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Liu J, Yang N, Yi X, Wang G, Wang C, Lin H, Sun L, Wang F, Zhu D. Integration of transcriptomics and metabolomics to reveal the effect of ginsenoside Rg3 on allergic rhinitis in mice. Food Funct 2023; 14:2416-2431. [PMID: 36786409 DOI: 10.1039/d2fo03885d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Increasing studies have demonstrated that ginsenoside Rg3 (Rg3) plays an important role in the prevention and treatment of various diseases, including allergic lower airway inflammation such as asthma. To investigate the role of Rg3 in allergic upper airway disease, the effect and therapeutic mechanism of Rg3 in allergic rhinitis (AR) were studied. Ovalbumin-induced AR model mice were intragastrically administered with Rg3. Nasal symptoms, levels of IgE, IL-4, IL-5, IL-13, SOD and MDA in serum, and histopathological analysis of nasal mucosa were used to evaluate the effect of Rg3 on ameliorating AR in mice. Moreover, nasal mucosa samples from the normal control group, AR model group and high dosage of Rg3 were collected to perform omics analysis. The differentially expressed genes and significantly changed metabolites were screened based on transcriptomics and metabolomics analyses, respectively. Integrative analysis was further performed to confirm the hub genes, metabolites and pathways. After Rg3 intervention, the nasal symptoms and inflammatory infiltration were effectively improved, the levels of IgE, IL-4, IL-5, IL-13 and MDA were significantly reduced, and the level of SOD was obviously increased. The results of the qRT-PCR assay complemented the transcriptomic findings. Integrated analysis showed that Rg3 played an anti-AR role mainly by regulating the interaction network, which was constructed by 12 genes, 8 metabolites and 4 pathways. Our findings suggested that Rg3 had a therapeutic effect on ovalbumin-induced AR in mice by inhibiting inflammation development and reducing oxidative stress. The present study could provide a potential natural agent for the treatment of AR.
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Affiliation(s)
- Jianming Liu
- Department of Otolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, Changchun 130021, China.
| | - Na Yang
- Clinical Pharmacy Department, First Hospital of Jilin University, Changchun 130021, China
| | - Xingcheng Yi
- Laboratory of Cancer Precision Medicine, First Hospital of Jilin University, Changchun 130061, China
| | - Guoqiang Wang
- Department of Pathogen Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China.
| | - Cuizhu Wang
- School of Pharmaceutical Sciences, Jilin University, Changchun 130021, China
| | - Hongqiang Lin
- Department of Pathogen Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China.
| | - Liwei Sun
- Department of Otolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, Changchun 130021, China.
| | - Fang Wang
- Department of Pathogen Biology, College of Basic Medical Sciences, Jilin University, Changchun 130021, China.
| | - Dongdong Zhu
- Department of Otolaryngology Head and Neck Surgery, China-Japan Union Hospital of Jilin University, Changchun 130021, China. .,Jilin Provincial Key Laboratory of Precise Diagnosis and Treatment of Upper Airway Allergic Diseases, Changchun 130021, China
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Harcourt-Smith EA, Krstic ET, Soekov-Pearce BJ, Colella AD, Chegeni N, Chataway TK, Woods CM, Aliakbari K, Carney AS. The Nasal Innate Immune Proteome After Saline Irrigation: A Pilot Study in Healthy Individuals. Am J Rhinol Allergy 2023:19458924231159176. [PMID: 36847244 DOI: 10.1177/19458924231159176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
BACKGROUND Previous research has shown diminished nasal immune function following nasal saline irrigation (NSI), returning to baseline at 6 hours. The aim of this study was to examine the immune nasal proteome before and after 14 days of nasal irrigation. METHODS Seventeen healthy volunteers received either isotonic (IsoSal) or low salt (LowNa) NSI. Nasal secretions were collected before and 30 min after NSI at baseline and again after 14 days. Specimens were analyzed using mass spectrometry to detect proteins of relevance to nasal immune function. RESULTS One thousand eight hundred and sixty-five proteins were identified with significant changes in 71 proteins, of which 23 were identified as part of the innate immune system. Baseline analysis demonstrated an increase of 9 innate proteins after NSI, most after IsoSal. After 14 days, a greater increase in innate peptides was present, with most now in the LowNa group. When NSI solutions were compared, a significant increase in 4 innate proteins, including a 211% in lysozyme, was detected in the LowNa group. CONCLUSION LowNa NSI demonstrates evidence of improving the innate immune secretions, especially lysozyme, in healthy volunteers.
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Affiliation(s)
| | - Emerson T Krstic
- College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | | | - Alex D Colella
- Proteomics Facility, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Nusha Chegeni
- Proteomics Facility, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Timothy K Chataway
- Proteomics Facility, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Charmaine M Woods
- College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - Kamelya Aliakbari
- Proteomics Facility, College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
| | - A Simon Carney
- College of Medicine and Public Health, Flinders University, Bedford Park, SA, Australia
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Genes related to allergen exposure in allergic rhinitis: a gene-chip-based study in a mouse model. BMC Med Genomics 2022; 15:243. [PMID: 36434595 PMCID: PMC9701046 DOI: 10.1186/s12920-022-01389-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 11/03/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND The typical clinical symptoms of allergic rhinitis (AR) are known to be associated with allergen exposure; however, the underlying mechanisms are not fully understood. We wanted to gain a comprehensive view of the molecular mechanisms related to allergen exposure in a well-controlled mouse model of AR. METHODS An OVA-induced AR model was developed. Two hours and 4 weeks after the last OVA challenge, AR symptoms and local immune responses were assessed. At the same time, differentially expressed genes (DEG) in nasal mucosa were identified by gene expression microarray and further analyzed by bioinformatics methods. Verification of DEG was done by quantitative RT-PCR and immunohistochemistry. RESULTS The number of nasal rubbings and sneezes, serum OVA-specific IgE concentrations, and the number of neutrophils and eosinophils in the nasal mucosa were significantly increased at 2 h and decreased at 4 weeks after the last allergen challenge compared to controls. A total of 2119 DEG were identified, and their expression dynamics were clustered into 8 profiles. Enriched functions in Profile 5, which had a similar trend to clinical features, were mainly related to inflammatory and immune response to environmental factors, eosinophils and neutrophils chemotaxis, and cell migration. Gene co-expression Network for genes from profile 5 identified BCL3, NFKB2, SOCS3, and CD53 having a higher degree. Profile 6 showed persistence of inflammatory and immune response at 4 weeks after the last allergen challenge. Olfactory and coagulation functions were enriched mainly in profiles with downward trends. CONCLUSIONS A wide range of genes with sequential cooperative action were identified to be associated with allergen exposure in AR. BCL3 may be the most vital in symptoms manifestation. Moreover, some inflammatory responses persisted for a period after allergen exposure, supporting a new treatment strategy of targeting inflammation out of season. This study may contribute to a better understanding of AR pathogenesis and provide potential therapeutic targets for AR patients.
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Vizuet-de-Rueda JC, Montero-Vargas JM, Galván-Morales MÁ, Porras-Gutiérrez-de-Velasco R, Teran LM. Current Insights on the Impact of Proteomics in Respiratory Allergies. Int J Mol Sci 2022; 23:ijms23105703. [PMID: 35628512 PMCID: PMC9144092 DOI: 10.3390/ijms23105703] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/13/2022] [Accepted: 05/17/2022] [Indexed: 12/11/2022] Open
Abstract
Respiratory allergies affect humans worldwide, causing extensive morbidity and mortality. They include allergic rhinitis (AR), asthma, pollen food allergy syndrome (PFAS), aspirin-exacerbated respiratory disease (AERD), and nasal polyps (NPs). The study of respiratory allergic diseases requires new technologies for early and accurate diagnosis and treatment. Omics technologies provide the tools required to investigate DNA, RNA, proteins, and other molecular determinants. These technologies include genomics, transcriptomics, proteomics, and metabolomics. However, proteomics is one of the main approaches to studying allergic disorders' pathophysiology. Proteins are used to indicate normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention. In this field, the principal goal of proteomics has been to discover new proteins and use them in precision medicine. Multiple technologies have been applied to proteomics, but that most used for identifying, quantifying, and profiling proteins is mass spectrometry (MS). Over the last few years, proteomics has enabled the establishment of several proteins for diagnosing and treating respiratory allergic diseases.
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Darnhofer B, Tomin T, Liesinger L, Schittmayer M, Tomazic PV, Birner‐Gruenberger R. Comparative proteomics of common allergenic tree pollens of birch, alder, and hazel. Allergy 2021; 76:1743-1753. [PMID: 33301602 PMCID: PMC8248232 DOI: 10.1111/all.14694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/26/2020] [Accepted: 11/14/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND In addition to known allergens, other proteins in pollen can aid the development of an immune response in allergic individuals. The contribution of the "unknown" protein allergens is apparent in phylogenetically related species where, despite of high homology of the lead allergens, the degree of allergenic potential can vary greatly. The aim of this study was to identify other potentially allergenic proteins in pollen of three common and highly related allergenic tree species: birch (Betula pendula), hazel (Corylus avellana) and alder (Alnus glutinosa). METHODS For that purpose, we carried out a comprehensive, comparative proteomic screening of the pollen from the three species. In order to maximize protein recovery and coverage, different protein extraction and isolation strategies during sample preparation were employed. RESULTS As a result, we report 2500-3000 identified proteins per each of the pollen species. Identified proteins were further used for a number of annotation steps, providing insight into differential distribution of peptidases, peptidase inhibitors and other potential allergenic proteins across the three species. Moreover, we carried out functional enrichment analyses that, interestingly, corroborated high species similarity in spite of their relatively distinct protein profiles. CONCLUSION We provide to our knowledge first insight into proteomes of two very important allergenic pollen types, hazel and alder, where not even transcriptomics data are available, and compared them to birch. Datasets from this study can be readily used as protein databases and as such serve as basis for further functional studies.
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Affiliation(s)
- Barbara Darnhofer
- Diagnostic and Research Institute of PathologyMedical University of GrazGrazAustria
- Omics Center GrazBiotechMed‐GrazGrazAustria
| | - Tamara Tomin
- Diagnostic and Research Institute of PathologyMedical University of GrazGrazAustria
- Omics Center GrazBiotechMed‐GrazGrazAustria
- Faculty of Technical ChemistryInstitute of Chemical Technologies and AnalyticsTechnische Universität Wien (TU Wien)ViennaAustria
| | - Laura Liesinger
- Diagnostic and Research Institute of PathologyMedical University of GrazGrazAustria
- Omics Center GrazBiotechMed‐GrazGrazAustria
| | - Matthias Schittmayer
- Diagnostic and Research Institute of PathologyMedical University of GrazGrazAustria
- Omics Center GrazBiotechMed‐GrazGrazAustria
- Faculty of Technical ChemistryInstitute of Chemical Technologies and AnalyticsTechnische Universität Wien (TU Wien)ViennaAustria
| | - Peter Valentin Tomazic
- Division of PhoniatricsDepartment of OtorhinolaryngologyMedical University of GrazGrazAustria
| | - Ruth Birner‐Gruenberger
- Diagnostic and Research Institute of PathologyMedical University of GrazGrazAustria
- Omics Center GrazBiotechMed‐GrazGrazAustria
- Faculty of Technical ChemistryInstitute of Chemical Technologies and AnalyticsTechnische Universität Wien (TU Wien)ViennaAustria
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6
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Chung YW, Cha J, Han S, Chen Y, Gucek M, Cho HJ, Nakahira K, Choi AMK, Ryu JH, Yoon JH. Apolipoprotein E and Periostin Are Potential Biomarkers of Nasal Mucosal Inflammation. A Parallel Approach of In Vitro and In Vivo Secretomes. Am J Respir Cell Mol Biol 2020; 62:23-34. [PMID: 31194918 DOI: 10.1165/rcmb.2018-0248oc] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
No previously suggested biomarkers of nasal mucosal inflammation have been practically applied in clinical fields, and nasal epithelium-derived secreted proteins as biomarkers have not specifically been investigated. The goal of this study was to identify secreted proteins that dynamically change during the differentiation from basal cells to fully differentiated cells and examine whether nasal epithelium-derived proteins can be used as biomarkers of nasal mucosal inflammation, such as chronic rhinosinusitis. To achieve this goal, we analyzed two secretomes using the isobaric tag for relative and absolute quantification technique. From in vitro secretomes, we identified the proteins altered in apical secretions of primary human nasal epithelial cells according to the degree of differentiation; from in vivo secretomes, we identified the increased proteins in nasal lavage fluids obtained from patients 2 weeks after endoscopic sinus surgery for chronic sinusitis. We then used a parallel approach to identify specific biomarkers of nasal mucosal inflammation; first, we selected apolipoprotein E as a nasal epithelial cell-derived biomarker through screening proteins that were upregulated in both in vitro and in vivo secretomes, and verified highly secreted apolipoprotein E in nasal lavage fluids of the patients by Western blotting. Next, we selected periostin as an inflammatory mediator-inducible biomarker from in vivo secretomes, the secretion of which was not induced under in vitro culture conditions. We demonstrated that those two nasal epithelium-derived proteins are possible biomarkers of nasal mucosal inflammation.
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Affiliation(s)
- Youn Wook Chung
- The Airway Mucus Institute.,Global Research Laboratory for Allergic Airway Disease.,Severance Biomedical Science Institute
| | - Jimin Cha
- Severance Biomedical Science Institute.,Brain Korea 21 PLUS Project for Medical Science, and
| | - Seunghan Han
- Severance Biomedical Science Institute.,Brain Korea 21 PLUS Project for Medical Science, and
| | - Yong Chen
- Proteomics Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland; and
| | - Marjan Gucek
- Proteomics Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland; and
| | - Hyung-Ju Cho
- The Airway Mucus Institute.,Global Research Laboratory for Allergic Airway Disease.,Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
| | - Kiichi Nakahira
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Augustine M K Choi
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Ji-Hwan Ryu
- Severance Biomedical Science Institute.,Brain Korea 21 PLUS Project for Medical Science, and
| | - Joo-Heon Yoon
- The Airway Mucus Institute.,Global Research Laboratory for Allergic Airway Disease.,Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
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7
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Tomazic PV, Darnhofer B, Birner-Gruenberger R. Nasal mucus proteome and its involvement in allergic rhinitis. Expert Rev Proteomics 2020; 17:191-199. [PMID: 32266843 PMCID: PMC7261402 DOI: 10.1080/14789450.2020.1748502] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Nasal mucus is the first line defense barrier against various pathogens including allergens. Proteins in nasal mucus maybe used as biomarkers for diagnosis or future therapeutic strategies. Proteomics opens the possibility to investigate whole human proteomes. Areas Covered: We aimed to analyze the existing literature on nasal mucus and nasal secretions proteomic approaches especially in allergic rhinitis. A PubMed/Medline search was conducted entering the following keywords and combinations: “nasal mucus”, “nasal lavage fluid,” nasal secretions,” “nasal swabs,” “allergic rhinitis,” ”proteins,” and “proteomics.” Expert opinion: The majority of studies focus on single proteins or protein groups mainly using ELISA techniques. Four studies met the criteria using mass spectrometry in the analysis of nasal mucus proteomes in rhinologic diseases. In these studies, 7, 35, 267, and 430 proteins were identified, respectively. These four studies are discussed in this review and put in relation to seven other proteomic studies that focus on nasal lavage fluid and nasal secretions obtained by swabs or filter paper. To put it in a nutshell, proteomics facilitates the investigation of the nasal secretome and its role in healthy and diseased state and as potential biomarkers for new diagnostic or therapeutic approaches.
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Affiliation(s)
| | - Barbara Darnhofer
- Diagnostic and Research Institute of Pathology, Diagnostic and Research Center of Molecular Medicine, Medical University of Graz, Graz, Austria.,BioTechMed-Graz, The Omics Center Graz, Graz, Austria
| | - Ruth Birner-Gruenberger
- Diagnostic and Research Institute of Pathology, Diagnostic and Research Center of Molecular Medicine, Medical University of Graz, Graz, Austria.,BioTechMed-Graz, The Omics Center Graz, Graz, Austria.,Institute of Chemical Technologies and Analytics, Vienna University of Technology, Vienna, Austria
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8
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Tang HHF, Sly PD, Holt PG, Holt KE, Inouye M. Systems biology and big data in asthma and allergy: recent discoveries and emerging challenges. Eur Respir J 2020; 55:13993003.00844-2019. [PMID: 31619470 DOI: 10.1183/13993003.00844-2019] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 09/12/2019] [Indexed: 12/15/2022]
Abstract
Asthma is a common condition caused by immune and respiratory dysfunction, and it is often linked to allergy. A systems perspective may prove helpful in unravelling the complexity of asthma and allergy. Our aim is to give an overview of systems biology approaches used in allergy and asthma research. Specifically, we describe recent "omic"-level findings, and examine how these findings have been systematically integrated to generate further insight.Current research suggests that allergy is driven by genetic and epigenetic factors, in concert with environmental factors such as microbiome and diet, leading to early-life disturbance in immunological development and disruption of balance within key immuno-inflammatory pathways. Variation in inherited susceptibility and exposures causes heterogeneity in manifestations of asthma and other allergic diseases. Machine learning approaches are being used to explore this heterogeneity, and to probe the pathophysiological patterns or "endotypes" that correlate with subphenotypes of asthma and allergy. Mathematical models are being built based on genomic, transcriptomic and proteomic data to predict or discriminate disease phenotypes, and to describe the biomolecular networks behind asthma.The use of systems biology in allergy and asthma research is rapidly growing, and has so far yielded fruitful results. However, the scale and multidisciplinary nature of this research means that it is accompanied by new challenges. Ultimately, it is hoped that systems medicine, with its integration of omics data into clinical practice, can pave the way to more precise, personalised and effective management of asthma.
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Affiliation(s)
- Howard H F Tang
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia .,Cambridge Baker Systems Genomics Initiative, Dept of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,School of BioSciences, The University of Melbourne, Parkville, Australia
| | - Peter D Sly
- Queensland Children's Medical Research Institute, The University of Queensland, Brisbane, Australia.,Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Patrick G Holt
- Queensland Children's Medical Research Institute, The University of Queensland, Brisbane, Australia.,Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Kathryn E Holt
- Dept of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia.,London School of Hygiene and Tropical Medicine, London, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia.,Cambridge Baker Systems Genomics Initiative, Dept of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,School of BioSciences, The University of Melbourne, Parkville, Australia.,The Alan Turing Institute, London, UK
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Kim YS, Han D, Kim J, Kim DW, Kim YM, Mo JH, Choi HG, Park JW, Shin HW. In-Depth, Proteomic Analysis of Nasal Secretions from Patients With Chronic Rhinosinusitis and Nasal Polyps. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2019; 11:691-708. [PMID: 31332980 PMCID: PMC6658407 DOI: 10.4168/aair.2019.11.5.691] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/22/2019] [Accepted: 05/08/2019] [Indexed: 12/19/2022]
Abstract
Purpose Chronic rhinosinusitis (CRS) is a complex immunological condition, and novel experimental modalities are required to explore various clinical and pathophysiological endotypes; mere evaluation of nasal polyp (NP) status is inadequate. Therefore, we collected patient nasal secretions on filter paper and characterized the proteomes. Methods We performed liquid chromatography-mass spectrometry (MS)/MS in the data-dependent acquisition (DDA) and data-independent acquisition (DIA) modes. Nasal secretions were collected from 10 controls, 10 CRS without NPs (CRSsNP) and 10 CRS with NPs (CRSwNP). We performed Orbitrap MS-based proteomic analysis in the DDA (5 controls, 5 CRSsNP and 5 CRSwNP) and the DIA (5 controls, 5 CRSsNP and 5 CRSwNP) modes, followed by a statistical analysis and a hierarchical clustering to identify differentially expressed proteins in the 3 groups. Results We identified 2,020 proteins in nasal secretions. Canonical pathway analysis and gene ontology (GO) evaluation revealed that interleukin (IL)-7, IL-9, IL-17A and IL-22 signaling and neutrophil-mediated immune responses like neutrophil degranulation and activation were significantly increased in CRSwNP compared to control. The GO terms related to the iron ion metabolism that may be associated with CRS and NP development. Conclusions Collection of nasal secretions on the filter paper is a practical and non-invasive method for in-depth study of nasal proteomics. Our proteomic signatures also support that Asian NPs could be characterized as non-eosinophilic inflammation features. Therefore, the proteomic profiling of nasal secretions from CRS patients may enhance our understanding of CRS endotypes.
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Affiliation(s)
- Yi Sook Kim
- Obstructive Upper airway Research (OUaR) Laboratory, Department of Pharmacology, Seoul National University College of Medicine, Seoul, Korea.,Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
| | - Dohyun Han
- Proteomics core facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, Korea
| | - JinYoup Kim
- Department of Otorhinolaryngology, Armed Forces Capital Hospital, Seongnam, Korea
| | - Dae Woo Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Boramae Medical Center, Seoul, Korea.,Clinical Mucosal Immunology Study Group, Seoul, Korea
| | - Yong Min Kim
- Department of Otorhinolaryngology-Head and Neck Surgery, Chungnam National University Hospital, Daejeon, Korea.,Clinical Mucosal Immunology Study Group, Seoul, Korea
| | - Ji Hun Mo
- Department of Otorhinolaryngology-Head and Neck Surgery, Dankook University Hospital, Cheonan, Korea.,Clinical Mucosal Immunology Study Group, Seoul, Korea
| | - Hyo Geun Choi
- Department of Otorhinolaryngology-Head and Neck Surgery, Hallym University Hospital, Pyongchon, Korea
| | - Jong Wan Park
- Obstructive Upper airway Research (OUaR) Laboratory, Department of Pharmacology, Seoul National University College of Medicine, Seoul, Korea.,Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea.,Ischemic/hypoxic disease institute, Seoul National University College of Medicine, Seoul, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hyun Woo Shin
- Obstructive Upper airway Research (OUaR) Laboratory, Department of Pharmacology, Seoul National University College of Medicine, Seoul, Korea.,Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea.,Ischemic/hypoxic disease institute, Seoul National University College of Medicine, Seoul, Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea.,Department of Otorhinolaryngology-Head and Neck Surgery, Seoul National University Hospital, Seoul, Korea.,Clinical Mucosal Immunology Study Group, Seoul, Korea.
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10
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Wolf A, Liesinger L, Spoerk S, Schittmayer M, Lang-Loidolt D, Birner-Gruenberger R, Tomazic PV. Olfactory cleft proteome does not reflect olfactory performance in patients with idiopathic and postinfectious olfactory disorder: A pilot study. Sci Rep 2018; 8:17554. [PMID: 30510230 PMCID: PMC6277379 DOI: 10.1038/s41598-018-35776-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 11/09/2018] [Indexed: 01/15/2023] Open
Abstract
Technical advances including liquid chromatography-tandem mass spectrometry and its data analysis enable detailed proteomic analysis of the nasal mucus. Alterations of the nasal mucus proteome may provoke substantial changes of the nasal physiology and have already been associated with rhinologic diseases such as allergic rhinitis. This study was conducted as a pilot study to map the olfactory cleft proteome using current techniques for proteomic analysis. Furthermore, we aimed to investigate proteomic changes as potential biomarkers in patients suffering from idiopathic and postinfectious olfactory disorders compared to healthy controls. Seven patients with idiopathic hyposmia and anosmia, seven patients with postinfectious hyposmia and anosmia and seven healthy controls were included in this study. In total, 1117 different proteins were detected in at least five patients in at least one group. Results of this study did not reveal significant differences regarding the proteomic composition of the olfactory cleft mucus between patients versus healthy controls. Among proteins involved in olfactory perception the G protein family was detected but also found unchanged between groups. Investigation of protein composition by liquid chromatography-tandem mass spectrometry enabled us to perform an in-depth analysis of the olfactory cleft mucus proteome regarding the diversity of different proteins in individual patients. However untargeted proteomics of the olfactory cleft mucus may not be an applicable approach to develop biomarkers for olfactory disorders. Targeted analyses of distinct proteins known to be involved in olfactory perception but not detected by our approach, e.g. odorant binding proteins, may provide more information regarding pathophysiology of olfactory diseases.
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Affiliation(s)
- Axel Wolf
- Department of Otorhinolaryngology, Medical University of Graz, Auenbruggerplatz 26, 8036, Graz, Austria
| | - Laura Liesinger
- Gottfried Schatz Research Center, Medical University of Graz, Stiftingtalstrasse 24, 8010, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010, Graz, Austria
| | - Stefan Spoerk
- Gottfried Schatz Research Center, Medical University of Graz, Stiftingtalstrasse 24, 8010, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010, Graz, Austria
| | - Matthias Schittmayer
- Gottfried Schatz Research Center, Medical University of Graz, Stiftingtalstrasse 24, 8010, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010, Graz, Austria
| | - Doris Lang-Loidolt
- Department of Otorhinolaryngology, Medical University of Graz, Auenbruggerplatz 26, 8036, Graz, Austria
| | - Ruth Birner-Gruenberger
- Gottfried Schatz Research Center, Medical University of Graz, Stiftingtalstrasse 24, 8010, Graz, Austria.
- Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010, Graz, Austria.
| | - Peter V Tomazic
- Department of Otorhinolaryngology, Medical University of Graz, Auenbruggerplatz 26, 8036, Graz, Austria.
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Ndika J, Suojalehto H, Täubel M, Lehto M, Karvala K, Pallasaho P, Sund J, Auvinen P, Järvi K, Pekkanen J, Kinaret P, Greco D, Hyvärinen A, Alenius H. Nasal mucosa and blood cell transcriptome profiles do not reflect respiratory symptoms associated with moisture damage. INDOOR AIR 2018; 28:721-731. [PMID: 29729044 DOI: 10.1111/ina.12472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 04/25/2018] [Indexed: 06/08/2023]
Abstract
Upper and lower respiratory symptoms and asthma are adverse health effects associated with moisture-damaged buildings. Quantitative measures to detect adverse health effects related to exposure to dampness and mold are needed. Here, we investigate differences in gene expression between occupants of moisture-damaged and reference buildings. Moisture-damaged (N = 11) and control (N = 5) buildings were evaluated for dampness and mold by trained inspectors. The transcriptomics cohort consisted of nasal brushings and peripheral blood mononuclear cells (PBMCs) from 86 teachers, with/without self-perceived respiratory symptoms. Subject categories comprised reference (R) and damaged (D) buildings with (S) or without (NS) symptoms, that is, R-S, R-NS, DS, and D-NS. Component analyses and k-means clustering of transcriptome profiles did not distinguish building status (R/D) or presence of respiratory symptoms (S/NS). Only one nasal mucosa gene (YBX3P1) exhibited a significant change in expression between D-S and D-NS. Nine other nasal mucosa genes were differentially expressed between R-S and D-S teachers. No differentially expressed genes were identified in PBMCs. We conclude that the observed mRNA differences provide very weak biological evidence for adverse health effects associated with subject occupancy of the specified moisture-damaged buildings. This emphasizes the need to evaluate all potential factors (including those not related to toxicity) influencing perceived/self-reported ill health in moisture-damaged buildings.
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Affiliation(s)
- J Ndika
- Department of Bacteriology and Immunology, Medicum, University of Helsinki, Helsinki, Finland
| | - H Suojalehto
- Department of Occupational Medicine, Finnish Institute of Occupational Health, Helsinki, Finland
| | - M Täubel
- Department of Health Security, National Institute for Health and Welfare, Kuopio, Finland
| | - M Lehto
- Department of Occupational Medicine, Finnish Institute of Occupational Health, Helsinki, Finland
| | - K Karvala
- Department of Occupational Medicine, Finnish Institute of Occupational Health, Helsinki, Finland
| | - P Pallasaho
- Department of Occupational Medicine, Finnish Institute of Occupational Health, Helsinki, Finland
| | - J Sund
- Department of Occupational Medicine, Finnish Institute of Occupational Health, Helsinki, Finland
| | - P Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - K Järvi
- Department of Health Security, National Institute for Health and Welfare, Kuopio, Finland
- School of Engineering, Aalto University, Espoo, Finland
| | - J Pekkanen
- Department of Health Security, National Institute for Health and Welfare, Kuopio, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - P Kinaret
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - D Greco
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - A Hyvärinen
- Department of Health Security, National Institute for Health and Welfare, Kuopio, Finland
| | - H Alenius
- Department of Bacteriology and Immunology, Medicum, University of Helsinki, Helsinki, Finland
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
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12
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Suojalehto H, Lindström I, Wolff H, Puustinen A. Nasal protein profiles in work-related asthma caused by different exposures. Allergy 2018; 73:653-663. [PMID: 28960398 DOI: 10.1111/all.13325] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2017] [Indexed: 12/15/2022]
Abstract
BACKGROUND The mechanisms of work-related asthma (WRA) are incompletely delineated. Nasal cell samples may be informative about processes in the lower airways. Our aim was to determine the nasal protein expression profiles of WRA caused by different kind of exposures. METHODS We collected nasal brush samples from 82 nonsmoking participants, including healthy controls and WRA patients exposed to (i) protein allergens, (ii) isocyanates and (iii) welding fumes the day after relevant exposure. The proteome changes in samples were analysed by two-dimensional difference gel electrophoresis, and the differentially regulated proteins found were identified by mass spectrometry. Immunological comparison was carried out using Western blot. RESULTS We detected an average of 2500 spots per protein gel. Altogether, 228 protein spots were chosen for identification, yielding 77 different proteins. Compared to the controls, exposure to protein allergens had the largest effects on the proteome. Hierarchical clustering revealed that protein allergen- and isocyanate-related asthma had similar profiles, whereas asthma related to welding fumes differed. The highly overrepresented functional categories in the asthma groups were defence response, protease inhibitor activity, inflammatory and calcium signalling, complement activation and cellular response to oxidative stress. Immunological analysis confirmed the found abundance differences in galectin 10 and protein S100-A9 between the groups. CONCLUSIONS Work-related asthma patients exposed to protein allergens and isocyanates elicit similar nasal proteome responses and the profiles of welders and healthy controls were alike. Revealed biological activities of the protein expression changes are associated with allergic inflammation and asthma.
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Affiliation(s)
- H. Suojalehto
- Occupational Medicine; Finnish Institute of Occupational Health; Helsinki Finland
| | - I. Lindström
- Occupational Medicine; Finnish Institute of Occupational Health; Helsinki Finland
| | - H. Wolff
- Work Environment Laboratories; Finnish Institute of Occupational Health; Helsinki Finland
| | - A. Puustinen
- Unit of Systems Toxicology; Finnish Institute of Occupational Health; Helsinki Finland
- Verifin; Department of Chemistry; University of Helsinki; Helsinki Finland
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13
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Biswas K, Wagner Mackenzie B, Waldvogel-Thurlow S, Middleditch M, Jullig M, Zoing M, Taylor MW, Douglas RG. Differentially Regulated Host Proteins Associated with Chronic Rhinosinusitis Are Correlated with the Sinonasal Microbiome. Front Cell Infect Microbiol 2017; 7:504. [PMID: 29270391 PMCID: PMC5723659 DOI: 10.3389/fcimb.2017.00504] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/22/2017] [Indexed: 12/18/2022] Open
Abstract
The chronic inflammatory nature of chronic rhinosinusitis (CRS) makes it a morbid condition for individuals with the disease and one whose pathogenesis is poorly understood. To date, proteomic approaches have been applied successfully in a handful of CRS studies. In this study we use a multifaceted approach, including proteomics (iTRAQ labeling) and microbiome (bacterial 16S rRNA gene sequencing) analyses of middle meatus swabs, as well as immune cell analysis of the underlying tissue, to investigate the host-microbe interaction in individuals with CRS (n = 10) and healthy controls (n = 9). Of the total 606 proteins identified in this study, seven were significantly (p < 0.05) more abundant and 104 were significantly lower in the CRS cohort compared with healthy controls. The majority of detected proteins (82% of proteins identified) were not significantly correlated with disease status. Elevated levels of blood and immune cell proteins in the CRS cohort, together with significantly higher numbers of B-cells and macrophages in the underlying tissue, confirmed the inflammatory status of CRS individuals. Protein PRRC2C and Ras-related protein (RAB14) (two of the seven elevated proteins) showed the biggest fold difference between the healthy and CRS groups. Validation of the elevated levels of these two proteins in CRS samples was provided by immunohistochemistry. Members of the bacterial community in the two study cohorts were not associated with PRRC2C, however members of the genus Moraxella did correlate with RAB14 (p < 0.0001, rho = -0.95), which is a protein involved in the development of basement membrane. In addition, significant correlations between certain members of the CRS bacterial community and 33 lower abundant proteins in the CRS cohort were identified. Members of the genera Streptococcus, Haemophilus and Veillonella were strongly correlated with CRS and were significantly associated with a number of proteins with varying functions. The results from this study reveal a strong association between the host and microbes in the sinonasal cavity. Proteins identified as associated with CRS could be new targets for drug therapies and biomarkers for assessment of treatment efficacy.
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Affiliation(s)
- Kristi Biswas
- Department of Surgery, School of Medicine, University of Auckland, Auckland, New Zealand
| | - Brett Wagner Mackenzie
- Department of Surgery, School of Medicine, University of Auckland, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | | | - Martin Middleditch
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Auckland Science Analytical Services, University of Auckland, Auckland, New Zealand
| | - Mia Jullig
- Auckland Science Analytical Services, University of Auckland, Auckland, New Zealand
| | - Melissa Zoing
- Department of Surgery, School of Medicine, University of Auckland, Auckland, New Zealand
| | - Michael W. Taylor
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, New Zealand
| | - Richard G. Douglas
- Department of Surgery, School of Medicine, University of Auckland, Auckland, New Zealand
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14
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Ndika J, Airaksinen L, Suojalehto H, Karisola P, Fyhrquist N, Puustinen A, Alenius H. Epithelial proteome profiling suggests the essential role of interferon-inducible proteins in patients with allergic rhinitis. J Allergy Clin Immunol 2017. [PMID: 28633877 DOI: 10.1016/j.jaci.2017.05.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Seasonal allergic rhinitis (SAR) caused by intermittent exposure to seasonal pollen causes itching, nasal congestion, and repeated sneezing, with profound effects on quality of life, work productivity, and school performance. Although both the genotype and environmental factors can contribute to the immunologic basis of allergic reactions, the molecular underpinnings associated with the pathogenesis of allergic rhinitis are not entirely clear. METHODS To address these questions, nasal epithelial brushings were collected from 29 patients with SAR and 31 control subjects during and after the pollen season. We then implemented an orbitrap-based, bottom-up, label-free quantitative proteomics approach, followed by multivariate analyses to identify differentially abundant (DA) proteins among the 4 sample groups. RESULTS We identified a total of 133 DA proteins for which the most significantly overrepresented functional category was found to be interferon 1 signaling. Two proteins, cystatin 1 and myeloblastin, the former of which protects against protease activity of allergens and the latter with a role in epithelial barrier function, were DA in patients with SAR and control subjects, irrespective of season. Moreover, interferon-inducible protein with tetratricopeptide repeats 1, cystatin 1, and interferon-inducible protein with tetratricopeptide repeats 3 were found to be differentially regulated between patients with SAR and control subjects, with inverse abundance dynamics during the transition from fall to spring. CONCLUSION We identified type 1 interferon-regulated proteins as biomarkers in patients with SAR, potentially playing an important role in its pathogenesis. Moreover, when compared with patients with SAR, healthy subjects exhibit an antagonistic proteomic response across seasons, which might prove to be a therapeutic target for disease prevention.
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Affiliation(s)
- Joseph Ndika
- Department of Bacteriology and Immunology, Medicum, University of Helsinki, Helsinki, Finland
| | - Liisa Airaksinen
- Occupational Medicine, Finnish Institute of Occupational Health, Helsinki, Finland
| | - Hille Suojalehto
- Occupational Medicine, Finnish Institute of Occupational Health, Helsinki, Finland
| | - Piia Karisola
- Department of Bacteriology and Immunology, Medicum, University of Helsinki, Helsinki, Finland
| | - Nanna Fyhrquist
- Department of Bacteriology and Immunology, Medicum, University of Helsinki, Helsinki, Finland
| | - Anne Puustinen
- Department of Clinical Chemistry, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Harri Alenius
- Department of Bacteriology and Immunology, Medicum, University of Helsinki, Helsinki, Finland; Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
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15
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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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