,Department of Pharmaceutical Sciences School of Pharmacy, Northeast Ohio Medical University Rootstown, Ohio 44225, United States
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29
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Hammond DE, Claydon AJ, Simpson DM, Edward D, Stockley P, Hurst JL, Beynon RJ. Proteome Dynamics: Tissue Variation in the Kinetics of Proteostasis in Intact Animals. Mol Cell Proteomics 2016; 15:1204-19. [PMID: 26839000 PMCID: PMC4824850 DOI: 10.1074/mcp.m115.053488] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Indexed: 11/09/2022] Open
Abstract
Understanding the role of protein turnover in the maintenance of proteostasis requires accurate measurements of the rates of replacement of proteins in complex systems, such as intact animals. Moreover, any investigation of allometric scaling of protein turnover is likely to include species for which fully annotated proteomes are not available. We have used dietary administration of stable isotope labeled lysine to assess protein turnover rates for proteins from four tissues in the bank vole, Myodes glareolus. The annotated genome for this species is not available, so protein identification was attained through cross-species matching to the mouse. For proteins for which confident identifications were derived, the pattern of lysine incorporation over 40 days was used to define the rate of synthesis of individual proteins in the four tissues. The data were heavily filtered to retain a very high quality dataset of turnover rates for 1088 proteins. Comparative analysis of the four tissues revealed different median rates of degradation (kidney: 0.099 days−1; liver 0.136 days−1; heart, 0.054 days−1, and skeletal muscle, 0.035 days−1). These data were compared with protein degradation rates from other studies on intact animals or from cells in culture and indicate that both cell type and analytical methodology may contribute to variance in turnover data between different studies. These differences were not only due to tissue-specific proteins but were reflected in gene products common to all tissues. All data are available via ProteomeXchange with identifier PXD002054.
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Affiliation(s)
- Dean E Hammond
- From the ‡Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Crown Street, L697ZB, UK
| | - Amy J Claydon
- From the ‡Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Crown Street, L697ZB, UK
| | - Deborah M Simpson
- From the ‡Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Crown Street, L697ZB, UK
| | - Dominic Edward
- §Mammalian Behaviour and Evolution Group, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK
| | - Paula Stockley
- §Mammalian Behaviour and Evolution Group, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK
| | - Jane L Hurst
- §Mammalian Behaviour and Evolution Group, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston, CH64 7TE, UK
| | - Robert J Beynon
- From the ‡Centre for Proteome Research, Institute of Integrative Biology, University of Liverpool, Crown Street, L697ZB, UK;
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30
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Wang Z, Han QQ, Zhou MT, Chen X, Guo L. Protein turnover analysis in Salmonella Typhimurium during infection by dynamic SILAC, Topograph, and quantitative proteomics. J Basic Microbiol 2016; 56:801-11. [PMID: 26773230 DOI: 10.1002/jobm.201500315] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 12/18/2015] [Indexed: 12/17/2022]
Abstract
Protein turnover affects protein abundance and phenotypes. Comprehensive investigation of protein turnover dynamics has the potential to provide substantial information about gene expression. Here we report a large-scale protein turnover study in Salmonella Typhimurium during infection by quantitative proteomics. Murine macrophage-like RAW 264.7 cells were infected with SILAC labeled Salmonella. Bacterial cells were extracted after 0, 30, 60, 120, and 240 min. Mass spectrometry analyses yielded information about Salmonella protein turnover dynamics and a software program named Topograph was used for the calculation of protein half lives. The half lives of 311 proteins from intracellular Salmonella were obtained. For bacteria cultured in control medium (DMEM), the half lives for 870 proteins were obtained. The calculated median of protein half lives was 69.13 and 99.30 min for the infection group and the DMEM group, respectively, indicating an elevated protein turnover at the initial stage of infection. Gene ontology analyses revealed that a number of protein functional groups were significantly regulated by infection, including proteins involved in ribosome, periplasmic space, cellular amino acid metabolic process, ion binding, and catalytic activity. The half lives of proteins involved in purine metabolism pathway were found to be significantly shortened during infection.
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Affiliation(s)
- Zhe Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Qiang-Qiang Han
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Mao-Tian Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xi Chen
- Wuhan Institute of Biotechnology, Wuhan, China
| | - Lin Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China
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31
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Previs SF, Herath K, Castro-Perez J, Mahsut A, Zhou H, McLaren DG, Shah V, Rohm RJ, Stout SJ, Zhong W, Wang SP, Johns DG, Hubbard BK, Cleary MA, Roddy TP. Effect of Error Propagation in Stable Isotope Tracer Studies: An Approach for Estimating Impact on Apparent Biochemical Flux. Methods Enzymol 2015; 561:331-58. [PMID: 26358910 DOI: 10.1016/bs.mie.2015.06.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Stable isotope tracers are widely used to quantify metabolic rates, and yet a limited number of studies have considered the impact of analytical error on estimates of flux. For example, when estimating the contribution of de novo lipogenesis, one typically measures a minimum of four isotope ratios, i.e., the precursor and product labeling pre- and posttracer administration. This seemingly simple problem has 1 correct solution and 80 erroneous outcomes. In this report, we outline a methodology for evaluating the effect of error propagation on apparent physiological endpoints. We demonstrate examples of how to evaluate the influence of analytical error in case studies concerning lipid and protein synthesis; we have focused on (2)H2O as a tracer and contrast different mass spectrometry platforms including GC-quadrupole-MS, GC-pyrolysis-IRMS, LC-quadrupole-MS, and high-resolution FT-ICR-MS. The method outlined herein can be used to determine how to minimize variations in the apparent biology by altering the dose and/or the type of tracer. Likewise, one can facilitate biological studies by estimating the reduction in the noise of an outcome that is expected for a given increase in the number of replicate injections.
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Affiliation(s)
| | | | | | - Ablatt Mahsut
- Merck Research Laboratories, Kenilworth, New Jersey, USA
| | - Haihong Zhou
- Merck Research Laboratories, Kenilworth, New Jersey, USA
| | | | - Vinit Shah
- Merck Research Laboratories, Kenilworth, New Jersey, USA
| | - Rory J Rohm
- Merck Research Laboratories, Kenilworth, New Jersey, USA
| | - Steven J Stout
- Merck Research Laboratories, Kenilworth, New Jersey, USA
| | - Wendy Zhong
- Merck Research Laboratories, Kenilworth, New Jersey, USA
| | | | | | | | | | - Thomas P Roddy
- Merck Research Laboratories, Kenilworth, New Jersey, USA
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32
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Zhou H, Wang SP, Herath K, Kasumov T, Sadygov RG, Previs SF, Kelley DE. Tracer-based estimates of protein flux in cases of incomplete product renewal: evidence and implications of heterogeneity in collagen turnover. Am J Physiol Endocrinol Metab 2015; 309:E115-21. [PMID: 26015435 PMCID: PMC4596733 DOI: 10.1152/ajpendo.00435.2014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 05/04/2015] [Indexed: 11/22/2022]
Abstract
The synthesis of various molecules can be estimated by measuring the incorporation of a labeled precursor into a product of interest. Unfortunately, a central problem in many studies has been an inability to estimate the intracellular dilution of the precursor and therein correctly calculate the synthesis of the product; it is generally assumed that measuring the true product labeling is straightforward. We initiated a study to examine liver collagen synthesis and identified an apparent problem with assumptions regarding measurements of the product labeling. Since it is well known that collagen production is relatively slow, we relied on the use of [(2)H]H2O labeling (analogous to a primed infusion) and sampled animals over the course of 16 days. Although the water labeling (the precursor) remained stable and we observed the incorporation of labeled amino acids into collagen, the asymptotic protein labeling was considerably lower than what would be expected based on the precursor labeling. Although this observation is not necessarily surprising (i.e., one might expect that a substantial fraction of the collagen pool would appear "inert" or turn over at a very slow rate), its implications are of interest in certain areas. Herein, we discuss a novel situation in which tracers are used to quantify rates of flux under conditions where a product may not undergo complete replacement. We demonstrate how heterogeneity in the product pool can lead one to the wrong conclusions regarding estimates of flux, and we outline an approach that may help to minimize errors surrounding data interpretation.
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Affiliation(s)
- Haihong Zhou
- Cardiometabolic Disease, Merck Research Laboratories, Kenilworth, New Jersey
| | - Sheng-Ping Wang
- Cardiometabolic Disease, Merck Research Laboratories, Kenilworth, New Jersey
| | - Kithsiri Herath
- Cardiometabolic Disease, Merck Research Laboratories, Kenilworth, New Jersey
| | - Takhar Kasumov
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, Ohio; and
| | - Rovshan G Sadygov
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas
| | - Stephen F Previs
- Cardiometabolic Disease, Merck Research Laboratories, Kenilworth, New Jersey;
| | - David E Kelley
- Cardiometabolic Disease, Merck Research Laboratories, Kenilworth, New Jersey
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33
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Ma Y, Yabluchanskiy A, Lindsey ML. Heavy hitting: Using water to label humans. Proteomics Clin Appl 2015; 8:477-9. [PMID: 25044642 DOI: 10.1002/prca.201400066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 07/01/2014] [Indexed: 11/12/2022]
Abstract
Monitoring protein dynamics, compared to measuring static protein expression profiles taken with snapshot evaluations, have recently been the focus of proteomics studies examining tissue or blood samples where time course changes occur. Using deuterium oxide ((2) H2 O) to label amino acids is a useful method to monitor protein turnover rates. The synthesis rate for individual proteins is calculated from the rate of (2) H incorporation into specific proteins analyzed by high resolution MS. In this issue, Wang and colleagues measured the plasma protein turnover dynamics in healthy humans by in vivo (2) H2 O labeling [Wang, D. et al., Proteomics Clin. Appl. 2014, 8, 610-619]. The authors developed and validated a safe and accessible (2) H2 O administration protocol to record the turnover dynamics of 542 plasma proteins using MS. Their study demonstrates a promising new way to evaluate plasma protein dynamics in clinical trials where such knowledge could help for prognosis and evaluating treatment efficacy.
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Affiliation(s)
- Yonggang Ma
- San Antonio Cardiovascular Proteomics Center and Mississippi Center for Heart Research, Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
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34
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Wang D, Liem DA, Lau E, Ng DCM, Bleakley BJ, Cadeiras M, Deng MC, Lam MPY, Ping P. Characterization of human plasma proteome dynamics using deuterium oxide. Proteomics Clin Appl 2015; 8:610-9. [PMID: 24946186 DOI: 10.1002/prca.201400038] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 05/23/2014] [Accepted: 06/11/2014] [Indexed: 11/06/2022]
Abstract
PURPOSE High-throughput quantification of human protein turnover via in vivo administration of deuterium oxide ((2) H2 O) is a powerful new approach to examine potential disease mechanisms. Its immediate clinical translation is contingent upon characterizations of the safety and hemodynamic effects of in vivo administration of (2) H2 O to human subjects. EXPERIMENTAL DESIGN We recruited ten healthy human subjects with a broad demographic variety to evaluate the safety, feasibility, efficacy, and reproducibility of (2) H2 O intake for studying protein dynamics. We designed a protocol where each subject orally consumed weight-adjusted doses of 70% (2) H2 O daily for 14 days to enrich body water and proteins with deuterium. Plasma proteome dynamics was measured using a high-resolution MS method we recently developed. RESULTS This protocol was successfully applied in ten human subjects to characterize the endogenous turnover rates of 542 human plasma proteins, the largest such human dataset to-date. Throughout the study, we did not detect physiological effects or signs of discomfort from (2) H2 O consumption. CONCLUSIONS AND CLINICAL RELEVANCE Our investigation supports the utility of a (2) H2 O intake protocol that is safe, accessible, and effective for clinical investigations of large-scale human protein turnover dynamics. This workflow shows promising clinical translational value for examining plasma protein dynamics in human diseases.
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Affiliation(s)
- Ding Wang
- The NHLBI Proteomics Center at UCLA, Los Angeles, CA, USA; Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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35
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Lau E, Huang D, Cao Q, Dincer TU, Black CM, Lin AJ, Lee JM, Wang D, Liem DA, Lam MP, Ping P. Spatial and temporal dynamics of the cardiac mitochondrial proteome. Expert Rev Proteomics 2015; 12:133-46. [PMID: 25752359 PMCID: PMC4721584 DOI: 10.1586/14789450.2015.1024227] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mitochondrial proteins alter in their composition and quantity drastically through time and space in correspondence to changing energy demands and cellular signaling events. The integrity and permutations of this dynamism are increasingly recognized to impact the functions of the cardiac proteome in health and disease. This article provides an overview on recent advances in defining the spatial and temporal dynamics of mitochondrial proteins in the heart. Proteomics techniques to characterize dynamics on a proteome scale are reviewed and the physiological consequences of altered mitochondrial protein dynamics are discussed. Lastly, we offer our perspectives on the unmet challenges in translating mitochondrial dynamics markers into the clinic.
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Affiliation(s)
- Edward Lau
- Departments of Physiology, The NHLBI Proteomics Center at UCLA, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Derrick Huang
- Departments of Physiology, The NHLBI Proteomics Center at UCLA, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Quan Cao
- Departments of Physiology, The NHLBI Proteomics Center at UCLA, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - T. Umut Dincer
- Departments of Physiology, The NHLBI Proteomics Center at UCLA, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Caitie M. Black
- Departments of Physiology, The NHLBI Proteomics Center at UCLA, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Amanda J. Lin
- Departments of Physiology, The NHLBI Proteomics Center at UCLA, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Jessica M. Lee
- Departments of Physiology, The NHLBI Proteomics Center at UCLA, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Ding Wang
- Departments of Physiology, The NHLBI Proteomics Center at UCLA, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - David A. Liem
- Departments of Physiology, The NHLBI Proteomics Center at UCLA, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Maggie P.Y. Lam
- Departments of Physiology, The NHLBI Proteomics Center at UCLA, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Peipei Ping
- Departments of Physiology, The NHLBI Proteomics Center at UCLA, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
- Departments of Medicine, and Bioinformatics, NIH Center of Excellence in Big Data Computing at UCLA, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
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36
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Chan XCY, Black CM, Lin AJ, Ping P, Lau E. Mitochondrial protein turnover: methods to measure turnover rates on a large scale. J Mol Cell Cardiol 2014; 78:54-61. [PMID: 25451168 DOI: 10.1016/j.yjmcc.2014.10.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/20/2014] [Accepted: 10/21/2014] [Indexed: 12/27/2022]
Abstract
Mitochondrial proteins carry out diverse cellular functions including ATP synthesis, ion homeostasis, cell death signaling, and fatty acid metabolism and biogenesis. Compromised mitochondrial quality control is implicated in various human disorders including cardiac diseases. Recently it has emerged that mitochondrial protein turnover can serve as an informative cellular parameter to characterize mitochondrial quality and uncover disease mechanisms. The turnover rate of a mitochondrial protein reflects its homeostasis and dynamics under the quality control systems acting on mitochondria at a particular cell state. This review article summarizes some recent advances and outstanding challenges for measuring the turnover rates of mitochondrial proteins in health and disease. This article is part of a Special Issue entitled "Mitochondria: From Basic Mitochondrial Biology to Cardiovascular Disease".
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Affiliation(s)
- X'avia C Y Chan
- The NHLBI Proteomics Center at UCLA, Los Angeles, CA 90095, USA; Department of Physiology, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Caitlin M Black
- The NHLBI Proteomics Center at UCLA, Los Angeles, CA 90095, USA; Department of Physiology, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Amanda J Lin
- The NHLBI Proteomics Center at UCLA, Los Angeles, CA 90095, USA; Department of Physiology, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | - Peipei Ping
- The NHLBI Proteomics Center at UCLA, Los Angeles, CA 90095, USA; Department of Physiology, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA; Department of Medicine, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA; Department of Bioinformatics, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA.
| | - Edward Lau
- The NHLBI Proteomics Center at UCLA, Los Angeles, CA 90095, USA; Department of Physiology, UCLA David Geffen School of Medicine, Los Angeles, CA 90095, USA.
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37
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Shekar KC, Li L, Dabkowski ER, Xu W, Ribeiro RF, Hecker PA, Recchia FA, Sadygov RG, Willard B, Kasumov T, Stanley WC. Cardiac mitochondrial proteome dynamics with heavy water reveals stable rate of mitochondrial protein synthesis in heart failure despite decline in mitochondrial oxidative capacity. J Mol Cell Cardiol 2014; 75:88-97. [PMID: 24995939 DOI: 10.1016/j.yjmcc.2014.06.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 06/07/2014] [Accepted: 06/16/2014] [Indexed: 11/19/2022]
Abstract
We recently developed a method to measure mitochondrial proteome dynamics with heavy water ((2)H2O)-based metabolic labeling and high resolution mass spectrometry. We reported the half-lives and synthesis rates of several proteins in the two cardiac mitochondrial subpopulations, subsarcolemmal and interfibrillar (SSM and IFM), in Sprague Dawley rats. In the present study, we tested the hypothesis that the mitochondrial protein synthesis rate is reduced in heart failure, with possible differential changes in SSM versus IFM. Six to seven week old male Sprague Dawley rats underwent transverse aortic constriction (TAC) and developed moderate heart failure after 22weeks. Heart failure and sham rats of the same age received heavy water (5% in drinking water) for up to 80days. Cardiac SSM and IFM were isolated from both groups and the proteins were separated by 1D gel electrophoresis. Heart failure reduced protein content and increased the turnover rate of several proteins involved in fatty acid oxidation, electron transport chain and ATP synthesis, while it decreased the turnover of other proteins, including pyruvate dehydrogenase subunit in IFM, but not in SSM. Because of these bidirectional changes, the average overall half-life of proteins was not altered by heart failure in both SSM and IFM. The kinetic measurements of individual mitochondrial proteins presented in this study may contribute to a better understanding of the mechanisms responsible for mitochondrial alterations in the failing heart.
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Affiliation(s)
| | - Ling Li
- Proteomics Core, Department of Research Core Services, Cleveland Clinic, Cleveland, OH, USA
| | - Erinne R Dabkowski
- Division of Cardiology and Department of Medicine, University of Maryland, Baltimore, MD, USA
| | - Wenhong Xu
- Division of Cardiology and Department of Medicine, University of Maryland, Baltimore, MD, USA
| | | | - Peter A Hecker
- Division of Cardiology and Department of Medicine, University of Maryland, Baltimore, MD, USA
| | - Fabio A Recchia
- Department of Physiology, Temple University School of Medicine, Philadelphia, PA, USA; Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Rovshan G Sadygov
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Belinda Willard
- Proteomics Core, Department of Research Core Services, Cleveland Clinic, Cleveland, OH, USA
| | - Takhar Kasumov
- Department of Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH, USA.
| | - William C Stanley
- Division of Cardiology and Department of Medicine, University of Maryland, Baltimore, MD, USA; Discipline of Physiology, University of Sydney, Anderson Stuart Building (F13) Sydney, NSW 2006 Australia
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Quantitation of human peptides and proteins via MS: review of analytically validated assays. Bioanalysis 2014; 6:1843-57. [DOI: 10.4155/bio.14.145] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Since the development of monoclonal antibodies in the 1970s, antibody-based assays have been used for the quantitation of proteins and peptides and, today, they are the most widely used technology in routine laboratory medicine and bioanalysis. However, in the last couple of decades, liquid chromatography-mass spectrometry/mass spectrometry (LC–MS/MS) techniques have been adopted in the quantitation of small molecules, and more recently have made significant contributions in the quantitation of proteins and peptides. In this article, we will review clinical MS-based assays for endogenous peptides, proteins, and therapeutic antibodies, for which validated methods exist. We will also cover the measurement of protein turnover and the unique solutions that MS can offer in this field.
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Lam MPY, Wang D, Lau E, Liem DA, Kim AK, Ng DCM, Liang X, Bleakley BJ, Liu C, Tabaraki JD, Cadeiras M, Wang Y, Deng MC, Ping P. Protein kinetic signatures of the remodeling heart following isoproterenol stimulation. J Clin Invest 2014; 124:1734-44. [PMID: 24614109 DOI: 10.1172/jci73787] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 01/09/2014] [Indexed: 02/02/2023] Open
Abstract
Protein temporal dynamics play a critical role in time-dimensional pathophysiological processes, including the gradual cardiac remodeling that occurs in early-stage heart failure. Methods for quantitative assessments of protein kinetics are lacking, and despite knowledge gained from single-protein studies, integrative views of the coordinated behavior of multiple proteins in cardiac remodeling are scarce. Here, we developed a workflow that integrates deuterium oxide (2H2O) labeling, high-resolution mass spectrometry (MS), and custom computational methods to systematically interrogate in vivo protein turnover. Using this workflow, we characterized the in vivo turnover kinetics of 2,964 proteins in a mouse model of β-adrenergic-induced cardiac remodeling. The data provided a quantitative and longitudinal view of cardiac remodeling at the molecular level, revealing widespread kinetic regulations in calcium signaling, metabolism, proteostasis, and mitochondrial dynamics. We translated the workflow to human studies, creating a reference dataset of 496 plasma protein turnover rates from 4 healthy adults. The approach is applicable to short, minimal label enrichment and can be performed on as little as a single biopsy, thereby overcoming critical obstacles to clinical investigations. The protein turnover quantitation experiments and computational workflow described here should be widely applicable to large-scale biomolecular investigations of human disease mechanisms with a temporal perspective.
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Herath KB, Zhong W, Yang J, Mahsut A, Rohm RJ, Shah V, Castro-Perez J, Zhou H, Attygalle AB, Kang L, Singh S, Johns DG, Cleary MA, Hubbard BK, Previs SF, Roddy TP. Determination of low levels of 2H-labeling using high-resolution mass spectrometry: application in studies of lipid flux and beyond. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:239-244. [PMID: 24375874 DOI: 10.1002/rcm.6776] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 10/23/2013] [Accepted: 10/27/2013] [Indexed: 06/03/2023]
Abstract
RATIONALE The ability to measure low levels of (2)H-labeling is important in studies of metabolic flux, e.g. one can estimate lipid synthesis by administering (2)H2O and then measuring the incorporation of (2)H into fatty acids. Unfortunately, the analyses are complicated by the presence of more abundant naturally occurring stable isotopes, e.g. (13)C. Conventional approaches rely on coupling gas chromatographic separation of lipids with either quadrupole-mass spectrometry (q-MS) and/or pyrolysis-isotope ratio mass spectrometry (IRMS). The former is limited by high background labeling (primarily from (13)C) whereas the latter is not suitable for routine high-throughput analyses. METHODS We have contrasted the use of continuous flow-pyrolysis-IRMS against high-resolution mass spectrometry (i.e. Qq-FT-ICR MS) for measuring the (2)H-enrichment of fatty acids and peptides. RESULTS In contrast to IRMS, which requires ~30 min per analysis, it is possible to measure the (2)H-enrichment of palmitate via direct infusion high-resolution mass spectrometry (HRMS) in ~3 min per sample. In addition, Qq-FT-ICR MS enabled measurements of the (2)H-enrichment of peptides (which is not possible using IRMS). CONCLUSIONS High-resolution mass spectrometry can be used to measure low levels of (2)H-labeling so we expect that this approach will enhance studies of metabolic flux that rely on (2)H-labeled tracers, e.g. (2)H2O. However, since the high-resolution analyses require greater amounts of a given analyte one potential limitation centers on the overall sensitivity. Presumably, future advances can overcome this barrier.
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De Riva A, Busch R. MHC Class II Protein Turnover In vivo and Its Relevance for Autoimmunity in Non-Obese Diabetic Mice. Front Immunol 2013; 4:399. [PMID: 24324466 PMCID: PMC3839011 DOI: 10.3389/fimmu.2013.00399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/08/2013] [Indexed: 11/19/2022] Open
Abstract
Major histocompatibility complex class II (MHCII) proteins are loaded with endosomal peptides and reside at the surface of antigen-presenting cells (APCs) for a time before being degraded. In vitro, MHCII protein levels and turnover are affected by peptide loading and by rates of ubiquitin-dependent internalization from the cell surface, which is in turn affected by APC type and activation state. Prior work suggested that fast turnover of disease-associated MHCII alleles may contribute to autoimmunity. We recently developed novel stable isotope tracer techniques to test this hypothesis in vivo. In non-obese diabetic (NOD) mice, a model of type 1 diabetes (T1D), MHCII turnover was affected by APC type, but unaffected by disease-associated structural polymorphism. Differences in MHCII turnover were observed between NOD colonies with high and low T1D incidence, but fast turnover was dispensable for autoimmunity. Moreover, NOD mice with gene knockouts of peptide loading cofactors do not develop T1D. Thus, fast turnover does not appear pathogenic, and conventional antigen presentation is critical for autoimmunity in NOD mice. However, shared environmental factors may underpin colony differences in MHCII protein turnover, immune regulation, and pathogenesis.
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Affiliation(s)
| | - Robert Busch
- Department of Medicine, University of Cambridge, Cambridge, UK
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Nemutlu E, Zhang S, Juranic NO, Terzic A, Macura S, Dzeja P. 18O-assisted dynamic metabolomics for individualized diagnostics and treatment of human diseases. Croat Med J 2013; 53:529-34. [PMID: 23275318 PMCID: PMC3541579 DOI: 10.3325/cmj.2012.53.529] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Technological innovations and translation of basic discoveries to clinical practice drive advances in medicine. Today's innovative technologies enable comprehensive screening of the genome, transcriptome, proteome, and metabolome. The detailed knowledge, converged in the integrated "omics" (genomics, transcriptomics, proteomics, and metabolomics), holds an immense potential for understanding mechanism of diseases, facilitating their early diagnostics, selecting personalized therapeutic strategies, and assessing their effectiveness. Metabolomics is the newest "omics" approach aimed to analyze large metabolite pools. The next generation of metabolomic screening requires technologies for high throughput and robust monitoring of metabolite levels and their fluxes. In this regard, stable isotope 18O-based metabolite tagging technology expands quantitative measurements of metabolite levels and turnover rates to all metabolites that include water as a reactant, most notably phosphometabolites. The obtained profiles and turnover rates are sensitive indicators of energy and metabolic imbalances like the ones created by genetic deficiencies, myocardial ischemia, heart failure, neurodegenerative disorders, etc. Here we describe and discuss briefly the potential use of dynamic phosphometabolomic platform for disease diagnostics currently under development at Mayo Clinic.
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Affiliation(s)
- Emirhan Nemutlu
- Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic, 200 1st Street SW, Rochester, Minnesota 55905, USA.
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De Riva A, Varley MC, Bluck LJ, Cooke A, Deery MJ, Busch R. Accelerated turnover of MHC class II molecules in nonobese diabetic mice is developmentally and environmentally regulated in vivo and dispensable for autoimmunity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2013; 190:5961-71. [PMID: 23677470 PMCID: PMC3785126 DOI: 10.4049/jimmunol.1300551] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The H2-A(g7) (A(g7)) MHC class II (MHCII) allele is required for type 1 diabetes (T1D) in NOD mice. A(g7) not only has a unique peptide-binding profile, it was reported to exhibit biochemical defects, including accelerated protein turnover. Such defects were proposed to impair Ag presentation and, thus, self-tolerance. Here, we report measurements of MHCII protein synthesis and turnover in vivo. NOD mice and BALB/c controls were labeled continuously with heavy water, and splenic B cells and dendritic cells were isolated. MHCII molecules were immunoprecipitated and digested with trypsin. Digests were analyzed by liquid chromatography/mass spectrometry to quantify the fraction of newly synthesized MHCII molecules and, thus, turnover. MHCII turnover was faster in dendritic cells than in B cells, varying slightly between mouse strains. Some A(g7) molecules exhibited accelerated turnover in B cells from young, but not older, prediabetic female NOD mice. This acceleration was not detected in a second NOD colony with a high incidence of T1D. Turnover rates of A(g7) and H2-A(d) were indistinguishable in (NOD × BALB/c) F1 mice. In conclusion, accelerated MHCII turnover may occur in NOD mice, but it reflects environmental and developmental regulation, rather than a structural deficit of the A(g7) allele. Moreover, this phenotype wanes before the onset of overt T1D and is dispensable for the development of autoimmune diabetes. Our observations highlight the importance of in vivo studies in understanding the role of protein turnover in genotype/phenotype relationships and offer a novel approach for addressing this fundamental research challenge.
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Affiliation(s)
| | - Mark C. Varley
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Engineering, University of Cambridge, Cambridge, UK
| | - Leslie J. Bluck
- Elsie Widdowson Laboratories, Medical Research Council Human Nutrition Research, Fulbourn, Cambridge, UK
| | - Anne Cooke
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Michael J. Deery
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
| | - Robert Busch
- Department of Medicine, University of Cambridge, Cambridge, UK
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44
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Kasumov T, Willard B, Li L, Li M, Conger H, Buffa JA, Previs S, McCullough A, Hazen SL, Smith JD. 2H2O-based high-density lipoprotein turnover method for the assessment of dynamic high-density lipoprotein function in mice. Arterioscler Thromb Vasc Biol 2013; 33:1994-2003. [PMID: 23766259 DOI: 10.1161/atvbaha.113.301700] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE High-density lipoprotein (HDL) promotes reverse cholesterol transport from peripheral tissues to the liver for clearance. Reduced HDL-cholesterol (HDLc) is associated with atherosclerosis; however, as a predictor of cardiovascular disease, HDLc has limitations because it is not a direct marker of HDL functionality. Our objective was to develop a mass spectrometry-based method for the simultaneous measurement of HDLc and ApoAI kinetics in mice, using a single (2)H2O tracer, and use it to examine genetic and drug perturbations on HDL turnover in vivo. APPROACH AND RESULTS Mice were given (2)H2O in the drinking water, and serial blood samples were collected at different time points. HDLc and ApoAI gradually incorporated (2)H, allowing experimental measurement of fractional catabolic rates and production rates for HDLc and ApoAI. ApoE(-/-) mice displayed increased fractional catabolic rates (P<0.01) and reduced production rates of both HDLc and ApoAI (P<0.05) compared with controls. In human ApoAI transgenic mice, levels and production rates of HDLc and human ApoAI were strikingly higher than in wild-type mice. Myriocin, an inhibitor of sphingolipid synthesis, significantly increased both HDL flux and macrophage-to-feces reverse cholesterol transport, indicating compatibility of this HDL turnover method with the macrophage-specific reverse cholesterol transport assay. CONCLUSIONS (2)H2O-labeling can be used to measure HDLc and ApoAI flux in vivo, and to assess the role of genetic and pharmacological interventions on HDL turnover in mice. Safety, simplicity, and low cost of the (2)H2O-based HDL turnover approach suggest that this assay can be scaled for human use to study effects of HDL targeted therapies on dynamic HDL function.
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Affiliation(s)
- Takhar Kasumov
- Department of Gastroenterology and Hepatology, Case Western Reserve University School of Medicine, Cleveland Clinic, Cleveland, OH 44195, USA
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45
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Holm L, O'Rourke B, Ebenstein D, Toth MJ, Bechshoeft R, Holstein-Rathlou NH, Kjaer M, Matthews DE. Determination of steady-state protein breakdown rate in vivo by the disappearance of protein-bound tracer-labeled amino acids: a method applicable in humans. Am J Physiol Endocrinol Metab 2013; 304:E895-907. [PMID: 23423170 PMCID: PMC3625778 DOI: 10.1152/ajpendo.00579.2012] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A method to determine the rate of protein breakdown in individual proteins was developed and tested in rats and confirmed in humans, using administration of deuterium oxide and incorporation of the deuterium into alanine that was subsequently incorporated into body proteins. Measurement of the fractional breakdown rate of proteins was determined from the rate of disappearance of deuterated alanine from the proteins. The rate of disappearance of deuterated alanine from the proteins was calculated using an exponential decay, giving the fractional breakdown rate (FBR) of the proteins. The applicability of this protein-specific FBR approach is suitable for human in vivo experimentation. The labeling period of deuterium oxide administration is dependent on the turnover rate of the protein of interest.
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Affiliation(s)
- Lars Holm
- Institute of Sports Medicine, Department of Orthopedic Surgery M81, Bispebjerg Hospital, and Center for Healthy Aging, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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46
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Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR. Protein analysis by shotgun/bottom-up proteomics. Chem Rev 2013; 113:2343-94. [PMID: 23438204 PMCID: PMC3751594 DOI: 10.1021/cr3003533] [Citation(s) in RCA: 970] [Impact Index Per Article: 88.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yaoyang Zhang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan R. Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bing Shan
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Moon-Chang Baek
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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47
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Kasumov T, Dabkowski ER, Shekar KC, Li L, Ribeiro RF, Walsh K, Previs SF, Sadygov RG, Willard B, Stanley WC. Assessment of cardiac proteome dynamics with heavy water: slower protein synthesis rates in interfibrillar than subsarcolemmal mitochondria. Am J Physiol Heart Circ Physiol 2013; 304:H1201-14. [PMID: 23457012 DOI: 10.1152/ajpheart.00933.2012] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Traditional proteomics provides static assessment of protein content, but not synthetic rates. Recently, proteome dynamics with heavy water ((2)H2O) was introduced, where (2)H labels amino acids that are incorporated into proteins, and the synthesis rate of individual proteins is calculated using mass isotopomer distribution analysis. We refine this approach with a novel algorithm and rigorous selection criteria that improve the accuracy and precision of the calculation of synthesis rates and use it to measure protein kinetics in spatially distinct cardiac mitochondrial subpopulations. Subsarcolemmal mitochondria (SSM) and interfibrillar mitochondria (IFM) were isolated from adult rats, which were given (2)H2O in the drinking water for up to 60 days. Plasma (2)H2O and myocardial (2)H-enrichment of amino acids were stable throughout the experimental protocol. Multiple tryptic peptides were identified from 28 proteins in both SSM and IFM and showed a time-dependent increase in heavy mass isotopomers that was consistent within a given protein. Mitochondrial protein synthesis was relatively slow (average half-life of 30 days, 2.4% per day). Although the synthesis rates for individual proteins were correlated between IFM and SSM (R(2) = 0.84; P < 0.0001), values in IFM were 15% less than SSM (P < 0.001). In conclusion, administration of (2)H2O results in stable enrichment of the cardiac precursor amino acid pool, with the use of refined analytical and computational methods coupled with cell fractionation one can measure synthesis rates for cardiac proteins in subcellular compartments in vivo, and protein synthesis is slower in mitochondria located among the myofibrils than in the subsarcolemmal region.
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Affiliation(s)
- Takhar Kasumov
- Department of Gastroenterology and Hepatology, Cleveland Clinic, Cleveland, Ohio 44195, USA.
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48
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Ilchenko S, Previs S, Rachdaoui N, Willard B, McCullough A, Kasumov T. An improved measurement of isotopic ratios by high resolution mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:309-12. [PMID: 23283729 PMCID: PMC3893058 DOI: 10.1007/s13361-012-0536-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 10/17/2012] [Accepted: 11/04/2012] [Indexed: 05/25/2023]
Abstract
The study of protein kinetics requires an accurate measurement of isotopic ratios of peptides. Although Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometers yield accurate mass measurements of analytes, the isotopologue ratios are consistently lower than predicted. Recently, we demonstrated that the magnitude of the spectral error in the FT-ICR mass spectrometer is proportional to the scan duration of ions. Here, we present a novel isotopic ratio extrapolation (IRE) method for obtaining accurate isotopic ratio measurements. Accuracy is achieved by performing scans with different duration and extrapolation of the data to the initial moment of the ion rotation; IRE minimizes the absolute isotopic ratio error to ≤1%. We demonstrate the application of IRE in protein turnover studies using (2)H(2)O-metabolic labeling. Overall, this technique allows accurate measurements of the isotopic ratios of proteolytic peptides, a critical step for enabling routine studies of proteome dynamics.
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Affiliation(s)
- S. Ilchenko
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
| | - S.F. Previs
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
| | - N. Rachdaoui
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
| | - B. Willard
- Department of Research Core Services, Cleveland Clinic, Cleveland, OH 44195
| | - A. McCullough
- Department of Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH 44195
| | - T. Kasumov
- Department of Gastroenterology & Hepatology, Cleveland Clinic, Cleveland, OH 44195
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49
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Claydon AJ, Beynon R. Proteome dynamics: revisiting turnover with a global perspective. Mol Cell Proteomics 2012; 11:1551-65. [PMID: 23125033 DOI: 10.1074/mcp.o112.022186] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Although bulk protein turnover has been measured with the use of stable isotope labeled tracers for over half a century, it is only recently that the same approach has become applicable to the level of the proteome, permitting analysis of the turnover of many proteins instead of single proteins or an aggregated protein pool. The optimal experimental design for turnover studies is dependent on the nature of the biological system under study, which dictates the choice of precursor label, protein pool sampling strategy, and treatment of data. In this review we discuss different approaches and, in particular, explore how complexity in experimental design and data processing increases as we shift from unicellular to multicellular systems, in particular animals.
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Affiliation(s)
- Amy J Claydon
- Protein Function Group, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
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50
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Claydon AJ, Thom MD, Hurst JL, Beynon RJ. Protein turnover: measurement of proteome dynamics by whole animal metabolic labelling with stable isotope labelled amino acids. Proteomics 2012; 12:1194-206. [PMID: 22577021 DOI: 10.1002/pmic.201100556] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The measurement of protein turnover in tissues of intact animals is obtained by whole animal dynamic labelling studies, requiring dietary administration of precursor label. It is difficult to obtain full labelling of precursor amino acids in the diet and if partial labelling is used, calculation of the rate of turnover of each protein requires knowledge of the precursor relative isotope abundance (RIA). We describe an approach to dynamic labelling of proteins in the mouse with a commercial diet supplemented with a pure, deuterated essential amino acid. The pattern of isotopomer labelling can be used to recover the precursor RIA, and sampling of urinary secreted proteins can monitor the development of liver precursor RIA non-invasively. Time-series analysis of the labelling trajectories for individual proteins allows accurate determination of the first order rate constant for degradation. The acquisition of this parameter over multiple proteins permits turnover profiling of cellular proteins and comparisons of different tissues. The median rate of degradation of muscle protein is considerably lower than liver or kidney, with heart occupying an intermediate position.
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Affiliation(s)
- Amy J Claydon
- Protein Function Group, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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