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Mass spectrometric immunoassays for discovery, screening and quantification of clinically relevant proteoforms. Bioanalysis 2016; 8:1623-1633. [PMID: 27396364 DOI: 10.4155/bio-2016-0060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Human proteins can exist as multiple proteoforms with potential diagnostic or prognostic significance. MS top-down approaches are ideally suited for proteoforms identification because there is no prerequisite for a priori knowledge of the specific proteoform. One such top-down approach, termed mass spectrometric immunoassay utilizes antibody-derivatized microcolumns for rapid and contained proteoforms isolation and detection via MALDI-TOF MS. The mass spectrometric immunoassay can also provide quantitative measurement of the proteoforms through inclusion of an internal reference standard into the analytical sample, serving as normalizer for all sample processing and data acquisition steps. Reviewed here are recent developments and results from the application of mass spectrometric immunoassays for discovery of clinical correlations of specific proteoforms for the protein biomarkers RANTES, retinol binding protein, serum amyloid A and apolipoprotein C-III.
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Dattilo S, Mancuso C, Koverech G, Di Mauro P, Ontario ML, Petralia CC, Petralia A, Maiolino L, Serra A, Calabrese EJ, Calabrese V. Heat shock proteins and hormesis in the diagnosis and treatment of neurodegenerative diseases. Immun Ageing 2015; 12:20. [PMID: 26543490 PMCID: PMC4634585 DOI: 10.1186/s12979-015-0046-8] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 10/15/2015] [Indexed: 12/16/2022]
Abstract
Modulation of endogenous cellular defense mechanisms via the vitagene system represents an innovative approach to therapeutic intervention in diseases causing chronic tissue damage, such as in neurodegeneration. The possibility of high-throughoutput screening using proteomic techniques, particularly redox proteomics, provide more comprehensive overview of the interaction of proteins, as well as the interplay among processes involved in neuroprotection. Here by introducing the hormetic dose response concept, the mechanistic foundations and applications to the field of neuroprotection, we discuss the emerging role of heat shock protein as prominent member of vitagene network in neuroprotection and redox proteomics as a tool for investigating redox modulation of stress responsive vitagenes. Hormetic mechanisms are reviewed as possibility of targeted therapeutic manipulation in a cell-, tissue- and/or pathway-specific manner at appropriate points in the neurodegenerative disease process.
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Affiliation(s)
- Sandro Dattilo
- />Department of Biomedical and Biotechnological Sciences, University of Catania, Via Andrea Doria, 95100 Catania, Italy
| | - Cesare Mancuso
- />Institute of Pharmacology, Catholic University School of Medicine, Rome, Italy
| | - Guido Koverech
- />Department of Biomedical and Biotechnological Sciences, University of Catania, Via Andrea Doria, 95100 Catania, Italy
| | - Paola Di Mauro
- />Department of Medical and Surgery Specialties, University of Catania, Catania, Italy
| | - Maria Laura Ontario
- />Department of Biomedical and Biotechnological Sciences, University of Catania, Via Andrea Doria, 95100 Catania, Italy
| | | | - Antonino Petralia
- />Department of Clinical and Experimental Medicine, School of Medicine, University of Catania, Catania, Italy
| | - Luigi Maiolino
- />Department of Medical and Surgery Specialties, University of Catania, Catania, Italy
| | - Agostino Serra
- />Department of Medical and Surgery Specialties, University of Catania, Catania, Italy
| | - Edward J. Calabrese
- />Environmental Health Sciences Division, School of Public Health, University of Massachusetts, Amherst, MA USA
| | - Vittorio Calabrese
- />Department of Biomedical and Biotechnological Sciences, University of Catania, Via Andrea Doria, 95100 Catania, Italy
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Calabrese V, Dattilo S, Petralia A, Parenti R, Pennisi M, Koverech G, Calabrese V, Graziano A, Monte I, Maiolino L, Ferreri T, Calabrese EJ. Analytical approaches to the diagnosis and treatment of aging and aging-related disease: redox status and proteomics. Free Radic Res 2015; 49:511-24. [PMID: 25824967 DOI: 10.3109/10715762.2015.1020799] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Basal levels of oxidants are indispensible for redox signaling to produce adaptive cellular responses such as vitagenes linked to cell survival; however, at higher levels, they are detrimental to cells, contributing to aging and to the pathogenesis of numerous age-related diseases. Aging is a complex systemic process and the major gap in aging research reminds the insufficient knowledge about pathways shifting from normal "healthy" aging to disease-associated pathological aging. The major complication of normal "healthy" aging is in fact the increasing risk of age-related diseases such as cardiovascular diseases, diabetes mellitus, and neurodegenerative pathologies that can adversely affect the quality of life in general, with enhanced incidences of comorbidities and mortality. In this context, global "omics" approaches may help to dissect and fully study the cellular and molecular mechanisms of aging and age-associated processes. The proteome, being more close to the phenotype than the transcriptome and more stable than the metabolome, represents the most promising "omics" field in aging research. In the present study, we exploit recent advances in the redox biology of aging and discuss the potential of proteomics approaches as innovative tools for monitoring at the proteome level the extent of protein oxidative insult and related modifications with the identification of targeted proteins.
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Affiliation(s)
- V Calabrese
- Department of Biomedical and Biotechnological Sciences, University of Catania , Catania , Italy
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Butterfield DA, Gu L, Di Domenico F, Robinson RAS. Mass spectrometry and redox proteomics: applications in disease. MASS SPECTROMETRY REVIEWS 2014; 33:277-301. [PMID: 24930952 DOI: 10.1002/mas.21374] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 02/07/2013] [Accepted: 02/07/2013] [Indexed: 06/03/2023]
Abstract
Proteomics techniques are continuously being developed to further understanding of biology and disease. Many of the pathways that are relevant to disease mechanisms rely on the identification of post-translational modifications (PTMs) such as phosphorylation, acetylation, and glycosylation. Much attention has also been focused on oxidative PTMs which include protein carbonyls, protein nitration, and the incorporation of fatty acids and advanced glycation products to amino acid side chains, amongst others. The introduction of these PTMs in the cell can occur due to the attack of reactive oxygen and nitrogen species (ROS and RNS, respectively) on proteins. ROS and RNS can be present as a result of normal metabolic processes as well as external factors such as UV radiation, disease, and environmental toxins. The imbalance of ROS and RNS with antioxidant cellular defenses leads to a state of oxidative stress, which has been implicated in many diseases. Redox proteomics techniques have been used to characterize oxidative PTMs that result as a part of normal cell signaling processes as well as oxidative stress conditions. This review highlights many of the redox proteomics techniques which are currently available for several oxidative PTMs and brings to the reader's attention the application of redox proteomics for understanding disease pathogenesis in neurodegenerative disorders and others such as cancer, kidney, and heart diseases.
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Affiliation(s)
- D Allan Butterfield
- Department of Chemistry, Center of Membrane Sciences, Sanders-Brown Center on Aging, University of Kentucky, Lexington, Kentucky, 40506
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Delineation of concentration ranges and longitudinal changes of human plasma protein variants. PLoS One 2014; 9:e100713. [PMID: 24955979 PMCID: PMC4067327 DOI: 10.1371/journal.pone.0100713] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 05/28/2014] [Indexed: 12/14/2022] Open
Abstract
Human protein diversity arises as a result of alternative splicing, single nucleotide polymorphisms (SNPs) and posttranslational modifications. Because of these processes, each protein can exists as multiple variants in vivo. Tailored strategies are needed to study these protein variants and understand their role in health and disease. In this work we utilized quantitative mass spectrometric immunoassays to determine the protein variants concentration of beta-2-microglobulin, cystatin C, retinol binding protein, and transthyretin, in a population of 500 healthy individuals. Additionally, we determined the longitudinal concentration changes for the protein variants from four individuals over a 6 month period. Along with the native forms of the four proteins, 13 posttranslationally modified variants and 7 SNP-derived variants were detected and their concentration determined. Correlations of the variants concentration with geographical origin, gender, and age of the individuals were also examined. This work represents an important step toward building a catalog of protein variants concentrations and examining their longitudinal changes.
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Wright P, Noirel J, Ow SY, Fazeli A. A review of current proteomics technologies with a survey on their widespread use in reproductive biology investigations. Theriogenology 2012; 77:738-765.e52. [DOI: 10.1016/j.theriogenology.2011.11.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 11/08/2011] [Accepted: 11/11/2011] [Indexed: 12/27/2022]
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Babaei-Jadidi R, Li N, Saadeddin A, Spencer-Dene B, Jandke A, Muhammad B, Ibrahim EE, Muraleedharan R, Abuzinadah M, Davis H, Lewis A, Watson S, Behrens A, Tomlinson I, Nateri AS. FBXW7 influences murine intestinal homeostasis and cancer, targeting Notch, Jun, and DEK for degradation. ACTA ACUST UNITED AC 2011; 208:295-312. [PMID: 21282377 PMCID: PMC3039859 DOI: 10.1084/jem.20100830] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The E3 ubiquitin ligase component FBXW7 modulates homeostasis and inhibits tumorigenesis in the murine intestine. The Fbxw7 (F-box/WD repeat–containing protein 7; also called CDC4, Sel10, Ago, and Fbw7) component of the SCF (Skp1/Cullin/F-box protein) E3 ubiquitin ligase complex acts as a tumor suppressor in several tissues and targets multiple transcriptional activators and protooncogenes for ubiquitin-mediated degradation. To understand Fbxw7 function in the murine intestine, in this study, we specifically deleted Fbxw7 in the murine gut using Villin-Cre (Fbxw7ΔG). In wild-type mice, loss of Fbxw7 in the gut altered homeostasis of the intestinal epithelium, resulted in elevated Notch and c-Jun expression, and induced development of adenomas at 9–10 mo of age. In the context of APC (adenomatous polyposis coli) deficiency (ApcMin/+ mice), loss of Fbxw7 accelerated intestinal tumorigenesis and death and promoted accumulation of β-catenin in adenomas at late but not early time points. At early time points, Fbxw7 mutant tumors showed accumulation of the DEK protooncogene. DEK expression promoted cell division and altered splicing of tropomyosin (TPM) RNA, which may also influence cell proliferation. DEK accumulation and altered TPM RNA splicing were also detected in FBXW7 mutant human colorectal tumor tissues. Given their reduced lifespan and increased incidence of intestinal tumors, ApcMin/+Fbxw7ΔG mice may be used for testing carcinogenicity and drug screening.
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Affiliation(s)
- Roya Babaei-Jadidi
- Division of Pre-Clinical Oncology, School of Clinical Sciences, University of Nottingham, Nottingham, England, UK
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Data processing pipelines for comprehensive profiling of proteomics samples by label-free LC–MS for biomarker discovery. Talanta 2011; 83:1209-24. [DOI: 10.1016/j.talanta.2010.10.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Revised: 10/18/2010] [Accepted: 10/21/2010] [Indexed: 01/30/2023]
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Woods AG, Sokolowska I, Yakubu R, Butkiewicz M, LaFleur M, Talbot C, Darie CC. Blue Native PAGE and Mass Spectrometry as an Approach for the Investigation of Stable and Transient Protein-Protein Interactions. ACS SYMPOSIUM SERIES 2011. [DOI: 10.1021/bk-2011-1083.ch012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Alisa G. Woods
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810
- These authors contributed equally to this work
| | - Izabela Sokolowska
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810
- These authors contributed equally to this work
| | - Rama Yakubu
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810
- These authors contributed equally to this work
| | - Melissa Butkiewicz
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810
- These authors contributed equally to this work
| | - Martin LaFleur
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810
- These authors contributed equally to this work
| | - Christopher Talbot
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810
- These authors contributed equally to this work
| | - Costel C. Darie
- Department of Chemistry & Biomolecular Science, Biochemistry & Proteomics Group, Clarkson University, 8 Clarkson Avenue, Potsdam, New York, 13699-5810
- These authors contributed equally to this work
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Zhao Z, Liu J, Wasinger VC, Malouf T, Nguyen-Khuong T, Walsh B, Willcox MD. Tear lipocalin is the predominant phosphoprotein in human tear fluid. Exp Eye Res 2010; 90:344-9. [DOI: 10.1016/j.exer.2009.11.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2009] [Revised: 11/19/2009] [Accepted: 11/23/2009] [Indexed: 10/20/2022]
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Baroli B. From natural bone grafts to tissue engineering therapeutics: Brainstorming on pharmaceutical formulative requirements and challenges. J Pharm Sci 2009; 98:1317-75. [PMID: 18729202 DOI: 10.1002/jps.21528] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Tissue engineering is an emerging multidisciplinary field of investigation focused on the regeneration of diseased or injured tissues through the delivery of appropriate molecular and mechanical signals. Therefore, bone tissue engineering covers all the attempts to reestablish a normal physiology or to speed up healing of bone in all musculoskeletal disorders and injuries that are lashing modern societies. This article attempts to give a pharmaceutical perspective on the production of engineered man-made bone grafts that are described as implantable tissue engineering therapeutics, and to highlight the importance of understanding bone composition and structure, as well as osteogenesis and bone healing processes, to improve the design and development of such implants. In addition, special emphasis is given to pharmaceutical aspects that are frequently minimized, but that, instead, may be useful for formulation developments and in vitro/in vivo correlations.
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Affiliation(s)
- Biancamaria Baroli
- Dip. Farmaco Chimico Tecnologico, Università di Cagliari, Via Ospedale, 72, 09124 Cagliari, Italy
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High-resolution mass spectrometry analysis of protein oxidations and resultant loss of function. Biochem Soc Trans 2008; 36:1037-44. [PMID: 18793185 DOI: 10.1042/bst0361037] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
MS, with or without pre-analysis peptide fractionation, can be used to decipher the residues on proteins where oxidative modifications caused by peroxynitrite, singlet oxygen or electrophilic lipids have occurred. Peroxynitrite nitrates tyrosine and tryptophan residues on the surface of actin. Singlet oxygen, formed by the interaction of UVA light with tryptophan, can oxidize neighbouring cysteine, histidine, methionine, tyrosine and tryptophan residues. Dose-response inactivation by 4HNE (4-hydroxynonenal) of hBAT (human bile acid CoA:amino acid N-acyltransferase) and CKBB (cytosolic brain isoform of creatine kinase) is associated with site-specific modifications. FT-ICR (Fourier-transform ion cyclotron resonance)-MS using nanoLC (nano-liquid chromatography)-ESI (electrospray ionization)-MS or direct-infusion ESI-MS with gas-phase fractionation identified 14 4HNE adducts on hBAT and 17 on CKBB respectively. At 4HNE concentrations in the physiological range, one member of the catalytic triad of hBAT (His362) was modified; for CKBB, although all four residues in the active site that were modifiable by 4HNE were ultimately modified, only one, Cys283, occurred at physiological concentrations of 4HNE. These results suggest that future in vivo studies should carefully assess the critical sites that are modified rather than using antibodies that do not distinguish between different modified sites.
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Ryckelynck M, A. Paulus C, Frugier M. Post-Translational Modifications Guard Yeast from Misaspartylation. Biochemistry 2008. [DOI: 10.1021/bi800931x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michaël Ryckelynck
- Architecture et Réactivité de l’ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg Cedex, France, and ISIS-ULP, Laboratoire de Biologie Chimique, 8 allée Gaspard Monge, BP 70028, 67083 Strasbourg Cedex, France
| | - Caroline A. Paulus
- Architecture et Réactivité de l’ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg Cedex, France, and ISIS-ULP, Laboratoire de Biologie Chimique, 8 allée Gaspard Monge, BP 70028, 67083 Strasbourg Cedex, France
| | - Magali Frugier
- Architecture et Réactivité de l’ARN, Université Louis Pasteur, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg Cedex, France, and ISIS-ULP, Laboratoire de Biologie Chimique, 8 allée Gaspard Monge, BP 70028, 67083 Strasbourg Cedex, France
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