1
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Das A, Chakrabarty S, Nag D, Paul S, Ganguli A, Chakrabarti G. Heavy water (D 2O) induces autophagy-dependent apoptotic cell death in non-small cell lung cancer A549 cells by generating reactive oxygen species (ROS) upon microtubule disruption. Toxicol In Vitro 2023; 93:105703. [PMID: 37751786 DOI: 10.1016/j.tiv.2023.105703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/13/2023] [Accepted: 09/22/2023] [Indexed: 09/28/2023]
Abstract
OBJECTIVE Deuterium oxide (D2O) or heavy water is known to have diverse biological activities and have a few therapeutic applications due to its limited toxicity to human subjects. In the present study, we investigated the mechanism of D2O-induced cytotoxicity in non-small cell lung cancer A549 cells. RESULTS We found that D2O-treatment resulted in cytotoxicity, cell cycle arrest, and apoptosis in A549 cells in a dose-dependent fashion. In contrast, limited cytotoxicity was observed in lung fibroblasts WI38 cells. Moreover, D2O-treatment resulted in the disruption of the cellular microtubule network, accompanied by the generation of ROS. On further investigation, we observed that the intracellular ROS triggered autophagic responses in D2O-treated cells, leading to apoptosis by inhibiting the oncogenic PI3K/ Akt/ mTOR signaling. D2O-treatment was also found to enhance the efficacy of paclitaxel in A549 cells. SIGNIFICANCE D2O induces autophagy-dependent apoptosis in A549 cells via ROS generation upon microtubule depolymerization and inhibition of PI3K/ Akt/ mTOR signaling. It augments the efficacy of other microtubule-targeting anticancer drug taxol, which indicates the potential therapeutic importance of D2O as an anticancer agent either alone or in combination with other chemotherapeutic drugs.
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Affiliation(s)
- Amlan Das
- Department of Biotechnology and Dr. B.C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, West Bengal 700019, India; Department of Biochemistry, Royal School of Biosciences, The Assam Royal Global University, Assam 781035, India.
| | - Subhendu Chakrabarty
- Department of Biotechnology and Dr. B.C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, West Bengal 700019, India; Department of Microbiology, M.U.C. Women's College, Burdwan, West Bengal 713104, India
| | - Debasish Nag
- Department of Biotechnology and Dr. B.C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, West Bengal 700019, India
| | - Santanu Paul
- Department of Biotechnology and Dr. B.C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, West Bengal 700019, India; Department of Biotechnology, School of Life Sciences, Swami Vivekananda University, Barrackpore, West Bengal 700121, India
| | - Arnab Ganguli
- Department of Microbiology, Techno India University, West Bengal 700091, India
| | - Gopal Chakrabarti
- Department of Biotechnology and Dr. B.C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, West Bengal 700019, India.
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2
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Monteiro C, Mesgarzadeh JS, Anselmo J, Fernandes J, Novais M, Rodrigues C, Powers DL, Powers ET, Coelho T, Kelly JW. Tafamidis polyneuropathy amelioration requires modest increases in transthyretin stability even though increases in plasma native TTR and decreases in non-native TTR do not predict response. Amyloid 2023; 30:81-95. [PMID: 36178172 PMCID: PMC9992127 DOI: 10.1080/13506129.2022.2126308] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 08/23/2022] [Accepted: 09/13/2022] [Indexed: 11/01/2022]
Abstract
BACKGROUND TTR aggregation causes hereditary transthyretin (TTR) polyneuropathy (ATTRv-PN) in individuals with destabilised TTR variants. ATTRv-PN can be treated with ligands that bind TTR and prevent aggregation. One such ligand, tafamidis, is widely approved to treat ATTRv-PN. We explore how TTR stabilisation markers relate to clinical efficacy in 210 ATTRv-PN patients taking tafamidis. METHODS TTR concentration in patient plasma was measured before and after tafamidis treatment using assays for native or combined native + non-native TTR. TTR tetramer dissociation kinetics, which are slowed by tafamidis binding, were also measured. RESULTS Native TTR levels increased by 56.8% while combined native + non-native TTR levels increased by 3.1% after 24 months of tafamidis treatment, implying that non-native TTR decreased. Accordingly, the fraction of native TTR increased from 0.54 to 0.71 with tafamidis administration. Changes in native and non-native TTR levels were uncorrelated with clinical response to tafamidis. TTR tetramer dissociation generally slowed to an extent consistent with ∼40% of TTR being tafamidis-bound. Male non-responders had a lower extent of binding. CONCLUSIONS Native and non-native TTR concentration changes cannot be used as surrogate measures for therapeutic efficacy. Also, successful tafamidis therapy requires only moderate TTR stabilisation. Male patients may benefit from higher tafamidis doses.
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Affiliation(s)
- Cecília Monteiro
- Department of Chemistry, The Scripps Research Institute,
10550 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Jaleh S. Mesgarzadeh
- Department of Chemistry, The Scripps Research Institute,
10550 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - João Anselmo
- Unidade Corino de Andrade, Centro Hospitalar do Porto,
Largo do Prof. Abel Salazar, 4099-001 Porto, Portugal
| | - Joana Fernandes
- Unidade Corino de Andrade, Centro Hospitalar do Porto,
Largo do Prof. Abel Salazar, 4099-001 Porto, Portugal
| | - Marta Novais
- Unidade Corino de Andrade, Centro Hospitalar do Porto,
Largo do Prof. Abel Salazar, 4099-001 Porto, Portugal
| | - Carla Rodrigues
- Unidade Corino de Andrade, Centro Hospitalar do Porto,
Largo do Prof. Abel Salazar, 4099-001 Porto, Portugal
| | - David L. Powers
- Department of Mathematics, Clarkson University, Potsdam, NY
13676, USA
| | - Evan T. Powers
- Department of Chemistry, The Scripps Research Institute,
10550 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Teresa Coelho
- Unidade Corino de Andrade, Centro Hospitalar do Porto,
Largo do Prof. Abel Salazar, 4099-001 Porto, Portugal
- Department of Neurophysiology, Centro Hospitalar do Porto,
Largo do Prof. Abel Salazar, 4099-001 Porto, Portugal
| | - Jeffery W. Kelly
- Department of Chemistry, The Scripps Research Institute,
10550 N Torrey Pines Rd, La Jolla, CA 92037, USA
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3
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Naylor B, Anderson CNK, Hadfield M, Parkinson DH, Ahlstrom A, Hannemann A, Quilling CR, Cutler KJ, Denton RL, Adamson R, Angel TE, Burlett RS, Hafen PS, Dallon JC, Transtrum MK, Hyldahl RD, Price JC. Utilizing Nonequilibrium Isotope Enrichments to Dramatically Increase Turnover Measurement Ranges in Single Biopsy Samples from Humans. J Proteome Res 2022; 21:2703-2714. [PMID: 36099490 PMCID: PMC9639613 DOI: 10.1021/acs.jproteome.2c00380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Indexed: 11/30/2022]
Abstract
The synthesis of new proteins and the degradation of old proteins in vivo can be quantified in serial samples using metabolic isotope labeling to measure turnover. Because serial biopsies in humans are impractical, we set out to develop a method to calculate the turnover rates of proteins from single human biopsies. This method involved a new metabolic labeling approach and adjustments to the calculations used in previous work to calculate protein turnover. We demonstrate that using a nonequilibrium isotope enrichment strategy avoids the time dependent bias caused by variable lag in label delivery to different tissues observed in traditional metabolic labeling methods. Turnover rates are consistent for the same subject in biopsies from different labeling periods, and turnover rates calculated in this study are consistent with previously reported values. We also demonstrate that by measuring protein turnover we can determine where proteins are synthesized. In human subjects a significant difference in turnover rates differentiated proteins synthesized in the salivary glands versus those imported from the serum. We also provide a data analysis tool, DeuteRater-H, to calculate protein turnover using this nonequilibrium metabolic 2H2O method.
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Affiliation(s)
- Bradley
C. Naylor
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| | | | - Marcus Hadfield
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| | - David H. Parkinson
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| | - Austin Ahlstrom
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| | - Austin Hannemann
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| | - Chad R. Quilling
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| | - Kyle J. Cutler
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| | - Russell L. Denton
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| | - Robert Adamson
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| | - Thomas E. Angel
- In-vitro/In-vivo
Translation Platform Group, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Rebecca S. Burlett
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
| | - Paul S. Hafen
- Department
of Exercise Sciences, Brigham Young University, Provo, Utah 84602, United States
| | - John. C. Dallon
- Department
of Mathematics, Brigham Young University, Provo, Utah 84602, United States
| | - Mark K. Transtrum
- Department
of Physics and Astronomy, Brigham Young
University, Provo, Utah 84602, United States
| | - Robert D. Hyldahl
- Department
of Exercise Sciences, Brigham Young University, Provo, Utah 84602, United States
| | - John C. Price
- Department
of Chemistry and Biochemistry, Brigham Young
University, Provo, Utah 84602, United States
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4
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Muliaditan M, Sepp A. Application of quantitative protein mass spectrometric data in the early predictive analysis of target engagement by monoclonal antibodies. Clin Transl Sci 2022; 15:1634-1643. [PMID: 35445800 PMCID: PMC9283736 DOI: 10.1111/cts.13278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/08/2022] [Accepted: 02/17/2022] [Indexed: 11/29/2022] Open
Abstract
Model‐informed drug discovery is endorsed by the US Food and Drug Administration (FDA) to improve the flow of medicines from bench to bedside. In the case of monoclonal antibodies, this necessitates taking into account not only the pharmacokinetic (PK) properties of the drug, but also the tissue distribution, concentration, and turnover of the target to guide dose and affinity selection, as well as serve as a link to downstream pharmacology. Relevant information (e.g., tissue proteomic data from quantitative mass spectrometry), is increasingly available from public domain data repositories, although not necessarily in the form that is directly usable for the purpose of quantitative, predictive, and mechanistic PK/pharmacodynamic (PD) modeling based on molarity or similar frameworks instead. Using secreted plasma protein concentrations measured both by immunochemical methods and mass spectrometry, we addressed this gap and derived an optimized nonlinear empirical function that establishes the correlation between the two data sets and validated the approach taken using a wider data set of all proteins found in plasma. In addition, we present a semimechanistic framework for the plasma half‐life of soluble proteins where clearance is expressed as a nonlinear function of the molecular weight of the protein. Finally, we apply the approach to two established therapeutic antibody targets: complement factor C5 and PCSK9 to demonstrate how the described framework can be applied to predictive PK/PD modeling.
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Affiliation(s)
- Morris Muliaditan
- Leiden Experts on Advanced Pharmacokinetics and Pharmacodynamics (LAP&P), Leiden, The Netherlands
| | - Armin Sepp
- Certara UK Ltd., Simcyp Division, 1 Concourse Way, Level 2-Acero, Sheffield, S1 2BJ, United Kingdom
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5
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Pauwaert K, Bodé S, Alwis US, Mylle T, Boeckx P, Delanghe J, Everaert K, Roggeman S. Observing the water handling in humans to resolve the role of the interstitium: preliminary results of the usability of deuterium oxide and bio-impedance analysis - a pilot analysis. ISOTOPES IN ENVIRONMENTAL AND HEALTH STUDIES 2022; 58:99-110. [PMID: 35072572 DOI: 10.1080/10256016.2022.2026349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 12/02/2021] [Indexed: 06/14/2023]
Abstract
The aim of this research was to evaluate the relevance of using deuterium oxide (2H2O) and bio-impedance analysis (BIA) to assess size and function of the interstitium for urological research. Nineteen volunteers were recruited to this prospective trial combining ingestion of 2H2O and BIA. Blood samples were obtained every 10 min after ingestion of 2H2O. Urine was collected before and after the experiment. BIA was performed every 5 min. Body position was alternated to study the effect on fluid distribution. First order kinetics were assumed for the uptake of 2H2O from the gastrointestinal tract to the blood. Sex seemed to have an influence with a significantly slower exchange for women (p = 0.041, men: 0.052 min-1, women: 0.038 min-1). Impedance measured in legs (men: p = 0.012, women: p = 0.008) and trunk (both p < 0.001) decreased significantly with posture change. These changes probably reflect the orthostatic redistribution of fluid with an increase of fluid in both trunk and legs. Both methods were tested and found to be useful for further urological research. Significant gender differences in 2H2O uptake dynamics from the gastrointestinal pool were observed. An impact of posture changes on the electrical impedance measured was observed.
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Affiliation(s)
- Kim Pauwaert
- Department of Urology, University Hospital Ghent, Ghent, Belgium
| | - Samuel Bodé
- Isotope Bioscience Laboratory - ISOFYS, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | | | - Toon Mylle
- Department of Urology, University Hospital Ghent, Ghent, Belgium
| | - Pascal Boeckx
- Isotope Bioscience Laboratory - ISOFYS, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Joris Delanghe
- Department of Diagnostic Sciences, University Hospital Ghent, Ghent, Belgium
| | - Karel Everaert
- Department of Urology, University Hospital Ghent, Ghent, Belgium
| | - Saskia Roggeman
- Department of Urology, University Hospital Ghent, Ghent, Belgium
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6
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Wilkinson DJ, Brook MS, Smith K. Principles of stable isotope research - with special reference to protein metabolism. CLINICAL NUTRITION OPEN SCIENCE 2021; 36:111-125. [PMID: 33969338 PMCID: PMC8083121 DOI: 10.1016/j.nutos.2021.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 02/06/2021] [Indexed: 12/13/2022] Open
Abstract
The key to understanding the mechanisms regulating disease stems from the ability to accurately quantify the dynamic nature of the metabolism underlying the physiological and pathological changes occurring as a result of the disease. Stable isotope tracer technologies have been at the forefront of this for almost 80 years now, and through a combination of both intense theoretical and technological development over these decades, it is now possible to utilise stable isotope tracers to investigate the complexities of in vivo human metabolism from a whole body perspective, down to the regulation of sub-nanometer cellular components (i.e organelles, nucleotides and individual proteins). This review therefore aims to highlight; 1) the advances made in these stable isotope tracer approaches - with special reference given to their role in understanding the nutritional regulation of protein metabolism, 2) some considerations required for the appropriate application of these stable isotope techniques to study protein metabolism, 3) and finally how new stable isotopes approaches and instrument/technical developments will help to deliver greater clinical insight in the near future.
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Key Words
- A-V, Arterial Venous
- AA, Amino Acids
- AP(E), Atom percent (excess)
- FBR, Fractional Breakdown Rate
- FSR, Fractional Synthesis Rate
- GC-MS, Gas Chromatography Mass Spectrometry
- LC-MS, Liquid Chromatography Mass Spectrometry
- MPS, Muscle Protein Synthesis
- Muscle
- Protein turnover
- Ra, Rate of Appearance
- Rd, Rate of Disappearance
- Stable isotope tracers
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Affiliation(s)
- Daniel J. Wilkinson
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, NIHR Nottingham BRC, UK
- Division of Health Sciences and Graduate Entry Medicine, School of Medicine, University of Nottingham, Royal Derby Hospital Centre, Derby, UK
| | - Matthew S. Brook
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, NIHR Nottingham BRC, UK
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Ken Smith
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, NIHR Nottingham BRC, UK
- Division of Health Sciences and Graduate Entry Medicine, School of Medicine, University of Nottingham, Royal Derby Hospital Centre, Derby, UK
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7
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Sénécaut N, Alves G, Weisser H, Lignières L, Terrier S, Yang-Crosson L, Poulain P, Lelandais G, Yu YK, Camadro JM. Novel Insights into Quantitative Proteomics from an Innovative Bottom-Up Simple Light Isotope Metabolic (bSLIM) Labeling Data Processing Strategy. J Proteome Res 2021; 20:1476-1487. [PMID: 33573382 PMCID: PMC8459934 DOI: 10.1021/acs.jproteome.0c00478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Simple light isotope metabolic labeling (SLIM labeling) is an innovative method to quantify variations in the proteome based on an original in vivo labeling strategy. Heterotrophic cells grown in U-[12C] as the sole source of carbon synthesize U-[12C]-amino acids, which are incorporated into proteins, giving rise to U-[12C]-proteins. This results in a large increase in the intensity of the monoisotope ion of peptides and proteins, thus allowing higher identification scores and protein sequence coverage in mass spectrometry experiments. This method, initially developed for signal processing and quantification of the incorporation rate of 12C into peptides, was based on a multistep process that was difficult to implement for many laboratories. To overcome these limitations, we developed a new theoretical background to analyze bottom-up proteomics data using SLIM-labeling (bSLIM) and established simple procedures based on open-source software, using dedicated OpenMS modules, and embedded R scripts to process the bSLIM experimental data. These new tools allow computation of both the 12C abundance in peptides to follow the kinetics of protein labeling and the molar fraction of unlabeled and 12C-labeled peptides in multiplexing experiments to determine the relative abundance of proteins extracted under different biological conditions. They also make it possible to consider incomplete 12C labeling, such as that observed in cells with nutritional requirements for nonlabeled amino acids. These tools were validated on an experimental dataset produced using various yeast strains of Saccharomyces cerevisiae and growth conditions. The workflows are built on the implementation of appropriate calculation modules in a KNIME working environment. These new integrated tools provide a convenient framework for the wider use of the SLIM-labeling strategy.
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Affiliation(s)
- Nicolas Sénécaut
- ≪ Mitochondria, Metals, and Oxidative Stress ≫ Group, Université de Paris-CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Gelio Alves
- National Center for Biotechnology Information, NLM, NIH, Bethesda, Maryland 20894, United States
| | | | - Laurent Lignières
- ProteoSeine@IJM, Université de Paris-CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Samuel Terrier
- ProteoSeine@IJM, Université de Paris-CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Lilian Yang-Crosson
- ≪ Mitochondria, Metals, and Oxidative Stress ≫ Group, Université de Paris-CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Pierre Poulain
- ≪ Mitochondria, Metals, and Oxidative Stress ≫ Group, Université de Paris-CNRS, Institut Jacques Monod, 75013 Paris, France
| | - Gaëlle Lelandais
- Institut de Biologie Intégrative de la Cellule, 91190 Orsay, France
| | - Yi-Kuo Yu
- National Center for Biotechnology Information, NLM, NIH, Bethesda, Maryland 20894, United States
| | - Jean-Michel Camadro
- ≪ Mitochondria, Metals, and Oxidative Stress ≫ Group, Université de Paris-CNRS, Institut Jacques Monod, 75013 Paris, France
- ProteoSeine@IJM, Université de Paris-CNRS, Institut Jacques Monod, 75013 Paris, France
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8
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Singh SA, Andraski AB, Higashi H, Lee LH, Ramsaroop A, Sacks FM, Aikawa M. Metabolism of PLTP, CETP, and LCAT on multiple HDL sizes using the Orbitrap Fusion Lumos. JCI Insight 2021; 6:143526. [PMID: 33351780 PMCID: PMC7934878 DOI: 10.1172/jci.insight.143526] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/16/2020] [Indexed: 11/18/2022] Open
Abstract
Recent in vivo tracer studies demonstrated that targeted mass spectrometry (MS) on the Q Exactive Orbitrap could determine the metabolism of HDL proteins 100s-fold less abundant than apolipoprotein A1 (APOA1). In this study, we demonstrate that the Orbitrap Lumos can measure tracer in proteins whose abundances are 1000s-fold less than APOA1, specifically the lipid transfer proteins phospholipid transfer protein (PLTP), cholesterol ester transfer protein (CETP), and lecithin-cholesterol acyl transferase (LCAT). Relative to the Q Exactive, the Lumos improved tracer detection by reducing tracer enrichment compression, thereby providing consistent enrichment data across multiple HDL sizes from 6 participants. We determined by compartmental modeling that PLTP is secreted in medium and large HDL (alpha2, alpha1, and alpha0) and is transferred from medium to larger sizes during circulation from where it is catabolized. CETP is secreted mainly in alpha1 and alpha2 and remains in these sizes during circulation. LCAT is secreted mainly in medium and small HDL (alpha2, alpha3, prebeta). Unlike PLTP and CETP, LCAT’s appearance on HDL is markedly delayed, indicating that LCAT may reside for a time outside of systemic circulation before attaching to HDL in plasma. The determination of these lipid transfer proteins’ unique metabolic structures was possible due to advances in MS technologies.
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Affiliation(s)
- Sasha A Singh
- Center for Interdisciplinary Cardiovascular Sciences, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Allison B Andraski
- Department of Nutrition and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Hideyuki Higashi
- Center for Interdisciplinary Cardiovascular Sciences, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lang Ho Lee
- Center for Interdisciplinary Cardiovascular Sciences, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ashisha Ramsaroop
- Center for Interdisciplinary Cardiovascular Sciences, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Frank M Sacks
- Department of Nutrition and Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Channing Division of Network Medicine, Department of Medicine, and
| | - Masanori Aikawa
- Center for Interdisciplinary Cardiovascular Sciences, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Channing Division of Network Medicine, Department of Medicine, and.,Center for Excellence in Vascular Biology, Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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9
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Huang L, Shao D, Wang Y, Cui X, Li Y, Chen Q, Cui J. Human body-fluid proteome: quantitative profiling and computational prediction. Brief Bioinform 2021; 22:315-333. [PMID: 32020158 PMCID: PMC7820883 DOI: 10.1093/bib/bbz160] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/22/2019] [Accepted: 10/18/2019] [Indexed: 12/15/2022] Open
Abstract
Empowered by the advancement of high-throughput bio technologies, recent research on body-fluid proteomes has led to the discoveries of numerous novel disease biomarkers and therapeutic drugs. In the meantime, a tremendous progress in disclosing the body-fluid proteomes was made, resulting in a collection of over 15 000 different proteins detected in major human body fluids. However, common challenges remain with current proteomics technologies about how to effectively handle the large variety of protein modifications in those fluids. To this end, computational effort utilizing statistical and machine-learning approaches has shown early successes in identifying biomarker proteins in specific human diseases. In this article, we first summarized the experimental progresses using a combination of conventional and high-throughput technologies, along with the major discoveries, and focused on current research status of 16 types of body-fluid proteins. Next, the emerging computational work on protein prediction based on support vector machine, ranking algorithm, and protein-protein interaction network were also surveyed, followed by algorithm and application discussion. At last, we discuss additional critical concerns about these topics and close the review by providing future perspectives especially toward the realization of clinical disease biomarker discovery.
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Affiliation(s)
- Lan Huang
- College of Computer Science and Technology in the Jilin University
| | - Dan Shao
- College of Computer Science and Technology in the Jilin University
- College of Computer Science and Technology in Changchun University
| | - Yan Wang
- College of Computer Science and Technology in the Jilin University
| | - Xueteng Cui
- College of Computer Science and Technology in the Changchun University
| | - Yufei Li
- College of Computer Science and Technology in the Changchun University
| | - Qian Chen
- College of Computer Science and Technology in the Jilin University
| | - Juan Cui
- Department of Computer Science and Engineering in the University of Nebraska-Lincoln
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10
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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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11
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Brook MS, Wilkinson DJ. Contemporary stable isotope tracer approaches: Insights into skeletal muscle metabolism in health and disease. Exp Physiol 2020; 105:1081-1089. [PMID: 32362047 DOI: 10.1113/ep087492] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 04/27/2020] [Indexed: 12/18/2022]
Abstract
NEW FINDINGS What is the topic of this review? This review discusses the application of new stable isotope tracer techniques in understanding the control of skeletal muscle mass. What advances does it highlight? This review highlights current advances in stable isotope tracer techniques through their combination with high-throughput proteomics technologies. ABSTRACT Beyond its primary locomotory and key structural functions, skeletal muscle provides additional vital roles for maintenance of metabolic health, acting as a storage point for glucose and intramuscular lipids for energy production, alongside being the largest reservoir for amino acids in the body. Therefore, maintenance of muscle mass is key to the promotion of health and well-being across the lifespan and in several disease states. As such, when skeletal muscle is lost, in either clinical (cancer, organ failure etc.) or non-clinical (ageing, inactivity) situations, there are potentially devastating consequences attached, with robust links existing between muscle mass loss and mortality. Great efforts are being made to reverse or slow muscle mass declines in health and disease, through combinations of lifestyle changes and nutritional and/or pharmaceutical intervention. However, despite this comprehensive research effort, the underlying metabolic and molecular mechanisms have yet to be defined properly. However, with the rapid acceleration of analytical developments over recent years, the application of stable isotope tracers to the study of human muscle metabolism is providing unique insights into the mechanisms controlling skeletal muscle loss and allowing more targeted therapeutic strategies to be developed. The aim of this review is to highlight the technical breakthroughs in our understanding of muscle wasting in health and disease and how future directions and developments incorporating 'omics' with stable isotope tracers will allow for a more personalized and stratified therapeutic approach.
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Affiliation(s)
- Matthew S Brook
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK.,School of Life Science, Queen's Medical Centre, Nottingham, UK
| | - Daniel J Wilkinson
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, National Institute for Health Research Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK.,Division of Health Sciences and Graduate Entry Medicine, School of Medicine, Royal Derby Hospital Centre, Derby, UK
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12
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Choi H, Simpson D, Wang D, Prescott M, Pitsillides AA, Dudhia J, Clegg PD, Ping P, Thorpe CT. Heterogeneity of proteome dynamics between connective tissue phases of adult tendon. eLife 2020; 9:e55262. [PMID: 32393437 PMCID: PMC7217697 DOI: 10.7554/elife.55262] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/16/2020] [Indexed: 12/29/2022] Open
Abstract
Maintenance of connective tissue integrity is fundamental to sustain function, requiring protein turnover to repair damaged tissue. However, connective tissue proteome dynamics remain largely undefined, as do differences in turnover rates of individual proteins in the collagen and glycoprotein phases of connective tissue extracellular matrix (ECM). Here, we investigate proteome dynamics in the collagen and glycoprotein phases of connective tissues by exploiting the spatially distinct fascicular (collagen-rich) and interfascicular (glycoprotein-rich) ECM phases of tendon. Using isotope labelling, mass spectrometry and bioinformatics, we calculate turnover rates of individual proteins within rat Achilles tendon and its ECM phases. Our results demonstrate complex proteome dynamics in tendon, with ~1000 fold differences in protein turnover rates, and overall faster protein turnover within the glycoprotein-rich interfascicular matrix compared to the collagen-rich fascicular matrix. These data provide insights into the complexity of proteome dynamics in tendon, likely required to maintain tissue homeostasis.
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Affiliation(s)
- Howard Choi
- Department of Physiology and Medicine, David Geffen School of Medicine, UCLALos AngelesUnited States
| | - Deborah Simpson
- Centre for Proteome Research, Biosciences Building, Institute of Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Ding Wang
- Department of Physiology and Medicine, David Geffen School of Medicine, UCLALos AngelesUnited States
| | - Mark Prescott
- Centre for Proteome Research, Biosciences Building, Institute of Integrative Biology, University of LiverpoolLiverpoolUnited Kingdom
| | - Andrew A Pitsillides
- Department of Comparative Biomedical Sciences, Royal Veterinary CollegeLondonUnited Kingdom
| | - Jayesh Dudhia
- Department of Clinical Sciences and Services, Royal Veterinary CollegeHatfieldUnited Kingdom
| | - Peter D Clegg
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of LiverpoolLiverpoolUnited Kingdom
| | - Peipei Ping
- Department of Physiology and Medicine, David Geffen School of Medicine, UCLALos AngelesUnited States
| | - Chavaunne T Thorpe
- Department of Comparative Biomedical Sciences, Royal Veterinary CollegeLondonUnited Kingdom
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13
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Miller BF, Reid JJ, Price JC, Lin HJL, Atherton PJ, Smith K. CORP: The use of deuterated water for the measurement of protein synthesis. J Appl Physiol (1985) 2020; 128:1163-1176. [PMID: 32213116 DOI: 10.1152/japplphysiol.00855.2019] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The use of deuterium oxide (D2O) has greatly expanded the scope of what is possible for the measurement of protein synthesis. The greatest asset of D2O labeling is that it facilitates the measurement of synthesis rates over prolonged periods of time from single proteins through integrated tissue-based measurements. Because the ease of administration, the method is amenable for use in a variety of models and conditions. Although the method adheres to the same rules as other isotope methods, the flexibility can create conditions that are not the same as other approaches and thus requires careful execution to maintain validity and reliability. For this CORP article, we provide a history that gave rise to the method and discuss the advantages and disadvantages of the method, the critical assumptions, guidelines, and best practices based on instrumentation, models, and experimental design. The goal of this CORP article is to propagate additional use of D2O in a manner that produces reliable and valid data.
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Affiliation(s)
- Benjamin F Miller
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - Justin J Reid
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma
| | - John C Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Hsien-Jung L Lin
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Philip J Atherton
- MRC-ARUK Center for Musculoskeletal Ageing Research, School of Medicine, University of Nottingham, Derby, United Kingdom
| | - Kenneth Smith
- MRC-ARUK Center for Musculoskeletal Ageing Research, School of Medicine, University of Nottingham, Derby, United Kingdom
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14
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Endurance-Type Exercise Increases Bulk and Individual Mitochondrial Protein Synthesis Rates in Rats. Int J Sport Nutr Exerc Metab 2020; 30:153–164. [DOI: 10.1123/ijsnem.2019-0281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/22/2019] [Accepted: 11/27/2019] [Indexed: 11/18/2022]
Abstract
Physical activity increases muscle protein synthesis rates. However, the impact of exercise on the coordinated up- and/or downregulation of individual protein synthesis rates in skeletal muscle tissue remains unclear. The authors assessed the impact of exercise on mixed muscle, myofibrillar, and mitochondrial protein synthesis rates as well as individual protein synthesis rates in vivo in rats. Adult Lewis rats either remained sedentary (n = 3) or had access to a running wheel (n = 3) for the last 2 weeks of a 3-week experimental period. Deuterated water was injected and subsequently administered in drinking water over the experimental period. Blood and soleus muscle were collected and used to assess bulk mixed muscle, myofibrillar, and mitochondrial protein synthesis rates using gas chromatography–mass spectrometry and individual muscle protein synthesis rates using liquid chromatography–mass spectrometry (i.e., dynamic proteomic profiling). Wheel running resulted in greater myofibrillar (3.94 ± 0.26 vs. 3.03 ± 0.15%/day; p < .01) and mitochondrial (4.64 ± 0.24 vs. 3.97 ± 0.26%/day; p < .05), but not mixed muscle (2.64 ± 0.96 vs. 2.38 ± 0.62%/day; p = .71) protein synthesis rates, when compared with the sedentary condition. Exercise impacted the synthesis rates of 80 proteins, with the difference from the sedentary condition ranging between −64% and +420%. Significantly greater synthesis rates were detected for F1-ATP synthase, ATP synthase subunit alpha, hemoglobin, myosin light chain-6, and synaptopodin-2 (p < .05). The skeletal muscle protein adaptive response to endurance-type exercise involves upregulation of mitochondrial protein synthesis rates, but it is highly coordinated as reflected by the up- and downregulation of various individual proteins across different bulk subcellular protein fractions.
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15
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Kumar AA, Kelly DP, Chirinos JA. Mitochondrial Dysfunction in Heart Failure With Preserved Ejection Fraction. Circulation 2019; 139:1435-1450. [PMID: 30856000 DOI: 10.1161/circulationaha.118.036259] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Heart failure with preserved ejection fraction (HFpEF) is a complex syndrome with an increasingly recognized heterogeneity in pathophysiology. Exercise intolerance is the hallmark of HFpEF and appears to be caused by both cardiac and peripheral abnormalities in the arterial tree and skeletal muscle. Mitochondrial abnormalities can significantly contribute to impaired oxygen utilization and the resulting exercise intolerance in HFpEF. We review key aspects of the complex biology of this organelle, the clinical relevance of mitochondrial function, the methods that are currently available to assess mitochondrial function in humans, and the evidence supporting a role for mitochondrial dysfunction in the pathophysiology of HFpEF. We also discuss the role of mitochondrial function as a therapeutic target, some key considerations for the design of early-phase clinical trials using agents that specifically target mitochondrial function to improve symptoms in patients with HFpEF, and ongoing trials with mitochondrial agents in HFpEF.
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Affiliation(s)
- Anupam A Kumar
- From the University of Pennsylvania Perelman School of Medicine, Philadelphia (A.K., D.P.K., J.C.)
| | - Daniel P Kelly
- From the University of Pennsylvania Perelman School of Medicine, Philadelphia (A.K., D.P.K., J.C.)
| | - Julio A Chirinos
- From the University of Pennsylvania Perelman School of Medicine, Philadelphia (A.K., D.P.K., J.C.).,the Hospital of the University of Pennsylvania, Philadelphia (J.C.)
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16
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Lehmann S, Hirtz C, Vialaret J, Ory M, Combes GG, Corre ML, Badiou S, Cristol JP, Hanon O, Cornillot E, Bauchet L, Gabelle A, Colinge J. In Vivo Large-Scale Mapping of Protein Turnover in Human Cerebrospinal Fluid. Anal Chem 2019; 91:15500-15508. [PMID: 31730336 DOI: 10.1021/acs.analchem.9b03328] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The extraction of accurate physiological parameters from clinical samples provides a unique perspective to understand disease etiology and evolution, including under therapy. We introduce a new methodologic framework to map patient proteome dynamics in vivo, either proteome-wide or in large targeted panels. We applied it to ventricular cerebrospinal fluid (CSF) and could determine the turnover parameters of almost 200 proteins, whereas a handful were known previously. We covered a large number of neuron biology- and immune system-related proteins, including many biomarkers and drug targets. This first large data set unraveled a significant relationship between turnover and protein origin that relates to our ability to investigate organ physiology with protein-labeling strategy specifics. Our data constitute the first draft of CSF proteome dynamics as well as a repertoire of peptides for the community to design new analyses. The disclosed methods apply to other fluids or tissues provided sequential sample collection can be performed. We show that the proposed mathematical modeling applies to other analytical methods in the field.
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Affiliation(s)
- Sylvain Lehmann
- CHU de Montpellier , 34295 Montpellier , France.,IRMB, INSERM, Laboratoire de Biochimie Protéomique Clinique , 34295 Montpellier , France.,Université de Montpellier , 34090 Montpellier , France
| | - Christophe Hirtz
- CHU de Montpellier , 34295 Montpellier , France.,IRMB, INSERM, Laboratoire de Biochimie Protéomique Clinique , 34295 Montpellier , France.,Université de Montpellier , 34090 Montpellier , France
| | - Jérôme Vialaret
- CHU de Montpellier , 34295 Montpellier , France.,IRMB, INSERM, Laboratoire de Biochimie Protéomique Clinique , 34295 Montpellier , France
| | - Maxence Ory
- Institut de Recherche en Cancérologie de Montpellier, INSERM , 34298 Montpellier , France
| | - Guillaume Gras Combes
- Université de Montpellier , 34090 Montpellier , France.,Hôpital Gui de Chauliac, Service de Neurochirurgie , CHU de Montpellier , 34295 Montpellier , France.,INSERM U1051 , 34295 Montpellier , France
| | - Marine Le Corre
- Université de Montpellier , 34090 Montpellier , France.,Hôpital Gui de Chauliac, Service de Neurochirurgie , CHU de Montpellier , 34295 Montpellier , France.,INSERM U1051 , 34295 Montpellier , France
| | - Stéphanie Badiou
- Université de Montpellier , 34090 Montpellier , France.,Département de Biochimie et Hormonologie , CHU de Montpellier , 34295 Montpellier , France.,PhyMedExp , Université de Montpellier, INSERM, CNRS , 34090 Montpellier , France
| | - Jean-Paul Cristol
- Université de Montpellier , 34090 Montpellier , France.,Département de Biochimie et Hormonologie , CHU de Montpellier , 34295 Montpellier , France.,PhyMedExp , Université de Montpellier, INSERM, CNRS , 34090 Montpellier , France
| | - Olivier Hanon
- Service de Gériatrie , Hôpital Broca (AP-HP) , 75013 Paris , France.,Université Paris Descartes, Sorbonne Paris Cité , 75006 Paris , France
| | - Emmanuel Cornillot
- Université de Montpellier , 34090 Montpellier , France.,Institut de Recherche en Cancérologie de Montpellier, INSERM , 34298 Montpellier , France
| | - Luc Bauchet
- Université de Montpellier , 34090 Montpellier , France.,Hôpital Gui de Chauliac, Service de Neurochirurgie , CHU de Montpellier , 34295 Montpellier , France.,INSERM U1051 , 34295 Montpellier , France
| | - Audrey Gabelle
- Université de Montpellier , 34090 Montpellier , France.,Centre Mémoire de Ressources et de Recherche Languedoc-Roussillon , 34295 Montpellier , France.,Hôpital Gui de Chauliac , CHU de Montpellier , 34295 Montpellier , France
| | - Jacques Colinge
- Université de Montpellier , 34090 Montpellier , France.,Institut de Recherche en Cancérologie de Montpellier, INSERM , 34298 Montpellier , France.,Institut Régional du Cancer de Montpellier , 34298 Montpellier , France
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17
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Elevated Autotaxin and LPA Levels During Chronic Viral Hepatitis and Hepatocellular Carcinoma Associate with Systemic Immune Activation. Cancers (Basel) 2019; 11:cancers11121867. [PMID: 31769428 PMCID: PMC6966516 DOI: 10.3390/cancers11121867] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 11/20/2019] [Accepted: 11/21/2019] [Indexed: 12/16/2022] Open
Abstract
Circulating autotaxin (ATX) is elevated in persons with liver disease, particularly in the setting of chronic hepatitis C virus (HCV) and HCV/HIV infection. It is thought that plasma ATX levels are, in part, attributable to impaired liver clearance that is secondary to fibrotic liver disease. In a discovery data set, we identified plasma ATX to be associated with parameters of systemic immune activation during chronic HCV and HCV/HIV infection. We and others have observed a partial normalization of ATX levels within months of starting interferon-free direct-acting antiviral (DAA) HCV therapy, consistent with a non-fibrotic liver disease contribution to elevated ATX levels, or HCV-mediated hepatocyte activation. Relationships between ATX, lysophosphatidic acid (LPA) and parameters of systemic immune activation will be discussed in the context of HCV infection, age, immune health, liver health, and hepatocellular carcinoma (HCC).
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18
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Zlatska A, Gordiienko I, Vasyliev R, Zubov D, Gubar O, Rodnichenko A, Syroeshkin A, Zlatskiy I. In Vitro Study of Deuterium Effect on Biological Properties of Human Cultured Adipose-Derived Stem Cells. ScientificWorldJournal 2018; 2018:5454367. [PMID: 30519147 PMCID: PMC6241234 DOI: 10.1155/2018/5454367] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 08/27/2018] [Accepted: 09/27/2018] [Indexed: 01/08/2023] Open
Abstract
In current in vitro study we have shown the impact of deuterium content in growth medium on proliferation rate of human cultured adipose-derived stem cells (ADSC). ADSCs have also demonstrated morphological changes when cultured in deuterated growth medium: the cell cultures did not reach confluence but acquired polygonal morphology with pronounced stress fibers. At high deuterium concentrations the ADSCs population doubling time increased which indicated the cell cycle retardation and decrease of cell proliferation rate. The deuterated and deuterium-depleted growth media demonstrated acute and chronic cytotoxicity, respectively. The minimal migration ability was observed in deuterated medium whereas the highest migration activity was observed in the medium with the deuterium content close to natural. The cells in deuterated growth medium demonstrated decrease in metabolic activity after three days in culture. In contrast, in deuterium-depleted medium there was an increase in ADSC metabolic activity.
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Affiliation(s)
- Alona Zlatska
- State Institute of Genetic and Regenerative Medicine, National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
- Biotechnology Laboratory Ilaya Regeneration, Medical Company Ilaya®, Kyiv, Ukraine
| | - Inna Gordiienko
- Biotechnology Laboratory Ilaya Regeneration, Medical Company Ilaya®, Kyiv, Ukraine
- RE Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Roman Vasyliev
- State Institute of Genetic and Regenerative Medicine, National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
- Biotechnology Laboratory Ilaya Regeneration, Medical Company Ilaya®, Kyiv, Ukraine
| | - Dmitriy Zubov
- State Institute of Genetic and Regenerative Medicine, National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
- Biotechnology Laboratory Ilaya Regeneration, Medical Company Ilaya®, Kyiv, Ukraine
| | - Olga Gubar
- Biotechnology Laboratory Ilaya Regeneration, Medical Company Ilaya®, Kyiv, Ukraine
| | - Anzhela Rodnichenko
- State Institute of Genetic and Regenerative Medicine, National Academy of Medical Sciences of Ukraine, Kyiv, Ukraine
- Biotechnology Laboratory Ilaya Regeneration, Medical Company Ilaya®, Kyiv, Ukraine
| | - Anton Syroeshkin
- Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., Moscow 117198, Russia
| | - Igor Zlatskiy
- Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St., Moscow 117198, Russia
- Dumanskii Institute of Colloid Chemistry and Water Chemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
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19
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Quantitative temporal analysis of protein dynamics in cardiac remodeling. J Mol Cell Cardiol 2018; 121:163-172. [PMID: 30009778 DOI: 10.1016/j.yjmcc.2018.07.126] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 06/20/2018] [Accepted: 07/09/2018] [Indexed: 01/02/2023]
Abstract
Cardiac remodeling (CR) is a complex dynamic process common to many heart diseases. CR is characterized as a temporal progression of global adaptive and maladaptive perturbations. The complex nature of this process clouds a comprehensive understanding of CR, but greater insight into the processes and mechanisms has potential to identify new therapeutic targets. To provide a deeper understanding of this important cardiac process, we applied a new proteomic technique, PALM (Pulse Azidohomoalanine in Mammals), to quantitate the newly-synthesized protein (NSP) changes during the progression of isoproterenol (ISO)-induced CR in the mouse left ventricle. This analysis revealed a complex combination of adaptive and maladaptive alterations at acute and prolonged time points including the identification of proteins not previously associated with CR. We also combined the PALM dataset with our published protein turnover rate dataset to identify putative biochemical mechanisms underlying CR. The novel integration of analyzing NSPs together with their protein turnover rates demonstrated that alterations in specific biological pathways (e.g., inflammation and oxidative stress) are produced by differential regulation of protein synthesis and degradation.
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20
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Goh B, Kim J, Seo S, Kim TY. High-Throughput Measurement of Lipid Turnover Rates Using Partial Metabolic Heavy Water Labeling. Anal Chem 2018; 90:6509-6518. [DOI: 10.1021/acs.analchem.7b05428] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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21
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Zachleder V, Vítová M, Hlavová M, Moudříková Š, Mojzeš P, Heumann H, Becher JR, Bišová K. Stable isotope compounds - production, detection, and application. Biotechnol Adv 2018; 36:784-797. [PMID: 29355599 DOI: 10.1016/j.biotechadv.2018.01.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 01/12/2018] [Accepted: 01/15/2018] [Indexed: 12/14/2022]
Abstract
Stable isotopes are used in wide fields of application from natural tracers in biology, geology and archeology through studies of metabolic fluxes to their application as tracers in quantitative proteomics and structural biology. We review the use of stable isotopes of biogenic elements (H, C, N, O, S, Mg, Se) with the emphasis on hydrogen and its heavy isotope deuterium. We will discuss the limitations of enriching various compounds in stable isotopes when produced in living organisms. Finally, we overview methods for measuring stable isotopes, focusing on methods for detection in single cells in situ and their exploitation in modern biotechnologies.
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Affiliation(s)
- Vilém Zachleder
- Institute of Microbiology, CAS, Centre Algatech, Laboratory of Cell Cycles of Algae, CZ-379 81 Třeboň, Czech Republic
| | - Milada Vítová
- Institute of Microbiology, CAS, Centre Algatech, Laboratory of Cell Cycles of Algae, CZ-379 81 Třeboň, Czech Republic
| | - Monika Hlavová
- Institute of Microbiology, CAS, Centre Algatech, Laboratory of Cell Cycles of Algae, CZ-379 81 Třeboň, Czech Republic
| | - Šárka Moudříková
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic
| | - Peter Mojzeš
- Institute of Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, CZ-121 16 Prague 2, Czech Republic
| | | | | | - Kateřina Bišová
- Institute of Microbiology, CAS, Centre Algatech, Laboratory of Cell Cycles of Algae, CZ-379 81 Třeboň, Czech Republic.
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22
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Golizeh M, Lee K, Ilchenko S, Ösme A, Bena J, Sadygov RG, Kashyap SR, Kasumov T. Increased serotransferrin and ceruloplasmin turnover in diet-controlled patients with type 2 diabetes. Free Radic Biol Med 2017; 113:461-469. [PMID: 29079528 PMCID: PMC5739305 DOI: 10.1016/j.freeradbiomed.2017.10.373] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/22/2017] [Accepted: 10/22/2017] [Indexed: 01/07/2023]
Abstract
Type 2 diabetes mellitus (T2DM) is associated with oxidative stress and perturbed iron metabolism. Serotransferrin (Trf) and ceruloplasmin (Cp) are two key proteins involved in iron metabolism and anti-oxidant defense. Non-enzymatic glycation and oxidative modification of plasma proteins are known to occur under hyperglycemia and oxidative stress. In this study, shotgun proteomics and 2H2O-based metabolic labeling were used to characterize post-translational modifications and assess the kinetics of Trf and Cp in T2DM patients and matched controls in vivo. Six early lysine (Amadori) and one advanced arginine glycation were detected in Trf. No glycation, but five asparagine deamidations, were found in Cp. T2DM patients had increased fractional catabolic rates of both Trf and Cp that correlated with HbA1c (p < 0.05). The glycated Trf population was subject to an even faster degradation compared to the total Trf pool, suggesting that hyperglycemia contributed to an increased Trf degradation in T2DM patients. Enhanced production of Trf and Cp kept their levels stable. The changes in Trf and Cp turnover were associated with increased systemic oxidative stress without any alteration in iron status in T2DM. These findings can help better understand the potential role of altered Trf and Cp metabolism in the pathogenesis of T2DM and other diseases.
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Affiliation(s)
- Makan Golizeh
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, United States
| | - Kwangwon Lee
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, United States
| | - Serguei Ilchenko
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, United States
| | - Abdullah Ösme
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, United States
| | - James Bena
- Section of Biostatistics, Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH, United States
| | - Rovshan G Sadygov
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Sangeeta R Kashyap
- Department of Endocrinology, Cleveland Clinic, Cleveland, OH, United States
| | - Takhar Kasumov
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH, United States; Department of Endocrinology, Cleveland Clinic, Cleveland, OH, United States.
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23
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Farthing DE, Buxbaum NP, Lucas PJ, Maglakelidze N, Oliver B, Wang J, Hu K, Castro E, Bare CV, Gress RE. Comparing DNA enrichment of proliferating cells following administration of different stable isotopes of heavy water. Sci Rep 2017. [PMID: 28642474 PMCID: PMC5481421 DOI: 10.1038/s41598-017-04404-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Deuterated water (2H2O) is a label commonly used for safe quantitative measurement of deuterium enrichment into DNA of proliferating cells. More recently, it has been used for labeling proteins and other biomolecules. Our in vitro - in vivo research reports important stable isotopic labeling enrichment differences into the DNA nucleosides and their isotopologues (e.g. deoxyadenosine (dA) M + 1, dA M + 2, dA M + 3), as well as tumor cell proliferation effects for various forms of commercially available stable heavy water (2H2O, H218O, and 2H218O). Using an in vitro mouse thymus tumor cell line, we determined that H218O provides superior DNA labeling enrichment quantitation, as measured by GC-positive chemical ionization (PCI)-MS/MS. In addition, at higher but physiologically relevant doses, both 2H218O and 2H2O down modulated mouse thymus tumor cell proliferation, whereas H218O water had no observable effects on cell proliferation. The in vivo labeling studies, where normal mouse bone marrow cells (i.e. high turnover) were evaluated post labeling, demonstrated DNA enrichments concordant with measurements from the in vitro studies. Our research also reports a headspace-GC-NCI-MS method, which rapidly and quantitatively measures stable heavy water levels in total body water.
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Affiliation(s)
- Don E Farthing
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States.
| | - Nataliya P Buxbaum
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Philip J Lucas
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Natella Maglakelidze
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Brittany Oliver
- OCRT&ME, 10 Center Drive, Bethesda, MD, 20814, United States
| | - Jiun Wang
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Kevin Hu
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Ehydel Castro
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Catherine V Bare
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
| | - Ronald E Gress
- National Institutes of Health (NIH), National Cancer Institute (NCI), Experimental Transplantation and Immunology (ETIB), 10 Center Drive, Bethesda, MD, 20892, United States
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Stastna M, Gottlieb RA, Van Eyk JE. Exploring ribosome composition and newly synthesized proteins through proteomics and potential biomedical applications. Expert Rev Proteomics 2017; 14:529-543. [PMID: 28532181 DOI: 10.1080/14789450.2017.1333424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION Protein synthesis is the outcome of tightly regulated gene expression which is responsive to a variety of conditions. Efforts are ongoing to monitor individual stages of protein synthesis to ensure maximum efficiency and accuracy. Due to post-transcriptional regulation mechanisms, the correlation between translatome and proteome is higher than between transcriptome and proteome. However, the most accurate approach to assess the key modulators and final protein expression is directly by using proteomics. Areas covered: This review covers various proteomic strategies that were used to better understand post-transcriptional regulation, specifically during and early after translation. The methods that identify both regulatory proteins associated with translational components and newly synthesized proteins are discussed. Expert commentary: Emerging proteomic approaches make it possible to monitor protein dynamics in cells, tissues and whole animals. The ability to detect alteration in protein abundance soon after their synthesis enables earlier recognition of disease causing factors and candidates to prevent/rectify disease phenotype.
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Affiliation(s)
- Miroslava Stastna
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,b Advanced Clinical BioSystems Research Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,c Institute of Analytical Chemistry of the Czech Academy of Sciences, v. v. i ., Brno , Czech Republic
| | - Roberta A Gottlieb
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Jennifer E Van Eyk
- a Heart Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA.,b Advanced Clinical BioSystems Research Institute , Cedars-Sinai Medical Center , Los Angeles , CA , USA
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25
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Garlid AO, Polson JS, Garlid KD, Hermjakob H, Ping P. Equipping Physiologists with an Informatics Tool Chest: Toward an Integerated Mitochondrial Phenome. Handb Exp Pharmacol 2017; 240:377-401. [PMID: 27995389 DOI: 10.1007/164_2016_93] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Understanding the complex involvement of mitochondrial biology in disease development often requires the acquisition, analysis, and integration of large-scale molecular and phenotypic data. An increasing number of bioinformatics tools are currently employed to aid in mitochondrial investigations, most notably in predicting or corroborating the spatial and temporal dynamics of mitochondrial molecules, in retrieving structural data of mitochondrial components, and in aggregating as well as transforming mitochondrial centric biomedical knowledge. With the increasing prevalence of complex Big Data from omics experiments and clinical cohorts, informatics tools have become indispensable in our quest to understand mitochondrial physiology and pathology. Here we present an overview of the various informatics resources that are helping researchers explore this vital organelle and gain insights into its form, function, and dynamics.
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Affiliation(s)
- Anders Olav Garlid
- The NIH BD2K Center of Excellence in Biomedical Computing at UCLA, Department of Physiology, University of California, Los Angeles, CA, 90095, USA.
| | - Jennifer S Polson
- The NIH BD2K Center of Excellence in Biomedical Computing at UCLA, Department of Physiology, University of California, Los Angeles, CA, 90095, USA.
| | - Keith D Garlid
- The NIH BD2K Center of Excellence in Biomedical Computing at UCLA, Department of Physiology, University of California, Los Angeles, CA, 90095, USA
| | - Henning Hermjakob
- The NIH BD2K Center of Excellence in Biomedical Computing at UCLA, Department of Physiology, University of California, Los Angeles, CA, 90095, USA
- Molecular Systems Cluster, European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Peipei Ping
- The NIH BD2K Center of Excellence in Biomedical Computing at UCLA, Departments of Physiology, Medicine, and Bioinformatics, University of California, Los Angeles, CA, 90095, USA
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26
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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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27
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Li L, Zhang GF, Lee K, Lopez R, Previs SF, Willard B, McCullough A, Kasumov T. A Western diet induced NAFLD in LDLR(-/)(-) mice is associated with reduced hepatic glutathione synthesis. Free Radic Biol Med 2016; 96:13-21. [PMID: 27036364 PMCID: PMC5297627 DOI: 10.1016/j.freeradbiomed.2016.03.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/24/2016] [Accepted: 03/25/2016] [Indexed: 12/11/2022]
Abstract
Oxidative stress plays a key role in the pathogenesis of non-alcoholic fatty liver disease (NAFLD). Glutathione is the major anti-oxidant involved in cellular oxidative defense, however there are currently no simple non-invasive methods for assessing hepatic glutathione metabolism in patients with NAFLD. As a primary source of plasma glutathione, liver plays an important role in interorgan glutathione homeostasis. In this study, we have tested the hypothesis that measurements of plasma glutathione turnover could be used to assess the hepatic glutathione metabolism in LDLR(-/)(-) mice, a mouse model of diet-induced NAFLD. Mice were fed a standard low fat diet (LFD) or a high fat diet containing cholesterol (a Western type diet (WD)). The kinetics of hepatic and plasma glutathione were quantified using the (2)H2O metabolic labeling approach. Our results show that a WD leads to reduced fractional synthesis rates (FSR) of hepatic (25%/h in LFD vs. 18%/h in WD, P<0.05) and plasma glutathione (43%/h in LFD vs. 21%/h in WD, P<0.05), without any significant effect on their absolute production rates (PRs). WD-induced concordant changes in both hepatic and plasma glutathione turnover suggest that the plasma glutathione turnover measurements could be used to assess hepatic glutathione metabolism. The safety, simplicity, and low cost of the (2)H2O-based glutathione turnover approach suggest that this method has the potential for non-invasive probing of hepatic glutathione metabolism in patients with NAFLD and other diseases.
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Affiliation(s)
- Ling Li
- Department of Research Core Services, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Guo-Fang Zhang
- Department of Nutrition, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Kwangwon Lee
- Department of Pharmaceutical Sciences, College of Pharmacy, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Rocio Lopez
- Department of Quantitative Health Sciences, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Stephen F Previs
- Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - Belinda Willard
- Department of Research Core Services, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44106, USA
| | - Arthur McCullough
- Department of Hepatology and Gastroenterology, Digestive Disease Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Takhar Kasumov
- Department of Pharmaceutical Sciences, College of Pharmacy, Northeast Ohio Medical University, Rootstown, OH 44272, USA; Department of Hepatology and Gastroenterology, Digestive Disease Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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28
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Lau E, Cao Q, Ng DCM, Bleakley BJ, Dincer TU, Bot BM, Wang D, Liem DA, Lam MPY, Ge J, Ping P. A large dataset of protein dynamics in the mammalian heart proteome. Sci Data 2016; 3:160015. [PMID: 26977904 PMCID: PMC4792174 DOI: 10.1038/sdata.2016.15] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/12/2016] [Indexed: 01/03/2023] Open
Abstract
Protein stability is a major regulatory principle of protein function and cellular homeostasis. Despite limited understanding on mechanisms, disruption of protein turnover is widely implicated in diverse pathologies from heart failure to neurodegenerations. Information on global protein dynamics therefore has the potential to expand the depth and scope of disease phenotyping and therapeutic strategies. Using an integrated platform of metabolic labeling, high-resolution mass spectrometry and computational analysis, we report here a comprehensive dataset of the in vivo half-life of 3,228 and the expression of 8,064 cardiac proteins, quantified under healthy and hypertrophic conditions across six mouse genetic strains commonly employed in biomedical research. We anticipate these data will aid in understanding key mitochondrial and metabolic pathways in heart diseases, and further serve as a reference for methodology development in dynamics studies in multiple organ systems.
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Affiliation(s)
- Edward Lau
- The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles, California 90095, USA.,Department of Physiology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Quan Cao
- The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles, California 90095, USA.,Department of Physiology, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Dominic C M Ng
- The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles, California 90095, USA.,Department of Physiology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Brian J Bleakley
- The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles, California 90095, USA.,Department of Physiology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - T Umut Dincer
- The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles, California 90095, USA.,Department of Physiology, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Bioinformatics, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Brian M Bot
- The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles, California 90095, USA.,Department of Sage Bionetworks, Seattle, Washignton 98109, USA
| | - Ding Wang
- The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles, California 90095, USA.,Department of Physiology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - David A Liem
- The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles, California 90095, USA.,Department of Physiology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Maggie P Y Lam
- The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles, California 90095, USA.,Department of Physiology, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Bioinformatics, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Junbo Ge
- Department of Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Peipei Ping
- The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles, California 90095, USA.,Department of Physiology, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Bioinformatics, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Medicine,University of California at Los Angeles, Los Angeles, California 90095, USA
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Lindsey ML, Mayr M, Gomes AV, Delles C, Arrell DK, Murphy AM, Lange RA, Costello CE, Jin YF, Laskowitz DT, Sam F, Terzic A, Van Eyk J, Srinivas PR. Transformative Impact of Proteomics on Cardiovascular Health and Disease: A Scientific Statement From the American Heart Association. Circulation 2015. [PMID: 26195497 DOI: 10.1161/cir.0000000000000226] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The year 2014 marked the 20th anniversary of the coining of the term proteomics. The purpose of this scientific statement is to summarize advances over this period that have catalyzed our capacity to address the experimental, translational, and clinical implications of proteomics as applied to cardiovascular health and disease and to evaluate the current status of the field. Key successes that have energized the field are delineated; opportunities for proteomics to drive basic science research, facilitate clinical translation, and establish diagnostic and therapeutic healthcare algorithms are discussed; and challenges that remain to be solved before proteomic technologies can be readily translated from scientific discoveries to meaningful advances in cardiovascular care are addressed. Proteomics is the result of disruptive technologies, namely, mass spectrometry and database searching, which drove protein analysis from 1 protein at a time to protein mixture analyses that enable large-scale analysis of proteins and facilitate paradigm shifts in biological concepts that address important clinical questions. Over the past 20 years, the field of proteomics has matured, yet it is still developing rapidly. The scope of this statement will extend beyond the reaches of a typical review article and offer guidance on the use of next-generation proteomics for future scientific discovery in the basic research laboratory and clinical settings.
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Bederman IR, Lai N, Shuster J, Henderson L, Ewart S, Cabrera ME. Chronic hindlimb suspension unloading markedly decreases turnover rates of skeletal and cardiac muscle proteins and adipose tissue triglycerides. J Appl Physiol (1985) 2015; 119:16-26. [PMID: 25930021 DOI: 10.1152/japplphysiol.00004.2014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 04/25/2015] [Indexed: 11/22/2022] Open
Abstract
We previously showed that a single bolus of "doubly-labeled" water ((2)H2 (18)O) can be used to simultaneously determine energy expenditure and turnover rates (synthesis and degradation) of tissue-specific lipids and proteins by modeling labeling patterns of protein-bound alanine and triglyceride-bound glycerol (Bederman IR, Dufner DA, Alexander JC, Previs SF. Am J Physiol Endocrinol Metab 290: E1048-E1056, 2006). Using this novel method, we quantified changes in the whole body and tissue-specific energy balance in a rat model of simulated "microgravity" induced by hindlimb suspension unloading (HSU). After chronic HSU (3 wk), rats exhibited marked atrophy of skeletal and cardiac muscles and significant decrease in adipose tissue mass. For example, soleus muscle mass progressively decreased 11, 43, and 52%. We found similar energy expenditure between control (90 ± 3 kcal · kg(-1)· day(-1)) and hindlimb suspended (81 ± 6 kcal/kg day) animals. By comparing food intake (∼ 112 kcal · kg(-1) · day(-1)) and expenditure, we found that animals maintained positive calorie balance proportional to their body weight. From multicompartmental fitting of (2)H-labeling patterns, we found significantly (P < 0.005) decreased rates of synthesis (percent decrease from control: cardiac, 25.5%; soleus, 70.3%; extensor digitorum longus, 44.9%; gastrocnemius, 52.5%; and adipose tissue, 39.5%) and rates of degradation (muscles: cardiac, 9.7%; soleus, 52.0%; extensor digitorum longus, 27.8%; gastrocnemius, 37.4%; and adipose tissue, 50.2%). Overall, HSU affected growth of young rats by decreasing the turnover rates of proteins in skeletal and cardiac muscles and adipose tissue triglycerides. Specifically, we found that synthesis rates of skeletal and cardiac muscle proteins were affected to a much greater degree compared with the decrease in degradation rates, resulting in large negative balance and significant tissue loss. In contrast, we found a small decrease in adipose tissue triglyceride synthesis paired with a large decrease in degradation, resulting in smaller negative energy balance and loss of fat mass. We conclude that HSU in rats differentially affects turnover of muscle proteins vs. adipose tissue triglycerides.
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Affiliation(s)
| | - Nicola Lai
- Department of Pediatrics and Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio
| | | | | | | | - Marco E Cabrera
- Department of Pediatrics and Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio
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31
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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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32
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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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33
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Atherton PJ, Phillips BE, Wilkinson DJ. Exercise and Regulation of Protein Metabolism. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2015; 135:75-98. [DOI: 10.1016/bs.pmbts.2015.06.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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34
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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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