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El-Sabawi B, Huang S, Tanriverdi K, Perry AS, Amancherla K, Jackson N, Hulsey J, Freedman JE, Shah R, Lindman BR. Capillary blood self-collection for high-throughput proteomics. Proteomics 2024; 24:e2300607. [PMID: 38783781 DOI: 10.1002/pmic.202300607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/09/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
In this study, we sought to compare protein concentrations obtained from a high-throughput proteomics platform (Olink) on samples collected using capillary blood self-collection (with the Tasso+ device) versus standard venipuncture (control). Blood collection was performed on 20 volunteers, including one sample obtained via venipuncture and two via capillary blood using the Tasso+ device. Tasso+ samples were stored at 2°C-8°C for 24-hs (Tasso-24) or 48-h (Tasso-48) prior to processing to simulate shipping times from a study participant's home. Proteomics were analyzed using Olink (384 Inflammatory Panel). Tasso+ blood collection was successful in 37/40 attempts. Of 230 proteins included in our analysis, Pearson correlations (r) and mean coefficient of variation (CV) between Tasso-24 or Tasso-48 versus venipuncture were variable. In the Tasso-24 analysis, 34 proteins (14.8%) had both a correlation r > 0.5 and CV < 0.20. In the Tasso-48 analysis, 68 proteins (29.6%) had a correlation r > 0.5 and CV < 0.20. Combining the Tasso-24 and Tasso-48 analyses, 26 (11.3%) proteins met these thresholds. We concluded that protein concentrations from Tasso+ samples processed 24-48 h after collection demonstrated wide technical variability and variable correlation with a venipuncture gold-standard. Use of home capillary blood self-collection for large-scale proteomics should be limited to select proteins with good agreement with venipuncture.
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Affiliation(s)
- Bassim El-Sabawi
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Shi Huang
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Kahraman Tanriverdi
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Andrew S Perry
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kaushik Amancherla
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Natalie Jackson
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Structural Heart and Valve Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jenna Hulsey
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Structural Heart and Valve Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jane E Freedman
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Ravi Shah
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Brian R Lindman
- Department of Medicine, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Structural Heart and Valve Center, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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2
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Lachén-Montes M, Mendizuri N, Ausín K, Pérez-Mediavilla A, Azkargorta M, Iloro I, Elortza F, Kondo H, Ohigashi I, Ferrer I, de la Torre R, Robledo P, Fernández-Irigoyen J, Santamaría E. Smelling the Dark Proteome: Functional Characterization of PITH Domain-Containing Protein 1 (C1orf128) in Olfactory Metabolism. J Proteome Res 2020; 19:4826-4843. [PMID: 33185454 DOI: 10.1021/acs.jproteome.0c00452] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Human Proteome Project (HPP) consortium aims to functionally characterize the dark proteome. On the basis of the relevance of olfaction in early neurodegeneration, we have analyzed the dark proteome using data mining in public resources and omics data sets derived from the human olfactory system. Multiple dark proteins localize at synaptic terminals and may be involved in amyloidopathies such as Alzheimer's disease (AD). We have characterized the dark PITH domain-containing protein 1 (PITHD1) in olfactory metabolism using bioinformatics, proteomics, in vitro and in vivo studies, and neuropathology. PITHD1-/- mice exhibit olfactory bulb (OB) proteome changes related to synaptic transmission, cognition, and memory. OB PITHD1 expression increases with age in wild-type (WT) mice and decreases in Tg2576 AD mice at late stages. The analysis across 6 neurological disorders reveals that olfactory tract (OT) PITHD1 is specifically upregulated in human AD. Stimulation of olfactory neuroepithelial (ON) cells with PITHD1 alters the ON phosphoproteome, modifies the proliferation rate, and induces a pro-inflammatory phenotype. This workflow applied by the Spanish C-HPP and Human Brain Proteome Project (HBPP) teams across the ON-OB-OT axis can be adapted as a guidance to decipher functional features of dark proteins. Data are available via ProteomeXchange with identifiers PXD018784 and PXD021634.
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Affiliation(s)
- Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
| | - Naroa Mendizuri
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
| | - Karina Ausín
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
| | - Alberto Pérez-Mediavilla
- IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain.,Neurobiology of Alzheimer's Disease, Department of Biochemistry, Center for Applied Medical Research (CIMA), Neurosciences Division, University of Navarra, 31008 Pamplona, Spain
| | - Mikel Azkargorta
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Ibon Iloro
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Felix Elortza
- Proteomics Platform, CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Hiroyuki Kondo
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, Tokushima University, Tokushima 770-8503, Japan
| | - Isidre Ferrer
- Bellvitge Biomedical Research Institute (IDIBELL), 08908 Hospitalet de Llobregat, Spain.,CIBERNED (Network Centre of Biomedical Research of Neurodegenerative Diseases), Institute of Health Carlos III, 28029 Madrid, Spain.,Department of Pathology and Experimental Therapeutics, University of Barcelona, 08908 Hospitalet de Llobregat, Spain.,Institute of Neurosciences, University of Barcelona, 08007 Barcelona, Spain
| | - Rafael de la Torre
- Integrative Pharmacology and Systems Neuroscience Research Group, Neurosciences Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain.,Department of Experimental and Health Sciences, Pompeu Fabra University (CEXS-UPF), 08002 Barcelona, Spain.,School of Medicine, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.,CIBER de Fisiopatología de la Obesidad y Nutrición (CB06/03), CIBEROBN, 28029 Madrid, Spain
| | - Patricia Robledo
- Integrative Pharmacology and Systems Neuroscience Research Group, Neurosciences Research Program, IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain.,Department of Experimental and Health Sciences, Pompeu Fabra University (CEXS-UPF), 08002 Barcelona, Spain
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,Proteored-ISCIII, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), Irunlarrea 3, 31008 Pamplona, Spain.,IdiSNA, Navarra Institute for Health Research, Irunlarrea 3, 31008 Pamplona, Spain
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3
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Ijichi C, Wakabayashi H, Sugiyama S, Ihara Y, Nogi Y, Nagashima A, Ihara S, Niimura Y, Shimizu Y, Kondo K, Touhara K. Metabolism of Odorant Molecules in Human Nasal/Oral Cavity Affects the Odorant Perception. Chem Senses 2020; 44:465-481. [PMID: 31254383 DOI: 10.1093/chemse/bjz041] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In this study, we examined the mode of metabolism of food odorant molecules in the human nasal/oral cavity in vitro and in vivo. We selected 4 odorants, 2-furfurylthiol (2-FT), hexanal, benzyl acetate, and methyl raspberry ketone, which are potentially important for designing food flavors. In vitro metabolic assays of odorants with saliva/nasal mucus analyzed by gas chromatography mass spectrometry revealed that human saliva and nasal mucus exhibit the following 3 enzymatic activities: (i) methylation of 2-FT into furfuryl methylsulfide (FMS); (ii) reduction of hexanal into hexanol; and (iii) hydrolysis of benzyl acetate into benzyl alcohol. However, (iv) demethylation of methyl raspberry ketone was not observed. Real-time in vivo analysis using proton transfer reaction-mass spectrometry demonstrated that the application of 2-FT and hexanal through 3 different pathways via the nostril or through the mouth generated the metabolites FMS and hexanol within a few seconds. The concentration of FMS and hexanol in the exhaled air was above the perception threshold. A cross-adaptation study based on the activation pattern of human odorant receptors suggested that this metabolism affects odor perception. These results suggest that some odorants in food are metabolized in the human nasal mucus/saliva, and the resulting metabolites are perceived as part of the odor quality of the substrates. Our results help improve the understanding of the mechanism of food odor perception and may enable improved design and development of foods in relation to odor.
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Affiliation(s)
- Chiori Ijichi
- Chemosensory Research Group, Technology Development Center, Institute of Food Science and Technologies, Food Products Division, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Hidehiko Wakabayashi
- Taste & Flavor Technology Group, Technology Development Center, Institute of Food Sciences and Technologies, Food Products Division, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Shingo Sugiyama
- Taste & Flavor Technology Group, Technology Development Center, Institute of Food Sciences and Technologies, Food Products Division, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Yusuke Ihara
- Chemosensory Research Group, Technology Development Center, Institute of Food Science and Technologies, Food Products Division, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Yasuko Nogi
- Chemosensory Research Group, Technology Development Center, Institute of Food Science and Technologies, Food Products Division, Ajinomoto Co., Inc., Kawasaki, Japan
| | - Ayumi Nagashima
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,ERATO Touhara Chemosensory Signal Project, JST, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Sayoko Ihara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,ERATO Touhara Chemosensory Signal Project, JST, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yoshihito Niimura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,ERATO Touhara Chemosensory Signal Project, JST, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yuya Shimizu
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kenji Kondo
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kazushige Touhara
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.,ERATO Touhara Chemosensory Signal Project, JST, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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4
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Ali N, Ljunggren S, Karlsson HM, Wierzbicka A, Pagels J, Isaxon C, Gudmundsson A, Rissler J, Nielsen J, Lindh CH, Kåredal M. Comprehensive proteome analysis of nasal lavage samples after controlled exposure to welding nanoparticles shows an induced acute phase and a nuclear receptor, LXR/RXR, activation that influence the status of the extracellular matrix. Clin Proteomics 2018; 15:20. [PMID: 29760600 PMCID: PMC5946400 DOI: 10.1186/s12014-018-9196-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 05/02/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Epidemiological studies have shown that many welders experience respiratory symptoms. During the welding process a large number of airborne nanosized particles are generated, which might be inhaled and deposited in the respiratory tract. Knowledge of the underlying mechanisms behind observed symptoms is still partly lacking, although inflammation is suggested to play a central role. The aim of this study was to investigate the effects of welding fume particle exposure on the proteome expression level in welders suffering from respiratory symptoms, and changes in protein mediators in nasal lavage samples were analyzed. Such mediators will be helpful to clarify the pathomechanisms behind welding fume particle-induced effects. METHODS In an exposure chamber, 11 welders with work-related symptoms in the lower airways during the last month were exposed to mild-steel welding fume particles (1 mg/m3) and to filtered air, respectively, in a double-blind manner. Nasal lavage samples were collected before, immediately after, and the day after exposure. The proteins in the nasal lavage were analyzed with two different mass spectrometry approaches, label-free discovery shotgun LC-MS/MS and a targeted selected reaction monitoring LC-MS/MS analyzing 130 proteins and four in vivo peptide degradation products. RESULTS The analysis revealed 30 significantly changed proteins that were associated with two main pathways; activation of acute phase response signaling and activation of LXR/RXR, which is a nuclear receptor family involved in lipid signaling. Connective tissue proteins and proteins controlling the degradation of such tissues, including two different matrix metalloprotease proteins, MMP8 and MMP9, were among the significantly changed enzymes and were identified as important key players in the pathways. CONCLUSION Exposure to mild-steel welding fume particles causes measurable changes on the proteome level in nasal lavage matrix in exposed welders, although no clinical symptoms were manifested. The results suggested that the exposure causes an immediate effect on the proteome level involving acute phase proteins and mediators regulating lipid signaling. Proteases involved in maintaining the balance between the formation and degradation of extracellular matrix proteins are important key proteins in the induced effects.
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Affiliation(s)
- Neserin Ali
- Division of Occupational and Environmental Medicine, Lund University, Lund, Sweden
| | - Stefan Ljunggren
- Occupational and Environmental Medicine Center, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Helen M. Karlsson
- Occupational and Environmental Medicine Center, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Aneta Wierzbicka
- Department of Design Sciences, Ergonomics and Aerosol Technology, Lund University, Lund, Sweden
| | - Joakim Pagels
- Department of Design Sciences, Ergonomics and Aerosol Technology, Lund University, Lund, Sweden
| | - Christina Isaxon
- Department of Design Sciences, Ergonomics and Aerosol Technology, Lund University, Lund, Sweden
| | - Anders Gudmundsson
- Department of Design Sciences, Ergonomics and Aerosol Technology, Lund University, Lund, Sweden
| | - Jenny Rissler
- Department of Design Sciences, Ergonomics and Aerosol Technology, Lund University, Lund, Sweden
| | - Jörn Nielsen
- Division of Occupational and Environmental Medicine, Lund University, Lund, Sweden
| | - Christian H. Lindh
- Division of Occupational and Environmental Medicine, Lund University, Lund, Sweden
| | - Monica Kåredal
- Division of Occupational and Environmental Medicine, Lund University, Lund, Sweden
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5
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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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6
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Shi T, Song E, Nie S, Rodland KD, Liu T, Qian WJ, Smith RD. Advances in targeted proteomics and applications to biomedical research. Proteomics 2016; 16:2160-82. [PMID: 27302376 PMCID: PMC5051956 DOI: 10.1002/pmic.201500449] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 05/09/2016] [Accepted: 06/10/2016] [Indexed: 12/17/2022]
Abstract
Targeted proteomics technique has emerged as a powerful protein quantification tool in systems biology, biomedical research, and increasing for clinical applications. The most widely used targeted proteomics approach, selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), can be used for quantification of cellular signaling networks and preclinical verification of candidate protein biomarkers. As an extension to our previous review on advances in SRM sensitivity (Shi et al., Proteomics, 12, 1074-1092, 2012) herein we review recent advances in the method and technology for further enhancing SRM sensitivity (from 2012 to present), and highlighting its broad biomedical applications in human bodily fluids, tissue and cell lines. Furthermore, we also review two recently introduced targeted proteomics approaches, parallel reaction monitoring (PRM) and data-independent acquisition (DIA) with targeted data extraction on fast scanning high-resolution accurate-mass (HR/AM) instruments. Such HR/AM targeted quantification with monitoring all target product ions addresses SRM limitations effectively in specificity and multiplexing; whereas when compared to SRM, PRM and DIA are still in the infancy with a limited number of applications. Thus, for HR/AM targeted quantification we focus our discussion on method development, data processing and analysis, and its advantages and limitations in targeted proteomics. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale quantification of hundreds of target proteins are discussed.
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Affiliation(s)
- Tujin Shi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ehwang Song
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Song Nie
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karin D Rodland
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tao Liu
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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7
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Lachén-Montes M, Fernández-Irigoyen J, Santamaría E. Deconstructing the molecular architecture of olfactory areas using proteomics. Proteomics Clin Appl 2016; 10:1178-1190. [PMID: 27226001 DOI: 10.1002/prca.201500147] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 05/02/2016] [Accepted: 05/22/2016] [Indexed: 11/07/2022]
Abstract
The anatomy of the olfactory system is highly complex, comprising a system of olfactory receptors, pathways for the transmission of olfactory information, and structures for the recognition, discrimination, and memorization of odors. During the last years, proteomics has emerged as a large-scale comprehensive approach to characterize and quantify specific olfactory-related proteomes in different biological conditions such as olfactory learning, neurodegeneration, and ageing between others. The current work reviews recent applications of proteomics to olfaction with particular focus on quantitative proteome profiling studies performed on olfactory areas from laboratory animal models as well as proteomic characterizations performed on specific brain structures and fluids involved in human smell. Finally, we will also discuss the potential application of proteomics to study global proteome dynamics and posttranslationally modified proteomes in order to unravel cell-signaling networks that occur from peripheral structures to olfactory cortical areas during odor processing.
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Affiliation(s)
- Mercedes Lachén-Montes
- Clinical Neuroproteomics Group, Navarrabiomed, Instituto de investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Group, Navarrabiomed, Instituto de investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain.,Proteomics Unit, Navarrabiomed, Proteored-ISCIII, Instituto de investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Group, Navarrabiomed, Instituto de investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain.,Proteomics Unit, Navarrabiomed, Proteored-ISCIII, Instituto de investigación Sanitaria de Navarra (IdiSNA), Pamplona, Spain
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8
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Ali N, Mattsson K, Rissler J, Karlsson HM, Svensson CR, Gudmundsson A, Lindh CH, Jönsson BAG, Cedervall T, Kåredal M. Analysis of nanoparticle-protein coronas formed in vitro between nanosized welding particles and nasal lavage proteins. Nanotoxicology 2015; 10:226-34. [PMID: 26186033 PMCID: PMC4819849 DOI: 10.3109/17435390.2015.1048324] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 12/21/2014] [Accepted: 04/09/2015] [Indexed: 11/13/2022]
Abstract
Welding fumes include agglomerated particles built up of primary nanoparticles. Particles inhaled through the nose will to some extent be deposited in the protein-rich nasal mucosa, and a protein corona will be formed around the particles. The aim was to identify the protein corona formed between nasal lavage proteins and four types of particles with different parameters. Two of the particles were formed and collected during welding and two were manufactured iron oxides. When nasal lavage proteins were added to the particles, differences were observed in the sizes of the aggregates that were formed. Measurements showed that the amount of protein bound to particles correlated with the relative size increase of the aggregates, suggesting that the surface area was associated with the binding capacity. However, differences in aggregate sizes were detected when nasal proteins were added to UFWF and Fe2O3 particles (having similar agglomerated size) suggesting that yet parameters other than size determine the binding. Relative quantitative mass spectrometric and gel-based analyses showed differences in the protein content of the coronas. High-affinity proteins were further assessed for network interactions. Additional experiments showed that the inhibitory function of secretory leukocyte peptidase inhibitor, a highly abundant nasal protein, was influenced by particle binding suggesting that an understanding of protein function following particle binding is necessary to properly evaluate pathophysiological events. Our results underscore the importance of including particles collected from real working environments when studying the toxic effects of particles because these effects might be mediated by the protein corona.
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Affiliation(s)
- Neserin Ali
- Division of Occupational and Environmental Medicine, Lund University,
Lund,
Sweden
| | - Karin Mattsson
- Center for Molecular Protein Science, Biochemistry and Structural Biology, Lund University,
Lund,
Sweden
| | - Jenny Rissler
- Department of Design Sciences, Ergonomic and Aerosol Technology, Lund University,
Lund,
Sweden
| | - Helen Marg Karlsson
- Occupational and Environmental Medicine, County Council of Östergötland, Linköping University,
Linköping,
Sweden
| | - Christian R. Svensson
- Department of Design Sciences, Ergonomic and Aerosol Technology, Lund University,
Lund,
Sweden
| | - Anders Gudmundsson
- Department of Design Sciences, Ergonomic and Aerosol Technology, Lund University,
Lund,
Sweden
| | - Christian H. Lindh
- Division of Occupational and Environmental Medicine, Lund University,
Lund,
Sweden
| | - Bo A. G. Jönsson
- Division of Occupational and Environmental Medicine, Lund University,
Lund,
Sweden
| | - Tommy Cedervall
- Center for Molecular Protein Science, Biochemistry and Structural Biology, Lund University,
Lund,
Sweden
| | - Monica Kåredal
- Division of Occupational and Environmental Medicine, Lund University,
Lund,
Sweden
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Schoenebeck B, May C, Güldner C, Respondek G, Mollenhauer B, Hoeglinger G, Meyer HE, Marcus K. Improved preparation of nasal lavage fluid (NLF) as a noninvasive sample for proteomic biomarker discovery. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:741-5. [PMID: 25680929 DOI: 10.1016/j.bbapap.2015.01.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 01/21/2015] [Accepted: 01/26/2015] [Indexed: 10/24/2022]
Abstract
UNLABELLED Nasal lavage fluid (NLF) becomes more and more important as a noninvasive patient sample serving as a new opportunity to discover new biomarkers in diverse human diseases comprising mainly respiratory disorders. This was supported by the observation that the protein profile of NLF differs from conventional samples of i.e. whole blood, hence being capable to complement or even expand the so far biomarker index. Since sample acquisition and processing are the most crucial steps for a profound and sensitive identification we present here a modified protocol of NLF generation and measurement. We show that mild washing steps for sample generation followed by column-mediated concentration and acetone precipitation are appropriate steps to minimize serum leakage by concomitantly highlighting proteins which represent typical components of NLF. This is shown by separation of proteins via 2D-PAGE followed by LC-MS/MS as well as Gel-LC-MS/MS measurements of cut and digested protein spots/bands. SIGNIFICANCE For a better understanding of the molecular mechanisms underlying respiratory diseases NLF samples are favored sources for protein research. NLF acquisition and sample processing were impaired so far by the problem of blood serum leakage and high salt content. Here, we present a modified protocol of NLF generation leading to the display of typical inventory of NLF proteins combined with reduced salt and serum contaminants. By this, both assay reproducibility and the detection of up- or down-regulated proteins reliably can be discovered in the case of biomarker screenings in a disease versus control design. This article is part of a Special Issue entitled: Neuroproteomics: Applications in Neuroscience and Neurology.
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Affiliation(s)
- Bodo Schoenebeck
- Abteilung für Neuroanatomie und Molekulare Hirnforschung, Medizinische Fakultaet, Ruhr-Universitaet Bochum, 44801 Bochum, Germany
| | - Caroline May
- Abteilung für Medizinische Proteomik/Bioanalytik, Medizinisches Proteom-Center, Ruhr-Universitaet Bochum, 44801 Bochum, Germany
| | - Christian Güldner
- Department of Otolaryngology, Phillips Universität, Marburg, Germany
| | - Gesine Respondek
- Department of Neurology, Technische Universität München, Munich, Germany and German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | | | - Guenter Hoeglinger
- Lehrstuhl für Translationale Neurodegeneration, Technische Universität München, Germany; Deutsches Zentrum für Neurodegenerative Erkrankungen, 81377 München, Germany
| | - Helmut E Meyer
- Leibniz-Institut für Analytische Wissenschaften -ISAS- e.V., Dortmund, Germany
| | - Katrin Marcus
- Abteilung für Funktionelle Proteomik, Medizinisches Proteom-Center, Ruhr-Universitaet Bochum, 44801 Bochum, Germany.
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10
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Mörtstedt H, Ali N, Kåredal M, Jacobsson H, Rietz E, Diab KK, Nielsen J, Jönsson BAG, Lindh CH. Targeted proteomic analyses of nasal lavage fluid in persulfate-challenged hairdressers with bleaching powder-associated rhinitis. J Proteome Res 2015; 14:860-73. [PMID: 25546367 DOI: 10.1021/pr5009306] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Hairdressers have an increased risk for developing airway symptoms, for example, asthma and rhinitis. Persulfates, which are oxidizing agents in bleaching powder, are considered important causal agents for these symptoms. However, the underlying mechanisms are unclear. The aim was therefore to measure proteomic changes in nasal lavage fluid from persulfate-challenged subjects to identify proteins potentially involved in the pathogenesis of bleaching powder-associated rhinitis or candidate effect biomarkers for persulfate. Also, oxidized peptides were measured to evaluate their usefulness as biomarkers for persulfate exposure or effect, for example, oxidative stress. Samples from hairdressers with and without bleaching powder-associated rhinitis were analyzed with liquid chromatography tandem mass spectrometry using selected reaction monitoring to target 246 proteins and five oxidized peptides. Pathway analysis was applied to obtain a functional overview of the proteins. Several proteins involved in biologically meaningful pathways, functions, or disorders, for example, inflammatory responses, oxidative stress, epithelium integrity, and dermatological disorders, changed after the persulfate challenge. A list with nine proteins that appeared to be affected by the persulfate challenge and should be followed up was defined. An albumin peptide containing oxidized tryptophan increased 2 h and 5 h after the challenge but not after 20 min, which indicates that such peptides may be useful as oxidative stress biomarkers.
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Affiliation(s)
- Harriet Mörtstedt
- Division of Occupational and Environmental Medicine, Department of Laboratory Medicine, Lund University , SE-221 85 Lund, Sweden
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11
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Teran LM, Montes-Vizuet R, Li X, Franz T. Respiratory proteomics: from descriptive studies to personalized medicine. J Proteome Res 2014; 14:38-50. [PMID: 25382407 DOI: 10.1021/pr500935s] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Respiratory diseases are highly prevalent and affect humankind worldwide, causing extensive morbidity and mortality with the environment playing an important role. Given the complex structure of the airways, sophisticated tools are required for early diagnosis; initial symptoms are nonspecific, and the clinical diagnosis is made frequently late. Over the past few years, proteomics has made high technological progress in mass-spectrometry-based protein identification and has allowed us to gain new insights into disease mechanisms and identify potential novel therapeutic targets. This review will highlight the contributions of proteomics toward the understanding of the respiratory proteome listing potential biomarkers and its potential application to the clinic. We also outline the contributions of proteomics to creating a personalized approach in respiratory medicine.
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Affiliation(s)
- Luis M Teran
- Instituto Nacional de Enfermedades Respiratorias , Calz. de Tlalpan 4502, Distrito Federal 14080, Mexico
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12
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Tomazic PV, Birner-Gruenberger R, Leitner A, Darnhofer B, Spoerk S, Lang-Loidolt D. Apolipoproteins have a potential role in nasal mucus of allergic rhinitis patients: a proteomic study. Laryngoscope 2014; 125:E91-6. [PMID: 25363381 DOI: 10.1002/lary.25003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2014] [Indexed: 11/11/2022]
Abstract
OBJECTIVES/HYPOTHESIS Nasal mucus is a defense barrier against aeroallergens. We recently found apolipoproteins to be elevated in the nasal mucus of allergic rhinitis patients. Apolipoproteins are involved in lipid metabolism, have immunomodulatory properties, and may represent interesting novel biomarkers. This study aims to validate our findings and analyze whether the increased abundance of apolipoproteins in nasal mucus is a local or systemic phenomenon in allergic rhinitis. STUDY DESIGN Prospective controlled trial. METHODS Nasal mucus of allergic rhinitis patients (n = 10) and healthy controls (n = 12) was collected, tryptically digested, and analyzed by LC-MS/MS. Areas under the curve (AUCs) of the total peptides identified and matched to apolipoproteins were used to compare relative protein abundances of the same protein between groups. RESULTS In a total of 389 identified proteins in nasal mucus, apolipoproteins A-I, A-II, A-IV, and B 100 were detected. Apolipoprotein A-I (mean normalized AUC 1.49% [SEM = 0.5] vs. 0.42% [SEM = 0.2]) and A-II (mean normalized AUC 0.47% [SEM = 0.2] vs. 0.05% [SEM = 0.02]) were significantly more abundant in allergic rhinitis patients than controls (3.6-fold and 9.4-fold, respectively). Apolipoprotein A-IV (mean normalized AUC = 0.01%) and B-100 (mean normalized AUC = 0.02%) were each detected in only one allergic rhinitis patient out of 10. Myeloperoxidase was detected with a mean normalized AUC of 0.06% (SEM = 0.03) in allergic rhinitis patients and 0.18% (SEM = 0.08) in healthy controls without reaching significance. CONCLUSION This study confirms the significantly higher abundance of apolipoproteins A-I and AII in allergic rhinitis mucus. Their release seems to be triggered by local mechanisms as an antiinflammatory response to allergens.
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Affiliation(s)
- Peter V Tomazic
- ENT, University Hospital (p.v.t., a.l., d.l-l.); the Institute of Pathology (r.b-g., b.d., s.s.); the Center of Medical Research, Mass Spectrometry Core Facility (s.s.), Medical University of Graz; The Austrian Center of Industrial Biotechnology (r.b-g., b.d., s.s.); and the The Omics Center Graz, BioTechMed (r.b-g., b.d., s.s.), Graz, Austria
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13
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Law KP, Lim YP. Recent advances in mass spectrometry: data independent analysis and hyper reaction monitoring. Expert Rev Proteomics 2014; 10:551-66. [PMID: 24206228 DOI: 10.1586/14789450.2013.858022] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
New mass spectrometry (MS) methods, collectively known as data independent analysis and hyper reaction monitoring, have recently emerged. These methods hold promises to address the shortcomings of data-dependent analysis and selected reaction monitoring (SRM) employed in shotgun and targeted proteomics, respectively. They allow MS analyses of all species in a complex sample indiscriminately, or permit SRM-like experiments conducted with full high-resolution product ion spectra, potentially leading to higher sequence coverage or analytical selectivity. These methods include MS(E), all-ion fragmentation, Fourier transform-all reaction monitoring, SWATH Acquisition, multiplexed MS/MS, pseudo-SRM (pSRM) and parallel reaction monitoring (PRM). In this review, the strengths and pitfalls of these methods are discussed and illustrated with examples. In essence, the suitability of the use of each method is contingent on the biological questions posed. Although these methods do not fundamentally change the shape of proteomics, they are useful additional tools that should expedite biological discoveries.
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Affiliation(s)
- Kai Pong Law
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, MD4, Level 1, 14 Medical Drive, 117599, Singapore
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14
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Pavlou MP, Dimitromanolakis A, Martinez-Morillo E, Smid M, Foekens JA, Diamandis EP. Integrating Meta-Analysis of Microarray Data and Targeted Proteomics for Biomarker Identification: Application in Breast Cancer. J Proteome Res 2014; 13:2897-909. [DOI: 10.1021/pr500352e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Maria P. Pavlou
- Department
of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Department
of Pathology and Laboratory Medicine, Mount Sinai Hospital, 60 Murray
Street, Toronto, ON M5T 3L9, Canada
| | - Apostolos Dimitromanolakis
- Department
of Pathology and Laboratory Medicine, Mount Sinai Hospital, 60 Murray
Street, Toronto, ON M5T 3L9, Canada
| | - Eduardo Martinez-Morillo
- Lunenfeld-Tanenbaum
Research Institute, Joseph and Wolf Lebovic Health Complex, Mount Sinai Hospital, 60 Murray Street, Toronto, ON M5T 3L9, Canada
| | - Marcel Smid
- Department
of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Groene Hilledijk 301, 3075 EA Rotterdam, The Netherlands
| | - John A. Foekens
- Department
of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Groene Hilledijk 301, 3075 EA Rotterdam, The Netherlands
| | - Eleftherios P. Diamandis
- Department
of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Toronto, ON M5S 1A8, Canada
- Department
of Pathology and Laboratory Medicine, Mount Sinai Hospital, 60 Murray
Street, Toronto, ON M5T 3L9, Canada
- Lunenfeld-Tanenbaum
Research Institute, Joseph and Wolf Lebovic Health Complex, Mount Sinai Hospital, 60 Murray Street, Toronto, ON M5T 3L9, Canada
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Nasal mucus proteomic changes reflect altered immune responses and epithelial permeability in patients with allergic rhinitis. J Allergy Clin Immunol 2013; 133:741-50. [PMID: 24290289 DOI: 10.1016/j.jaci.2013.09.040] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 08/31/2013] [Accepted: 09/27/2013] [Indexed: 12/19/2022]
Abstract
BACKGROUND Nasal mucus is the first-line defense barrier against (aero-) allergens. However, its proteome and function have not been clearly investigated. OBJECTIVE The role of nasal mucus in the pathophysiology of allergic rhinitis was investigated by analyzing its proteome in patients with allergic rhinitis (n = 29) and healthy control subjects (n = 29). METHODS Nasal mucus was collected with a suction device, tryptically digested, and analyzed by using liquid chromatography-tandem mass spectrometry. Proteins were identified by searching the SwissProt database and annotated by collecting gene ontology data from databases and existing literature. Gene enrichment analysis was performed by using Cytoscape/BINGO software tools. Proteins were quantified with spectral counting, and selected proteins were confirmed by means of Western blotting. RESULTS In total, 267 proteins were identified, with 20 (7.5%) found exclusively in patients with allergic rhinitis and 25 (9.5%) found exclusively in healthy control subjects. Five proteins were found to be significantly upregulated in patients with allergic rhinitis (apolipoprotein A-2 [APOA2], 9.7-fold; α2-macroglobulin [A2M], 4.5-fold; apolipoprotein A-1 [APOA1], 3.2-fold; α1-antitrypsin [SERPINA1], 2.5-fold; and complement C3 [C3], 2.3-fold) and 5 were found to be downregulated (antileukoproteinase [SLPI], 0.6-fold; WAP 4-disulfide core domain protein [WFDC2], 0.5-fold; haptoglobin [HP], 0.7-fold; IgJ chain [IGJ], 0.7-fold; and Ig hc V-III region BRO, 0.8-fold) compared with levels seen in healthy control subjects. CONCLUSION The allergic rhinitis mucus proteome shows an enhanced immune response in which apolipoproteins might play an important role. Furthermore, an imbalance between cysteine proteases and antiproteases could be seen, which negatively affects epithelial integrity on exposure to pollen protease activity. This reflects the important role of mucus as the first-line defense barrier against allergens.
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