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Miura Y, Tsumoto H, Iwamoto M, Yamaguchi Y, Ko P, Soejima Y, Yoshida S, Toda T, Arai T, Hamamatsu A, Endo T, Sawabe M. Age‐associated proteomic alterations in human aortic media. Geriatr Gerontol Int 2019; 19:1054-1062. [DOI: 10.1111/ggi.13757] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/26/2019] [Accepted: 07/18/2019] [Indexed: 01/06/2023]
Affiliation(s)
- Yuri Miura
- Research Team for Mechanism of AgingTokyo Metropolitan Institute of Gerontology Tokyo Japan
| | - Hiroki Tsumoto
- Research Team for Mechanism of AgingTokyo Metropolitan Institute of Gerontology Tokyo Japan
| | - Machiko Iwamoto
- Research Team for Mechanism of AgingTokyo Metropolitan Institute of Gerontology Tokyo Japan
| | - Yuya Yamaguchi
- Department of Molecular Pathology, Graduate School of Medical and Dental SciencesTokyo Medical and Dental University Tokyo Japan
| | - Pojui Ko
- Department of Molecular Pathology, Graduate School of Medical and Dental SciencesTokyo Medical and Dental University Tokyo Japan
| | - Yurie Soejima
- Department of Molecular Pathology, Graduate School of Medical and Dental SciencesTokyo Medical and Dental University Tokyo Japan
| | - Shoko Yoshida
- Department of Molecular Pathology, Graduate School of Medical and Dental SciencesTokyo Medical and Dental University Tokyo Japan
| | - Tosifusa Toda
- Research Team for Mechanism of AgingTokyo Metropolitan Institute of Gerontology Tokyo Japan
| | - Tomio Arai
- Department of PathologyTokyo Metropolitan Geriatric Hospital Tokyo Japan
| | - Akihiko Hamamatsu
- Department of PathologyTokyo Metropolitan Geriatric Hospital Tokyo Japan
| | - Tamao Endo
- Research Team for Mechanism of AgingTokyo Metropolitan Institute of Gerontology Tokyo Japan
| | - Motoji Sawabe
- Department of Molecular Pathology, Graduate School of Medical and Dental SciencesTokyo Medical and Dental University Tokyo Japan
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Oxidation of protein-bound methionine in Photofrin-photodynamic therapy-treated human tumor cells explored by methionine-containing peptide enrichment and quantitative proteomics approach. Sci Rep 2017; 7:1370. [PMID: 28465586 PMCID: PMC5431048 DOI: 10.1038/s41598-017-01409-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 03/28/2017] [Indexed: 11/08/2022] Open
Abstract
In Photofrin-mediated photodynamic therapy (PDT), cell fate can be modulated by the subcellular location of Photofrin. PDT triggers oxidative damage to target cells, including the methionine (Met) oxidation of proteins. Here, we developed a new Met-containing peptide enrichment protocol combined with SILAC-based quantitative proteomics, and used this approach to explore the global Met oxidation changes of proteins in PDT-treated epidermoid carcinoma A431 cells preloaded with Photofrin at the plasma membrane, ER/Golgi, or ubiquitously. We identified 431 Met-peptides corresponding to 302 proteins that underwent severe oxidation upon PDT and observed overrepresentation of proteins related to the cell surface, plasma membrane, ER, Golgi, and endosome under all three conditions. The most frequently oxidized Met-peptide sequence was "QAMXXMM-E/G/M-S/G-A/G/F-XG". We also identified several hundred potential Photofrin-binding proteins using affinity purification coupled with LC-MS/MS, and confirmed the bindings of EGFR and cathepsin D with Photofrin. The enzyme activities of both proteins were significantly reduced by Photofrin-PDT. Our results shed light on the global and site-specific changes in Met-peptide oxidation among cells undergoing Photofrin-PDT-mediated oxidative stress originating from distinct subcellular sites, and suggest numerous potential Photofrin-binding proteins. These findings provide new insight into the molecular targets through which Photofrin-PDT has diverse effects on target cells.
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Ohlendieck K. Proteomic identification of biomarkers of skeletal muscle disorders. Biomark Med 2013; 7:169-86. [PMID: 23387498 DOI: 10.2217/bmm.12.96] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Disease-specific biomarkers play a central diagnostic and therapeutic role in muscle pathology. Serum levels of a variety of muscle-derived enzymes are routinely used for the detection of muscle damage in diagnostic procedures, as well as for the monitoring of physical training status in sports medicine. Over the last few years, the systematic application of mass spectrometry-based proteomics for studying skeletal muscle degeneration has greatly expanded the range of muscle biomarkers, including new fiber-associated proteins involved in muscle transformation, muscular atrophy, muscular dystrophy, motor neuron disease, inclusion body myositis, myotonia, hypoxia, diabetes, obesity and sarcopenia of old age. These mass spectrometric studies have clearly established skeletal muscle proteomics as a reliable method for the identification of novel indicators of neuromuscular diseases.
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Affiliation(s)
- Kay Ohlendieck
- Muscle Biology Laboratory, Department of Biology, National University of Ireland, Maynooth, County Kildare, Ireland.
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Fu Z, Wang M, Everett A, Lakatta E, Van Eyk J. Can proteomics yield insight into aging aorta? Proteomics Clin Appl 2013; 7:477-89. [PMID: 23788441 DOI: 10.1002/prca.201200138] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 06/13/2013] [Accepted: 06/14/2013] [Indexed: 12/16/2022]
Abstract
The aging aorta exhibits structural and physiological changes that are reflected in the proteome of its component cells types. The advance in proteomic technologies has made it possible to analyze the quantity of proteins associated with the natural history of aortic aging. These alterations reflect the molecular and cellular mechanisms of aging and could provide an opportunity to predict vascular health. This paper focuses on whether discoveries stemming from the application of proteomic approaches of the intact aging aorta or vascular smooth muscle cells can provide useful insights. Although there have been limited studies to date, a number of interesting proteins have been identified that are closely associated with aging in the rat aorta. Such proteins, including milk fat globule-EGF factor 8, matrix metalloproteinase type-2, and vitronectin, could be used as indicators of vascular health, or even explored as therapeutic targets for aging-related vascular diseases.
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Affiliation(s)
- Zongming Fu
- Department of Pediatrics, The Johns Hopkins University, Baltimore, MD 21224, USA
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Abstract
Cellular aging is a fundamental biological process, and mass spectrometry-based proteomics has been widely used for the global identification of age-related changes in a variety of tissues. The proteomic profiling of senescent skeletal muscles has revealed a variety of alterations in proteins associated with the contractile apparatus, cell signaling, ion homeostasis, metabolism, and the cellular stress response. Here, we outline the two-dimensional gel electrophoretic separation and fluorescent labeling of the urea-soluble protein complement from aged diaphragm muscle. This chapter describes the various experimental steps involved in gel electrophoresis-based proteomics, including protein extraction, isoelectric focusing, slab gel electrophoresis, fluorescence labeling, image analysis, protein digestion, mass spectrometric identification of proteins and immunoblotting.
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Affiliation(s)
- Steven Carberry
- Department of Biology, National University of Ireland Maynooth, Maynooth, Kildare, Ireland
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Dunston CR, Choudhury K, Griffiths HR. Terminal galactose residues on transferrin are increased in midlife adults compared to young adults. Proteomics 2012; 12:3147-53. [DOI: 10.1002/pmic.201100506] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 07/20/2012] [Accepted: 07/30/2012] [Indexed: 12/14/2022]
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Wieser D, Papatheodorou I, Ziehm M, Thornton JM. Computational biology for ageing. Philos Trans R Soc Lond B Biol Sci 2011; 366:51-63. [PMID: 21115530 PMCID: PMC3001313 DOI: 10.1098/rstb.2010.0286] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
High-throughput genomic and proteomic technologies have generated a wealth of publicly available data on ageing. Easy access to these data, and their computational analysis, is of great importance in order to pinpoint the causes and effects of ageing. Here, we provide a description of the existing databases and computational tools on ageing that are available for researchers. We also describe the computational approaches to data interpretation in the field of ageing including gene expression, comparative and pathway analyses, and highlight the challenges for future developments. We review recent biological insights gained from applying bioinformatics methods to analyse and interpret ageing data in different organisms, tissues and conditions.
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Affiliation(s)
- Daniela Wieser
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
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Sharov VS, Dremina ES, Galeva NA, Gerstenecker GS, Li X, Dobrowsky RT, Stobaugh JF, Schöneich C. Fluorogenic Tagging of Peptide and Protein 3-Nitrotyrosine with 4-(Aminomethyl)-benzenesulfonic Acid for Quantitative Analysis of Protein Tyrosine Nitration. Chromatographia 2009; 71:37-53. [PMID: 20703364 DOI: 10.1365/s10337-009-1409-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Protein 3-nitrotyrosine (3-NT) has been recognized as an important biomarker of nitroxidative stress associated with inflammatory and degenerative diseases, and biological aging. Analysis of protein-bound 3-NT continues to represent a challenge since in vivo it frequently does not accumulate on proteins in amounts detectable by quantitative analytical methods. Here, we describe a novel approach of fluorescent tagging and quantitation of peptide-bound 3-NT residues based on the selective reduction to 3-AT followed by reaction with 4-(amino-methyl)benzenesulfonic acid (ABS) in the presence of K(3)Fe(CN)(6) to form a highly fluorescent 2-phenylbenzoxazole product. Synthetic 3-NT peptide (0.005-1 μM) upon reduction with 10 mM sodium dithionite and tagging with 2 mM ABS and 5 μM K(3)Fe(CN)(6) in 0.1 M Na(2)HPO(4) buffer (pH 9.0) was converted with yields >95% to a single fluorescent product incorporating two ABS molecules per 3-NT residue, with fluorescence excitation and emission maxima at 360 ± 2 and 490 ± 2 nm, respectively, and a quantum yield of 0.77 ± 0.08, based on reverse-phase LC with UV and fluorescence detection, fluorescence spectroscopy and LC-MS-MS analysis. This protocol was successfully tested for quantitative analysis of in vitro Tyr nitration in a model protein, rabbit muscle phosphorylase b, and in a complex mixture of proteins from C2C12 cultured cells exposed to peroxynitrite, with a detection limit of ca. 1 pmol 3-NT by fluorescence spectrometry, and an apparent LOD of 12 and 40 pmol for nitropeptides alone or in the presence of 100 μg digested cell proteins, respectively. LC-MS-MS analysis of ABS tagged peptides revealed that the fluorescent derivatives undergo efficient backbone fragmentations, allowing for sequence-specific characterization of protein Tyr nitration in proteomic studies. Fluorogenic tagging with ABS also can be instrumental for detection and visualization of protein 3-NT in LC and gel-based protein separations.
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Affiliation(s)
- Victor S Sharov
- Department of Pharmaceutical Chemistry, University of Kansas, 2095 Constant Avenue, Lawrence, KS 66047, USA
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Doran P, Donoghue P, O'Connell K, Gannon J, Ohlendieck K. Proteomics of skeletal muscle aging. Proteomics 2009; 9:989-1003. [DOI: 10.1002/pmic.200800365] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Wilson S, Mazzatti DJ. Current status and future prospects in the search for protein biomarkers of immunosenescence. Expert Rev Proteomics 2008; 5:561-9. [PMID: 18761467 DOI: 10.1586/14789450.5.4.561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Complex adaptations including changes in cellular redox status, the production of high levels of pro-inflammatory cytokines and alterations in immunity occur as the result of aging of the immune system (immunosenescence). These events are thought to underlie the progression of chronic degenerative diseases of aging, such as atherosclerosis, Type 2 diabetes and Alzheimer's disease. It is envisaged that identifying early biomarkers of immune aging would aid in identifying individuals at risk of age-related disease and would allow the discovery of novel intervention strategies. Proteomics has emerged as a rapidly expanding and innovative field, investigating protein expression, interaction and function at a global level. Several proteomic strategies, including use of mass spectrometry and non-mass spectrometry-based detection systems (including secondary antibody labeling with fluorescent tags) may be particularly advantageous in identifying biomarkers of immune health. Application of these approaches may identify factors that both contribute to (and define) age-dependent deregulation of the immune system.
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Affiliation(s)
- Steve Wilson
- Unilever Corporate Research, Colworth Park, Sharnbrook, Bedfordshire, MK44 1LQ, UK.
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O’Connell K, Doran P, Gannon J, Ohlendieck K. Lectin-based proteomic profiling of aged skeletal muscle: Decreased pyruvate kinase isozyme M1 exhibits drastically increased levels of N-glycosylation. Eur J Cell Biol 2008; 87:793-805. [DOI: 10.1016/j.ejcb.2008.04.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2008] [Revised: 04/10/2008] [Accepted: 04/21/2008] [Indexed: 12/24/2022] Open
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Münch D, Amdam GV, Wolschin F. Ageing in a eusocial insect: molecular and physiological characteristics of life span plasticity in the honey bee. Funct Ecol 2008; 22:407-421. [PMID: 18728759 DOI: 10.1111/j.1365-2435.2008.01419.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Commonly held views assume that ageing, or senescence, represents an inevitable, passive, and random decline in function that is strongly linked to chronological age. In recent years, genetic intervention of life span regulating pathways, for example, in Drosophila as well as case studies in non-classical animal models, have provided compelling evidence to challenge these views.Rather than comprehensively revisiting studies on the established genetic model systems of ageing, we here focus on an alternative model organism with a wild type (unselected genotype) characterized by a unique diversity in longevity - the honey bee.Honey bee (Apis mellifera) life span varies from a few weeks to more than 2 years. This plasticity is largely controlled by environmental factors. Thereby, although individuals are closely related genetically, distinct life histories can emerge as a function of social environmental change.Another remarkable feature of the honey bee is the occurrence of reverted behavioural ontogeny in the worker (female helper) caste. This behavioural peculiarity is associated with alterations in somatic maintenance functions that are indicative of reverted senescence. Thus, although intraspecific variation in organismal life span is not uncommon, the honey bee holds great promise for gaining insights into regulatory pathways that can shape the time-course of ageing by delaying, halting or even reversing processes of senescence. These aspects provide the setting of our review.We will highlight comparative findings from Drosophila melanogaster and Caenorhabditis elegans in particular, and focus on knowledge spanning from molecular- to behavioural-senescence to elucidate how the honey bee can contribute to novel insights into regulatory mechanisms that underlie plasticity and robustness or irreversibility in ageing.
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Affiliation(s)
- D Münch
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, N-1432 Aas, Norway
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