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He B, Huang Z, Huang C, Nice EC. Clinical applications of plasma proteomics and peptidomics: Towards precision medicine. Proteomics Clin Appl 2022; 16:e2100097. [PMID: 35490333 DOI: 10.1002/prca.202100097] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 02/05/2023]
Abstract
In the context of precision medicine, disease treatment requires individualized strategies based on the underlying molecular characteristics to overcome therapeutic challenges posed by heterogeneity. For this purpose, it is essential to develop new biomarkers to diagnose, stratify, or possibly prevent diseases. Plasma is an available source of biomarkers that greatly reflects the physiological and pathological conditions of the body. An increasing number of studies are focusing on proteins and peptides, including many involving the Human Proteome Project (HPP) of the Human Proteome Organization (HUPO), and proteomics and peptidomics techniques are emerging as critical tools for developing novel precision medicine preventative measures. Excitingly, the emerging plasma proteomics and peptidomics toolbox exhibits a huge potential for studying pathogenesis of diseases (e.g., COVID-19 and cancer), identifying valuable biomarkers and improving clinical management. However, the enormous complexity and wide dynamic range of plasma proteins makes plasma proteome profiling challenging. Herein, we summarize the recent advances in plasma proteomics and peptidomics with a focus on their emerging roles in COVID-19 and cancer research, aiming to emphasize the significance of plasma proteomics and peptidomics in clinical applications and precision medicine.
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Affiliation(s)
- Bo He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China.,Department of Pharmacology, and Provincial Key Laboratory of Pathophysiology in Ningbo University School of Medicine, Ningbo, Zhejiang, China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
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Qin W, Wang T, Liu G, Sun L, Han W, Gao Y. Dynamic Urinary Proteome Changes in Ovalbumin-Induced Asthma Mouse Model Using Data-Independent Acquisition Proteomics. J Asthma Allergy 2021; 14:1355-1366. [PMID: 34785909 PMCID: PMC8590963 DOI: 10.2147/jaa.s330054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Accepted: 10/30/2021] [Indexed: 01/09/2023] Open
Abstract
Background In this work, we aim to investigate dynamic urinary proteome changes during asthma development and to identify potential urinary protein biomarkers for the diagnosis of asthma. Methods An ovalbumin (OVA)-induced mouse model was used to mimic asthma. The urinary proteome from asthma and control mice was determined using data-independent acquisition combined with high-resolution tandem mass spectrometry. Results Overall, 331 proteins were identified, among which 53 were differentially expressed (26, 24, 14 and 20 on days 2, 8, 15 and 18, respectively; 1.5-fold change, adjust P<0.05). Gene Ontology annotation of the differential proteins showed that the acute-phase response, innate immune response, B cell receptor signaling pathway, and complement activation were significantly enriched. Protein–protein interaction network revealed that these differential proteins were partially biologically connected in OVA-induced asthma, as a group. On days 2 and 8, after two episodes of OVA sensitization, six differential proteins (CRAMP, ECP, HP, F2, AGP1, and CFB) were also reported to be closely associated with asthma. These proteins may hold the potential for the early screening of asthma. On days 15 and 18, after challenged with 1% OVA by inhalation, seven differential proteins (VDBP, HP, CTSE, PIGR, AAT, TRFE, and HPX) were also reported to be closely associated with asthma. Thus, these proteins hold the potential to be biomarkers for the diagnosis of asthma attack. Conclusion Our results indicate that the urinary proteome could reflect dynamic pathophysiological changes in asthma progression.
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Affiliation(s)
- Weiwei Qin
- Department of Anesthesiology, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266071, People's Republic of China.,Department of Biochemistry and Molecular Biology, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Ting Wang
- Department of Biochemistry and Molecular Biology, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Guangwei Liu
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Institute of Cell Biology, College of Life Sciences, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Lixin Sun
- Department of Anesthesiology, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Wei Han
- Department of Respiratory Medicine, Qingdao Municipal Hospital, Qingdao University, Qingdao, 266071, People's Republic of China
| | - Youhe Gao
- Department of Biochemistry and Molecular Biology, Gene Engineering Drug and Biotechnology Beijing Key Laboratory, Beijing Normal University, Beijing, 100875, People's Republic of China
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Abstract
Peptides play a crucial role in many vitally important functions of living organisms. The goal of peptidomics is the identification of the "peptidome," the whole peptide content of a cell, organ, tissue, body fluid, or organism. In peptidomic or proteomic studies, capillary electrophoresis (CE) is an alternative technique for liquid chromatography. It is a highly efficient and fast separation method requiring extremely low amounts of sample. In peptidomic approaches, CE is commonly combined with mass spectrometric (MS) detection. Most often, CE is coupled with electrospray ionization MS and less frequently with matrix-assisted laser desorption/ionization MS. CE-MS has been employed in numerous studies dealing with determination of peptide biomarkers in different body fluids for various diseases, or in food peptidomic research for the analysis and identification of peptides with special biological activities. In addition to the above topics, sample preparation techniques commonly applied in peptidomics before CE separation and possibilities for peptide identification and quantification by CE-MS or CE-MS/MS methods are discussed in this chapter.
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González-Sálamo J, Varela-Martínez DA, González-Curbelo MÁ, Hernández-Borges J. The Role of Chromatographic and Electromigration Techniques in Foodomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1336:31-49. [PMID: 34628626 DOI: 10.1007/978-3-030-77252-9_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Foodomics is the discipline aimed at studying the prevention of diseases by food, identifying chemical, biological and biochemical food contaminants, determining changes in genetically modified foods, identifying biomarkers able to confirm the authenticity and quality of foods or studying the safety, quality and traceability of foods, among other issues. It is mainly based on the use of genomic, transcriptomic, proteomic and metabolomic tools, among others, in order to understand the effect of food on animals and humans at the level of genes, messenger ribonucleic acid, proteins and metabolites. Since the first definition of Foodomics, a reasonable number of works have shown the extremely high possibilities of this discipline, which is highly based on the use of advanced analytical hyphenated techniques - especially for proteomics and metabolomics. This book chapter aims at providing a general description of the role of chromatographic and electromigration techniques that are currently being applied to achieve the main objectives of Foodomics, particularly in the proteomic and metabolomic fields, since most published works have been focused on these approaches, and to highlight relevant applications.
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Affiliation(s)
- Javier González-Sálamo
- Departamento de Química, Unidad Departamental de Química Analítica, Facultad de Ciencias, Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain
| | - Diana Angélica Varela-Martínez
- Departamento de Química, Unidad Departamental de Química Analítica, Facultad de Ciencias, Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain.,Departamento de Ciencias Básicas, Facultad de Ingeniería, Universidad EAN, Bogotá D.C., Colombia
| | | | - Javier Hernández-Borges
- Departamento de Química, Unidad Departamental de Química Analítica, Facultad de Ciencias, Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain. .,Instituto Universitario de Enfermedades Tropicales y Salud Pública, Universidad de La Laguna (ULL), San Cristóbal de La Laguna, Spain.
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Vitorino R, Choudhury M, Guedes S, Ferreira R, Thongboonkerd V, Sharma L, Amado F, Srivastava S. Peptidomics and proteogenomics: background, challenges and future needs. Expert Rev Proteomics 2021; 18:643-659. [PMID: 34517741 DOI: 10.1080/14789450.2021.1980388] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION With available genomic data and related information, it is becoming possible to better highlight mutations or genomic alterations associated with a particular disease or disorder. The advent of high-throughput sequencing technologies has greatly advanced diagnostics, prognostics, and drug development. AREAS COVERED Peptidomics and proteogenomics are the two post-genomic technologies that enable the simultaneous study of peptides and proteins/transcripts/genes. Both technologies add a remarkably large amount of data to the pool of information on various peptides associated with gene mutations or genome remodeling. Literature search was performed in the PubMed database and is up to date. EXPERT OPINION This article lists various techniques used for peptidomic and proteogenomic analyses. It also explains various bioinformatics workflows developed to understand differentially expressed peptides/proteins and their role in disease pathogenesis. Their role in deciphering disease pathways, cancer research, and biomarker discovery using biofluids is highlighted. Finally, the challenges and future requirements to overcome the current limitations for their effective clinical use are also discussed.
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Affiliation(s)
- Rui Vitorino
- Faculdade de Medicina da Universidade do Porto, Porto, Portugal.,iBiMED, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.,Laqv/requimte, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Manisha Choudhury
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Powai, India
| | - Sofia Guedes
- Laqv/requimte, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Rita Ferreira
- Laqv/requimte, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Francisco Amado
- Laqv/requimte, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Powai, India
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Majerova P, Barath P, Michalicova A, Katina S, Novak M, Kovac A. Changes of Cerebrospinal Fluid Peptides due to Tauopathy. J Alzheimers Dis 2017; 58:507-520. [DOI: 10.3233/jad-170110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Petra Majerova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
- AXON Neuroscience R&D, Bratislava, Slovak Republic
| | - Peter Barath
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Alena Michalicova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
- AXON Neuroscience R&D, Bratislava, Slovak Republic
| | - Stanislav Katina
- AXON Neuroscience R&D, Bratislava, Slovak Republic
- Institute of Mathematics and Statistics, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michal Novak
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
- AXON Neuroscience R&D, Bratislava, Slovak Republic
| | - Andrej Kovac
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovak Republic
- AXON Neuroscience R&D, Bratislava, Slovak Republic
- Department of Pharmacology and Toxicology, The University of Veterinary Medicine and Pharmacy, Kosice, Slovak Republic
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Lombardo N, Preianò M, Maggisano G, Murfuni MS, Messina L, Pelaia G, Savino R, Terracciano R. A rapid differential display analysis of nasal swab fingerprints to distinguish allergic from non-allergic rhinitis subjects by mesoporous silica particles and MALDI-TOF mass spectrometry. Proteomics 2017; 17. [PMID: 28012241 DOI: 10.1002/pmic.201600215] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/01/2016] [Accepted: 12/19/2016] [Indexed: 12/13/2022]
Abstract
Discriminating different rhinitis cases can sometimes be difficult as the diagnostic criteria used to identify the various subgroups are not always unambiguous. The nasal fluid (NF) highly reflects the pathophysiology of these inflammatory diseases. However, its collection, as nasal lavage fluid, may cause discomfort. Due to the non-invasiveness and rapidity of collection, nasal swab might represent an alternative to overcome these problems and also an ideal source of biomarkers. In this study, we demonstrate that the combined use of mesoporous silica (MPS) with MALDI-TOF MS allows the rapid detection of differential nasal peptide profiles from nasal swabs of healthy (H), allergic rhinitis (AR) and non-allergic rhinitis (NAR) subjects. NF peptides from nasal swabs were captured by the mean of MPS then profiled by MALDI-TOF MS. As a proof-of-principle, we also explored the ability of our platform to discriminate between nasal swabs of patients with AR and NAR, and between these groups and H controls. Four peaks resulted differentially expressed between NAR and AR, two peaks discriminated AR from H while one peak segregated NAR from H group. Therefore, peptides selected and enriched by our platform could form a part of a diagnostic ''rhinomic'' profile of the allergic and non-allergic patients.
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Affiliation(s)
- Nicola Lombardo
- Department of Medical and Surgical Sciences, University "Magna Graecia", Catanzaro, Italy
| | - Mariaimmacolata Preianò
- Department of Health Sciences, Laboratory of Mass Spectrometry and Proteomics, University "Magna Graecia", Catanzaro, Italy
| | - Giuseppina Maggisano
- Department of Health Sciences, Laboratory of Mass Spectrometry and Proteomics, University "Magna Graecia", Catanzaro, Italy
| | - Maria Stella Murfuni
- Department of Health Sciences, Laboratory of Mass Spectrometry and Proteomics, University "Magna Graecia", Catanzaro, Italy
| | - Luigi Messina
- Department of Medical and Surgical Sciences, University "Magna Graecia", Catanzaro, Italy
| | - Girolamo Pelaia
- Department of Medical and Surgical Sciences, University "Magna Graecia", Catanzaro, Italy
| | - Rocco Savino
- Department of Health Sciences, Laboratory of Mass Spectrometry and Proteomics, University "Magna Graecia", Catanzaro, Italy
| | - Rosa Terracciano
- Department of Health Sciences, Laboratory of Mass Spectrometry and Proteomics, University "Magna Graecia", Catanzaro, Italy
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Kelly RS, Dahlin A, McGeachie MJ, Qiu W, Sordillo J, Wan ES, Wu AC, Lasky-Su J. Asthma Metabolomics and the Potential for Integrative Omics in Research and the Clinic. Chest 2016; 151:262-277. [PMID: 27776981 DOI: 10.1016/j.chest.2016.10.008] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 09/26/2016] [Accepted: 10/07/2016] [Indexed: 12/11/2022] Open
Abstract
Asthma is a complex disease well-suited to metabolomic profiling, both for the development of novel biomarkers and for the improved understanding of pathophysiology. In this review, we summarize the 21 existing metabolomic studies of asthma in humans, all of which reported significant findings and concluded that individual metabolites and metabolomic profiles measured in exhaled breath condensate, urine, plasma, and serum could identify people with asthma and asthma phenotypes with high discriminatory ability. There was considerable consistency across the studies in terms of the reported biomarkers, regardless of biospecimen, profiling technology, and population age. In particular, acetate, adenosine, alanine, hippurate, succinate, threonine, and trans-aconitate, and pathways relating to hypoxia response, oxidative stress, immunity, inflammation, lipid metabolism and the tricarboxylic acid cycle were all identified as significant in at least two studies. There were also a number of nonreplicated results; however, the literature is not yet sufficiently developed to determine whether these represent spurious findings or reflect the substantial heterogeneity and limited statistical power in the studies and their methods to date. This review highlights the need for additional asthma metabolomic studies to explore these issues, and, further, the need for standardized methods in the way these studies are conducted. We conclude by discussing the potential of translation of these metabolomic findings into clinically useful biomarkers and the crucial role that integrated omics is likely to play in this endeavor.
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Affiliation(s)
- Rachel S Kelly
- Channing Division of Network Medicine, Brigham Women's Hospital and Harvard Medical School, Boston, MA
| | - Amber Dahlin
- Channing Division of Network Medicine, Brigham Women's Hospital and Harvard Medical School, Boston, MA
| | - Michael J McGeachie
- Channing Division of Network Medicine, Brigham Women's Hospital and Harvard Medical School, Boston, MA
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham Women's Hospital and Harvard Medical School, Boston, MA
| | - Joanne Sordillo
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, MA
| | - Emily S Wan
- Channing Division of Network Medicine, Brigham Women's Hospital and Harvard Medical School, Boston, MA; VA Boston Healthcare System, Department of Veterans Affairs, Boston, MA
| | - Ann Chen Wu
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, MA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham Women's Hospital and Harvard Medical School, Boston, MA.
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Mani BM, Huerta-Ocampo JA, Garcia-Sanchez JR, Barrera-Pacheco A, de la Rosa APB, Teran LM. Identification of Ligustrum lucidum pollen allergens using a proteomics approach. Biochem Biophys Res Commun 2015; 468:788-92. [PMID: 26562528 DOI: 10.1016/j.bbrc.2015.11.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 11/05/2015] [Indexed: 10/22/2022]
Abstract
BACKGROUND Ligustrum spp. are members of the Oleaceae family, one of the most prominent allergic families worldwide. The genus Ligustrum contains approximately fifty species, including Ligustrum lucidum, which have been widely cultivated as ornamental plants, and its pollen is a source of inhalant allergens associated with respiratory allergic diseases. Little is known about the presence of allergenic proteins in L. lucidum. METHODS The L. lucidum pollen proteins were extracted by a modified phenolic extraction method. A pool of four sera from mono sensitive patients was analyzed by 2DE immunoblotting and mass spectrometric analysis was performed on 6 immunoreactive protein spots. RESULTS SDS-PAGE of L. lucidum pollen extract revealed proteins in ranges of 15-150 kDa. The 2DE gel profile of the L. lucidum pollen protein extract showed approximately 180 spots, and the 2DE immunoblots obtained using sera from Ligustrum monosensitive patients as the source of IgE antibodies revealed six allergen protein spots, corresponding to Profilin, Enolase, Fra e 9.01 (β-1,3-glucanase), Pollen-specific Polygalacturonases, Alanine aminotransferase, and two ATP synthase beta subunits. CONCLUSION We report for the first time the identification of IgE-reactive proteins from L. lucidum.
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Affiliation(s)
- Blessy Maruthukunnel Mani
- Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Casco de Santo Tomás, C.P.11340 México City, Mexico
| | - Jose Angel Huerta-Ocampo
- Centro de investigación en Alimentación y Desarrollo, A.C. Apartado Postal 1735, Hermosillo, Sonora, Mexico
| | - Jose Ruben Garcia-Sanchez
- Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Casco de Santo Tomás, C.P.11340 México City, Mexico
| | - Alberto Barrera-Pacheco
- División Biología Molecular, IPICyT, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, Col. Lomas 4a. Sección, 78216 San Luis Potosí, SLP, Mexico
| | - Ana Paulina Barba de la Rosa
- División Biología Molecular, IPICyT, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, Col. Lomas 4a. Sección, 78216 San Luis Potosí, SLP, Mexico
| | - Luis M Teran
- Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas", Calzada Tlalpan No. 4502, Sección XVI, C.P.14080 México City, Mexico.
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Viglio S, Stolk J, Iadarola P, Giuliano S, Luisetti M, Salvini R, Fumagalli M, Bardoni A. Respiratory Proteomics Today: Are Technological Advances for the Identification of Biomarker Signatures Catching up with Their Promise? A Critical Review of the Literature in the Decade 2004-2013. Proteomes 2014; 2:18-52. [PMID: 28250368 PMCID: PMC5302730 DOI: 10.3390/proteomes2010018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 01/08/2014] [Accepted: 01/10/2014] [Indexed: 01/14/2023] Open
Abstract
To improve the knowledge on a variety of severe disorders, research has moved from the analysis of individual proteins to the investigation of all proteins expressed by a tissue/organism. This global proteomic approach could prove very useful: (i) for investigating the biochemical pathways involved in disease; (ii) for generating hypotheses; or (iii) as a tool for the identification of proteins differentially expressed in response to the disease state. Proteomics has not been used yet in the field of respiratory research as extensively as in other fields, only a few reproducible and clinically applicable molecular markers, which can assist in diagnosis, having been currently identified. The continuous advances in both instrumentation and methodology, which enable sensitive and quantitative proteomic analyses in much smaller amounts of biological material than before, will hopefully promote the identification of new candidate biomarkers in this area. The aim of this report is to critically review the application over the decade 2004-2013 of very sophisticated technologies to the study of respiratory disorders. The observed changes in protein expression profiles from tissues/fluids of patients affected by pulmonary disorders opens the route for the identification of novel pathological mediators of these disorders.
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Affiliation(s)
- Simona Viglio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Via Taramelli 3/B, Pavia 27100, Italy.
| | - Jan Stolk
- Department of Pulmonology, Leiden University Medical Center, Leiden 2333, The Netherlands.
| | - Paolo Iadarola
- Department of Biology and Biotechnologies, Biochemistry Unit, University of Pavia, Via Taramelli 3/B, Pavia 27100, Italy.
| | - Serena Giuliano
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Via Taramelli 3/B, Pavia 27100, Italy.
- Faculty of Science "Parc Valrose", University of Nice "Sophia Antipolis", FRE 3472 CNRS, LP2M Nice, France.
| | - Maurizio Luisetti
- Department of Molecular Medicine, Division of Pneumology, University of Pavia & IRCCS Policlinico San Matteo, Via Taramelli 5, Pavia 27100, Italy.
| | - Roberta Salvini
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Via Taramelli 3/B, Pavia 27100, Italy.
| | - Marco Fumagalli
- Department of Biology and Biotechnologies, Biochemistry Unit, University of Pavia, Via Taramelli 3/B, Pavia 27100, Italy.
| | - Anna Bardoni
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Via Taramelli 3/B, Pavia 27100, Italy.
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Shahali Y, Sutra JP, Haddad I, Vinh J, Guilloux L, Peltre G, Sénéchal H, Poncet P. Proteomics of cypress pollen allergens using double and triple one-dimensional electrophoresis. Electrophoresis 2012; 33:462-9. [PMID: 22287175 DOI: 10.1002/elps.201100324] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Italian cypress (Cupressus sempervirens, Cups) pollen causes allergic diseases in inhabitants of many of the cities surrounding the Mediterranean basin. However, allergens of Cups pollen are still poorly known. We introduce here a novel proteomic approach based on double one-dimensional gel electrophoresis (D1-DE) as an alternative to the 2-DE immunoblot, for the specific IgE screening of allergenic proteins from pollen extracts. The sequential one-dimensional combination of IEF and SDS-PAGE associated with IgE immunoblotting allows a versatile multiplexed immunochemical analysis of selected groups of allergens by converting a single protein spot into an extended protein band. Moreover, the method appears to be valuable for MS/MS identification, without protein purification, of a new Cups pollen allergen at 43 kDa. D1-DE immunoblotting revealed that the prevalence of IgE sensitization to this allergen belonging to the polygalacturonase (PG) family was 70% in tested French allergic patients. In subsequent triple one-dimensional gel electrophoresis, the Cups pollen PG was shown to promote lectin-based protein-protein interactions. Therefore, D1-DE could be used in routine work as a convenient alternative to 2-DE immunoblotting for the simultaneous screening of allergenic components under identical experimental conditions, thereby saving considerable amounts of sera and allergen extracts.
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Racine J, Gerber V, Feutz MM, Riley CP, Adamec J, Swinburne JE, Couetil LL. Comparison of genomic and proteomic data in recurrent airway obstruction affected horses using Ingenuity Pathway Analysis®. BMC Vet Res 2011; 7:48. [PMID: 21843342 PMCID: PMC3174119 DOI: 10.1186/1746-6148-7-48] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Accepted: 08/15/2011] [Indexed: 11/19/2022] Open
Abstract
Background Recurrent airway obstruction (RAO) is a severe chronic respiratory disease affecting horses worldwide, though mostly in the Northern hemisphere. Environmental as well as genetic factors strongly influence the course and prognosis of the disease. Research has been focused on characterization of immunologic factors contributing to inflammatory responses, on genetic linkage analysis, and, more recently, on proteomic analysis of airway secretions from affected horses. The goal of this study was to investigate the interactions between eight candidate genes previously identified in a genetic linkage study and proteins expressed in bronchoalveolar lavage fluid (BALF) collected from healthy and RAO-affected horses. The analysis was carried out with Ingenuity Pathway Analysis® bioinformatics software. Results The gene with the greatest number of indirect interactions with the set of proteins identified is Interleukin 4 Receptor (IL-4R), whose protein has also been detected in BALF. Interleukin 21 receptor and chemokine (C-C motif) ligand 24 also showed a large number of interactions with the group of detected proteins. Protein products of other genes like that of SOCS5, revealed direct interactions with the IL-4R protein. The interacting proteins NOD2, RPS6KA5 and FOXP3 found in several pathways are reported regulators of the NFκB pathway. Conclusions The pathways generated with IL-4R highlight possible important intracellular signaling cascades implicating, for instance, NFκB. Furthermore, the proposed interaction between SOCS5 and IL-4R could explain how different genes can lead to identical clinical RAO phenotypes, as observed in two Swiss Warmblood half sibling families because these proteins interact upstream of an important cascade where they may act as a functional unit.
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Affiliation(s)
- Julien Racine
- Department of Clinical Veterinary Medicine, Vetsuisse-Faculty, University of Berne, Berne, Switzerland
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13
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Gutiérrez-Rodríguez A, Postigo I, Guisantes JA, Suñén E, Martínez J. Identification of allergens homologous to Alt a 1 from Stemphylium botryosum and Ulocladium botrytis. Med Mycol 2011; 49:892-6. [PMID: 21504377 DOI: 10.3109/13693786.2011.576350] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Several studies have demonstrated that proteins homologous to the Alt a 1 major allergen of Alternaria alternata are expressed in other members of the Pleosporaceae family. However, since no direct biochemical data have been reported concerning the presence of Alt a 1 allergen homologues capable of binding IgE in the excretion-secretion products of Stemphylium and Ulocladium, our objective was to explore their presence in Stemphylium botryosum and Ulocladium botrytis. S. botryosum and U. botrytis culture filtrate extracts were analyzed by two-dimensional (2D)-electrophoresis and 2D-immunoblotting using polyclonal rabbit antibodies raised against recombinant Alt a 1, as well as five human sera from patients allergic to Alternaria. Cross-reactivity immunoassays were performed by ImmunoCAP inhibition and 2D-immunoblotting inhibition. IgE-binding proteins recognized by the rabbit antiserum raised against Alt a 1, with apparent molecular weights of 17-18 kDa and isoelectric points of 4, were identified as Alt a 1-like proteins. Alt a 1 inhibited IgE-specific binding to the Alt a 1 homologues from S. botryosum and U. botrytis. In conclusion, it was demonstrated that allergens which are homologous to Alt a 1 are expressed in the excretory-secretory materials of the phylogenetically-related species S. botryosum and U. botrytis.
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Affiliation(s)
- Antonio Gutiérrez-Rodríguez
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country, Faculty of Pharmacy, Vitoria, Spain
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Haenen S, Vanoirbeek JAJ, De Vooght V, Maes E, Schoofs L, Nemery B, Hoet PHM, Clynen E. Proteome analysis of multiple compartments in a mouse model of chemical-induced asthma. J Proteome Res 2010; 9:5868-76. [PMID: 20860378 DOI: 10.1021/pr100638m] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Occupational asthma is the principal cause of work-related respiratory disease in the industrial world. Toluene-2,4-diisocyanate (TDI) is one of the most common respiratory sensitizers leading to occupational asthma. Using a mouse model of chemical-induced asthma, we explored proteome changes in multiple compartments of mice sensitized and challenged with TDI or acetone-olive oil (AOO; vehicle). Airway reactivity to methacholine and a bronchoalveolar lavage (BAL) cell count was assessed in treated and control mice, 1 day after challenge. Subsequently, two-dimensional differential gel electrophoresis (2D-DIGE) was performed on auricular lymph nodes, BAL, and serum comparing TDI-treated and vehicle-treated control mice. The differentially expressed proteins were identified by mass spectrometry and pathway analysis was performed. TDI-treated mice exhibit increased airway reactivity (2.6-fold increase) and a neutrophilic inflammation in the BAL fluid, compared to control mice. 2D-DIGE showed 53, 210, and 40 differentially expressed proteins in the auricular lymph nodes, BAL, and serum of TDI-treated versus vehicle-treated mice, respectively. Several of the identified proteins could be linked with inflammation, neutrophil chemotaxis, and/or oxidative stress. Physiologic and immunologic readouts of the asthmatic phenotype, such as inflammation, were confirmed in three compartments by several of the differentially expressed proteins via 2D-DIGE and computerized pathway analysis.
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Affiliation(s)
- Steven Haenen
- Katholieke Universiteit Leuven, Research Unit Lung Toxicology, 3000 Leuven, Belgium
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15
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Abstract
Proteomic approaches have already been successfully implemented in areas such as cancer research. Surprisingly, only a few proteomics analyses have been published reporting on the protein profiles associated with asthma. Although proteomics has its limitations and experimental challenges, it can successfully contribute to the understanding of a complex disease such as asthma. We have reviewed the current literature that has reported the use of proteomic techniques to identify proteins that may contribute to altered lung function in asthma. Only a few of these studies have used proteomic techniques on human tissues associated with asthma, while most research has been performed with animal models of asthma. Proteomic applications have been used as a complimentary technique to verify the suspected candidate proteins involved in asthma. In addition, novel proteins have been identified as potential therapeutic targets. Future collaboration between the different scientific disciplines using proteomic studies of animal models of asthma and confirmation of these findings in human tissues will significantly contribute to the understanding of the etiology of asthma and lead to the development of new therapeutic strategies for this highly prevalent disease.
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Affiliation(s)
- Annette Osei-Kumah
- Discipline of Obstetrics and Gynaecology, School of Paediatrics and Reproductive Health, University of Adelaide, SA 5005, Australia.
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Fens N, Zwinderman AH, van der Schee MP, de Nijs SB, Dijkers E, Roldaan AC, Cheung D, Bel EH, Sterk PJ. Exhaled breath profiling enables discrimination of chronic obstructive pulmonary disease and asthma. Am J Respir Crit Care Med 2009; 180:1076-82. [PMID: 19713445 DOI: 10.1164/rccm.200906-0939oc] [Citation(s) in RCA: 229] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Chronic obstructive pulmonary disease (COPD) and asthma can exhibit overlapping clinical features. Exhaled air contains volatile organic compounds (VOCs) that may qualify as noninvasive biomarkers. VOC profiles can be assessed using integrative analysis by electronic nose, resulting in exhaled molecular fingerprints (breathprints). OBJECTIVES We hypothesized that breathprints by electronic nose can discriminate patients with COPD and asthma. METHODS Ninety subjects participated in a cross-sectional study: 30 patients with COPD (age, 61.6 +/- 9.3 years; FEV(1), 1.72 +/- 0.69 L), 20 patients with asthma (age, 35.4 +/- 15.1 years; FEV(1) 3.32 +/- 0.86 L), 20 nonsmoking control subjects (age, 56.7 +/- 9.3 years; FEV(1), 3.44 +/- 0.76 L), and 20 smoking control subjects (age, 56.1 +/- 5.9 years; FEV(1), 3.58 +/- 0.78). After 5 minutes of tidal breathing through an inspiratory VOC filter, an expiratory vital capacity was collected in a Tedlar bag and sampled by electronic nose. Breathprints were analyzed by discriminant analysis on principal component reduction resulting in cross-validated accuracy values (accuracy). Repeatability and reproducibility were assessed by measuring samples in duplicate by two devices. MEASUREMENTS AND MAIN RESULTS Breathprints from patients with asthma were separated from patients with COPD (accuracy 96%; P < 0.001), from nonsmoking control subjects (accuracy, 95%; P < 0.001), and from smoking control subjects (accuracy, 92.5%; P < 0.001). Exhaled breath profiles of patients with COPD partially overlapped with those of asymptomatic smokers (accuracy, 66%; P = 0.006). Measurements were repeatable and reproducible. CONCLUSIONS Molecular profiling of exhaled air can distinguish patients with COPD and asthma and control subjects. Our data demonstrate a potential of electronic noses in the differential diagnosis of obstructive airway diseases and in the risk assessment in asymptomatic smokers. Clinical trial registered with www.trialregister.nl (NTR 1282).
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Affiliation(s)
- Niki Fens
- Department of Respiratory Medicine, F5-260, Academic Medical Centre, University of Amsterdam, P.O. Box 22700, Amsterdam NL-1100 DE, The Netherlands.
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Horgan RP, Clancy OH, Myers JE, Baker PN. An overview of proteomic and metabolomic technologies and their application to pregnancy research. BJOG 2008; 116:173-81. [DOI: 10.1111/j.1471-0528.2008.01997.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Hur GY, Choi GS, Sheen SS, Lee HY, Park HJ, Choi SJ, Ye YM, Park HS. Serum ferritin and transferrin levels as serologic markers of methylene diphenyl diisocyanate-induced occupational asthma. J Allergy Clin Immunol 2008; 122:774-780. [PMID: 19014769 DOI: 10.1016/j.jaci.2008.07.034] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Revised: 07/28/2008] [Accepted: 07/29/2008] [Indexed: 10/21/2022]
Abstract
BACKGROUND Although methylene diphenyl diisocyanate (MDI) may induce occupational asthma in the workplace, the pathogenic mechanisms are unclear. OBJECTIVES By using bronchoalveolar lavage fluid, we sought to identify proteins that were differentially expressed between subjects with MDI-induced occupational asthma (MDI-OA) and asymptomatic exposed controls (AECs). METHODS To find proteins that were differentially expressed between the MDI-OA and AEC groups, 2-dimensional electrophoresis was performed by using bronchoalveolar lavage fluid obtained from subjects after MDI-specific inhalation challenge. The selected protein spots were then identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The clinical relevance of the differentially expressed spots was compared by ELISA using sera from the MDI-OA/eosinophilic bronchitis, AEC, and unexposed healthy control groups. Receiver operating characteristic curves were then plotted, and the sensitivity and specificity were determined. RESULTS Twenty-three protein spots were identified that distinguished the subjects with MDI-OA from those in the AEC group. Among them, ferritin expression was downregulated whereas transferrin expression was upregulated in subjects with MDI-OA compared with AEC; these results were validated by ELISA using sera from the MDI-OA/EB and AEC groups. To identify subjects with MDI-OA, the optimal serum cutoff levels were 69.84 ng/mL for ferritin and 2.48 microg/mL for transferrin. When these 2 parameters were combined, the sensitivity was 71.43% and the specificity was 85.71%. CONCLUSION Serum ferritin and transferrin levels are associated with the phenotype of MDI-OA.
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Affiliation(s)
- Gyu-Young Hur
- Department of Allergy and Rheumatology, Ajou University School of Medicine, Suwon, South Korea
| | - Gil-Soon Choi
- Department of Allergy and Rheumatology, Ajou University School of Medicine, Suwon, South Korea
| | - Seung-Soo Sheen
- Pulmonary and Critical Care Medicine, Ajou University School of Medicine, Suwon, South Korea
| | - Hyun-Young Lee
- Department of Allergy and Rheumatology, Ajou University School of Medicine, Suwon, South Korea
| | - Han-Jung Park
- Department of Allergy and Rheumatology, Ajou University School of Medicine, Suwon, South Korea
| | - Sung-Jin Choi
- Department of Allergy and Rheumatology, Ajou University School of Medicine, Suwon, South Korea
| | - Young-Min Ye
- Department of Allergy and Rheumatology, Ajou University School of Medicine, Suwon, South Korea
| | - Hae-Sim Park
- Department of Allergy and Rheumatology, Ajou University School of Medicine, Suwon, South Korea.
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Wong WSF, Zhao J. Proteome analysis of chronically inflamed lungs in a mouse chronic asthma model. Int Arch Allergy Immunol 2008; 147:179-89. [PMID: 18594147 DOI: 10.1159/000142040] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2007] [Accepted: 03/07/2008] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Asthma is a chronic airway inflammatory disease characterized by airway wall remodeling. The mechanisms underlying airway remodeling in asthma are not fully understood. There is an urgent need to investigate global protein profiling of chronically inflamed lungs to identify novel pathogenic molecules and biomarkers for chronic asthma. In this study, we described the first differentially expressed proteome of lung tissue and bronchoalveolar lavage fluid from a mouse chronic asthma model. METHODS BALB/c mice sensitized to ovalbumin were challenged with ovalbumin aerosol 3 times per week for 8 weeks. The lung tissue and lavage fluid proteins were resolved by 2-dimensional gel electrophoresis, and differentially expressed proteins were identified by matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry. RESULTS Airway goblet cell hyperplasia, smooth muscle hyperplasia, subepithelial fibrosis, airway hyperresponsiveness, pulmonary inflammatory cell infiltration and elevated serum ovalbumin-specific IgE level were observed in our chronic asthma model. We have identified at least 100 protein spots that were differentially expressed in chronically inflamed lungs, and the identity of 66 protein spots was confirmed. CONCLUSIONS Many of these proteins, including cytoskeleton-related proteins, Ca2+-binding proteins and anti-oxidant proteins, may be related to the development of airway remodeling, and they should be evaluated further as potential therapeutic targets and biomarkers for chronic asthma.
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Affiliation(s)
- W S Fred Wong
- Department of Pharmacology, Yong Loo Ling School of Medicine, and Immunology Program, Center for Life Sciences, National University of Singapore, Singapore.
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Darewicz M, Dziuba J, Minkiewicz P. Celiac Disease—Background, Molecular, Bioinformatics and Analytical Aspects. FOOD REVIEWS INTERNATIONAL 2008. [DOI: 10.1080/87559120802089258] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Clynen E, Baggerman G, Husson SJ, Landuyt B, Schoofs L. Peptidomics in drug research. Expert Opin Drug Discov 2008; 3:425-40. [DOI: 10.1517/17460441.3.4.425] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Dragonieri S, Schot R, Mertens BJA, Le Cessie S, Gauw SA, Spanevello A, Resta O, Willard NP, Vink TJ, Rabe KF, Bel EH, Sterk PJ. An electronic nose in the discrimination of patients with asthma and controls. J Allergy Clin Immunol 2007; 120:856-62. [PMID: 17658592 DOI: 10.1016/j.jaci.2007.05.043] [Citation(s) in RCA: 273] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2007] [Revised: 05/24/2007] [Accepted: 05/29/2007] [Indexed: 12/22/2022]
Abstract
BACKGROUND Exhaled breath contains thousands of volatile organic compounds (VOCs) that could serve as biomarkers of lung disease. Electronic noses can distinguish VOC mixtures by pattern recognition. OBJECTIVE We hypothesized that an electronic nose can discriminate exhaled air of patients with asthma from healthy controls, and between patients with different disease severities. METHODS Ten young patients with mild asthma (25.1 +/- 5.9 years; FEV(1), 99.9 +/- 7.7% predicted), 10 young controls (26.8 +/- 6.4 years; FEV(1), 101.9 +/- 10.3), 10 older patients with severe asthma (49.5 +/- 12.0 years; FEV(1), 62.3 +/- 23.6), and 10 older controls (57.3 +/- 7.1 years; FEV(1), 108.3 +/- 14.7) joined a cross-sectional study with duplicate sampling of exhaled breath with an interval of 2 to 5 minutes. Subjects inspired VOC-filtered air by tidal breathing for 5 minutes, and a single expiratory vital capacity was collected into a Tedlar bag that was sampled by electronic nose (Cyranose 320) within 10 minutes. Smellprints were analyzed by linear discriminant analysis on principal component reduction. Cross-validation values (CVVs) were calculated. RESULTS Smellprints of patients with mild asthma were fully separated from young controls (CVV, 100%; Mahalanobis distance [M-distance], 5.32), and patients with severe asthma could be distinguished from old controls (CVV, 90%; M-distance, 2.77). Patients with mild and severe asthma could be less well discriminated (CVV, 65%; M-distance, 1.23), whereas the 2 control groups were indistinguishable (CVV, 50%; M-distance, 1.56). The duplicate samples replicated these results. CONCLUSION An electronic nose can discriminate exhaled breath of patients with asthma from controls but is less accurate in distinguishing asthma severities. CLINICAL IMPLICATION These findings warrant validation of electronic noses in diagnosing newly presented patients with asthma.
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Affiliation(s)
- Silvano Dragonieri
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
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Gupta MB, Seferovic MD, Liu S, Gratton RJ, Doherty-Kirby A, Lajoie GA, Han VKM. Altered proteome profiles in maternal plasma in pregnancies with fetal growth restriction. Clin Proteomics 2006. [DOI: 10.1007/bf02752499] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Abstract
Fetal growth restriction (FGR) affects 3–5% of pregnancies and is associated with increased perinatal morbidity and mortality. Currently, there is no reliable biochemical test to differentiate a pathological FGR from a nonpathological one. The objective of this study was to screen whole maternal plasma to identify differentially expressed relatively abundant proteins associated with FGR. We analyzed maternal plasma from FGR (n=28) and healthy (n=22) pregnancies using two-dimensional gel electrophoresis (2D-GE) followed by software image analysis. Three spots with molecular weight (Mr) 18 kDa corresponding to haptoglobin (hp) α2, as identified by LC-MS/MS and immunoblotting, showed differential expression patterns in FGR. The distribution of hp α2 variants in maternal plasma samples showed the hp α2 variant 1 was low in 72% of FGR, medium in 16%, whereas high in 12%. In comparison, hp α2 variant 1 was high in (41%) of controls, medium in 41%, and low in 18% of cases. Based on the software image analysis, the mean spot volume for hp α2 variant 1 was 0.12 (SD=0.18) for FGR compared to 0.26 (SD=0.19) for control (p=0.006). Given that hp turnover is indicative of its maturation process and is traceable in plasma by its dominant/suppressed variants, we propose that hp α2 is an important potential target for evaluation of its clinical and pathophysiological role and as a diagnostic biomarker in FGR.
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Magi B, Bargagli E, Bini L, Rottoli P. Proteome analysis of bronchoalveolar lavage in lung diseases. Proteomics 2006; 6:6354-69. [PMID: 17133372 DOI: 10.1002/pmic.200600303] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The proteomic approach is complementary to genomics and enables protein composition to be investigated under various clinical conditions. Its application to the study of bronchoalveolar lavage (BAL) is extremely promising. BAL proteomic studies were initially based on two-dimensional electrophoretic separation of complex protein samples and subsequent identification of proteins by different methods. With the techniques available today it is possible to attain many different research objectives. BAL proteomics can contribute to the identification of proteins in alveolar spaces with possible insights into pathogenesis and clinical application for diagnosis, prognosis and therapy. Many proteins with different functions have already been identified in BAL. Some could be biomarkers that need to be individually confirmed by correlation with clinical parameters and validation by other methods on larger cohorts of patients. The standardization of BAL sample preparation and processing for proteomic studies is an important goal that would promote and facilitate clinical applications. Here, we review the principal literature on BAL proteomic analysis applied to the study of lung diseases.
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Affiliation(s)
- Barbara Magi
- Department of Molecular Biology, University of Siena, Siena, Italy.
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Leszczynski D. The need for a new approach in studies of the biological effects of electromagnetic fields. Proteomics 2006; 6:4671-3. [PMID: 16933341 DOI: 10.1002/pmic.200690099] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Boot JD, Panzner P, Diamant Z. A critical appraisal of methods used in early clinical development of novel drugs for the treatment of asthma. Pulm Pharmacol Ther 2006; 20:201-19. [PMID: 16584905 DOI: 10.1016/j.pupt.2006.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Revised: 02/06/2006] [Accepted: 02/14/2006] [Indexed: 11/16/2022]
Abstract
Asthma is a heterogeneous disorder characterized by chronic airway inflammation, hyperresponsiveness and remodeling. Being the hallmark of asthma, airway inflammation has become the most important target for therapeutic agents. Consequently, during the past decade various semi-and non-invasive methods have been explored to sample the airway inflammation in asthma. In this review, we provide a practical overview of the current status of various sampling techniques including sputum induction, exhaled breath analysis, and bronchoprovocation tests (BPTs). We focus on their applicability for monitoring in clinical practice and in intervention trials in asthma.
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Affiliation(s)
- J D Boot
- Centre for Human Drug Research, Zernikedreef 10, 2333 CL Leiden, The Netherlands
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