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Najm M, Martignetti L, Cornet M, Kelly-Aubert M, Sermet I, Calzone L, Stoven V. From CFTR to a CF signalling network: a systems biology approach to study Cystic Fibrosis. BMC Genomics 2024; 25:892. [PMID: 39342081 PMCID: PMC11438383 DOI: 10.1186/s12864-024-10752-x] [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: 11/21/2023] [Accepted: 08/30/2024] [Indexed: 10/01/2024] Open
Abstract
BACKGROUND Cystic Fibrosis (CF) is a monogenic disease caused by mutations in the gene coding the Cystic Fibrosis Transmembrane Regulator (CFTR) protein, but its overall physio-pathology cannot be solely explained by the loss of the CFTR chloride channel function. Indeed, CFTR belongs to a yet not fully deciphered network of proteins participating in various signalling pathways. METHODS We propose a systems biology approach to study how the absence of the CFTR protein at the membrane leads to perturbation of these pathways, resulting in a panel of deleterious CF cellular phenotypes. RESULTS Based on publicly available transcriptomic datasets, we built and analyzed a CF network that recapitulates signalling dysregulations. The CF network topology and its resulting phenotypes were found to be consistent with CF pathology. CONCLUSION Analysis of the network topology highlighted a few proteins that may initiate the propagation of dysregulations, those that trigger CF cellular phenotypes, and suggested several candidate therapeutic targets. Although our research is focused on CF, the global approach proposed in the present paper could also be followed to study other rare monogenic diseases.
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Affiliation(s)
- Matthieu Najm
- Center for Computational Biology (CBIO), Mines Paris-PSL, 75006, Paris, France.
- Institut Curie, Université PSL, 75005, Paris, France.
- INSERM U900, 75005, Paris, France.
| | - Loredana Martignetti
- Center for Computational Biology (CBIO), Mines Paris-PSL, 75006, Paris, France
- Institut Curie, Université PSL, 75005, Paris, France
- INSERM U900, 75005, Paris, France
| | - Matthieu Cornet
- Center for Computational Biology (CBIO), Mines Paris-PSL, 75006, Paris, France
- Institut Curie, Université PSL, 75005, Paris, France
- INSERM U900, 75005, Paris, France
- Institut Necker Enfants Malades, INSERM U1151, 75015, Paris, France
| | - Mairead Kelly-Aubert
- Institut Necker Enfants Malades, INSERM U1151, 75015, Paris, France
- Université Paris Cité, 75015, Paris, France
| | - Isabelle Sermet
- Institut Necker Enfants Malades, INSERM U1151, 75015, Paris, France
- Université Paris Cité, 75015, Paris, France
- Centre de Référence Maladies Rares, Mucoviscidose et Maladies Apparentées, Hôpital Necker Enfants Malades AP-HP Centre Paris Cité, 75015, Paris, France
| | - Laurence Calzone
- Center for Computational Biology (CBIO), Mines Paris-PSL, 75006, Paris, France.
- Institut Curie, Université PSL, 75005, Paris, France.
- INSERM U900, 75005, Paris, France.
| | - Véronique Stoven
- Center for Computational Biology (CBIO), Mines Paris-PSL, 75006, Paris, France.
- Institut Curie, Université PSL, 75005, Paris, France.
- INSERM U900, 75005, Paris, France.
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Zhao S, Luo J, Hu J, Wang H, Zhao N, Cao M, Zhang C, Hu R, Liu L. Role of Ezrin in Asthma-Related Airway Inflammation and Remodeling. Mediators Inflamm 2022; 2022:6255012. [PMID: 36530558 PMCID: PMC9750775 DOI: 10.1155/2022/6255012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 08/13/2023] Open
Abstract
Ezrin is an actin binding protein connecting the cell membrane and the cytoskeleton, which is crucial to maintaining cell morphology, intercellular adhesion, and cytoskeleton remodeling. Asthma involves dysfunction of inflammatory cells, cytokines, and airway structural cells. Recent studies have shown that ezrin, whose function is affected by extensive phosphorylation and protein interactions, is closely associated with asthma, may be a therapeutic target for asthma treatment. In this review, we summarize studies on ezrin and discuss its role in asthma-related airway inflammation and remodeling.
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Affiliation(s)
- Shumei Zhao
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- Nanjing University of Chinese Medicine, Nanjing 210029, China
| | - Jiaqi Luo
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- Nanjing University of Chinese Medicine, Nanjing 210029, China
| | - Jun Hu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- Nanjing University of Chinese Medicine, Nanjing 210029, China
| | - Hesheng Wang
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- Nanjing University of Chinese Medicine, Nanjing 210029, China
| | - Ningwei Zhao
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- Shimadzu Biomedical Research Laboratory, Shanghai 200233, China
| | - Meng Cao
- Nanjing University of Chinese Medicine, Nanjing 210029, China
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine Nanjing University of Chinese Medicine, Nanjing 210028, China
| | - Cong Zhang
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- Nanjing University of Chinese Medicine, Nanjing 210029, China
| | - Rongkui Hu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- Nanjing University of Chinese Medicine, Nanjing 210029, China
| | - Lanying Liu
- Affiliated Hospital of Nanjing University of Chinese Medicine, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, China
- Nanjing University of Chinese Medicine, Nanjing 210029, China
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3
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Kanjanapruthipong T, Sukphopetch P, Reamtong O, Isarangkul D, Muangkaew W, Thiangtrongjit T, Sansurin N, Fongsodsri K, Ampawong S. Cytoskeletal Alteration Is an Early Cellular Response in Pulmonary Epithelium Infected with Aspergillus fumigatus Rather than Scedosporium apiospermum. MICROBIAL ECOLOGY 2022; 83:216-235. [PMID: 33890146 DOI: 10.1007/s00248-021-01750-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 04/02/2021] [Indexed: 06/12/2023]
Abstract
Invasive aspergillosis and scedosporiosis are life-threatening fungal infections with similar clinical manifestations in immunocompromised patients. Contrarily, Scedosporium apiospermum is susceptible to some azole derivative but often resistant to amphotericin B. Histopathological examination alone cannot diagnose these two fungal species. Pathogenesis studies could contribute to explore candidate protein markers for new diagnosis and treatment methods leading to a decrease in mortality. In the present study, proteomics was conducted to identify significantly altered proteins in A549 cells infected with or without Aspergillus fumigatus and S. apiospermum as measured at initial invasion. Protein validation was performed with immunogold labelling alongside immunohistochemical techniques in infected A549 cells and lungs from murine models. Further, cytokine production was measured, using the Bio-Plex-Multiplex immunoassay. The cytoskeletal proteins HSPA9, PA2G4, VAT1, PSMA2, PEX1, PTGES3, KRT1, KRT9, CLIP1 and CLEC20A were mainly changed during A. fumigatus infection, while the immunologically activated proteins WNT7A, GAPDH and ANXA2 were principally altered during S. apiospermum infection. These proteins are involved in fungal internalisation and structural destruction leading to pulmonary disorders. Interleukin (IL)-21, IL-1α, IL-22, IL-2, IL-8, IL-12, IL-17A, interferon-γ and tumour necrosis factor-α were upregulated in both aspergillosis and scedosporiosis, although more predominately in the latter, in accordance with chitin synthase-1 and matrix metalloproteinase levels. Our results demonstrated that during invasion, A. fumigatus primarily altered host cellular integrity, whereas S. apiospermum chiefly induced and extensively modulated host immune responses.
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Affiliation(s)
- Tapanee Kanjanapruthipong
- Department of Tropical Pathology, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Passanesh Sukphopetch
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetic, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Duangnate Isarangkul
- Department of Microbiology, Faculty of Science, Mahidol University, 272, Rama VI Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Watcharamat Muangkaew
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Tipparat Thiangtrongjit
- Department of Molecular Tropical Medicine and Genetic, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Nichapa Sansurin
- Northeast Laboratory Animal Center, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Kamonpan Fongsodsri
- Department of Tropical Pathology, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand
| | - Sumate Ampawong
- Department of Tropical Pathology, Faculty of Tropical Medicine, Mahidol University, Ratchawithi Road, Ratchathewi, Bangkok, 10400, Thailand.
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Abstract
Biomarkers may be diagnostic of asthma, they may predict or reflect response to therapy or they may identify patients at risk of asthma exacerbation. A biomarker is most often measured in biologic fluids that are sampled using relatively non-invasive sampling techniques such as blood, sputum, urine or exhaled breath. Biomarkers should be stable, readily quantifiable and their measurement should be reproducible and not confounded by other host factors, or the presence of comorbidities. However, asthma comprises multiple molecular endotypes and single, sensitive, specific, biomarkers reflecting these endotypes may not exist. Combining biomarkers may improve their predictive capability in asthma. The most well-established endotypes are those described as Type2 and non-Type2 asthma. Clinical trials established the fraction of exhaled nitric oxide (FeNO) and blood eosinophil counts as key biomarkers of response to corticosteroid or targeted anti-inflammatory therapy in Type2 asthma. However, these biomarkers may have limited value in the management of asthma in real-life settings or routine clinical practise. Biomarkers for Type2 asthma are not well described or validated and more research is needed. Breathomics has provided evidence to propose a number of exhaled volatile organic compounds (VOCs) as surrogate biomarkers for airway inflammatory phenotypes, disease activity and adherence to therapy. Analysis of urinary eicosanoids has identified eicosanoids related to Type2 and non-Type2 inflammation. Future clinical trials will be important in determining how exhaled VOCs or urinary eicosanoid profiles can be used to direct precision treatments. Their future clinical use will also depend on developing simplified instrumentation for biomarker analysis at the point-of-care.
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Affiliation(s)
- Janis Shute
- School of Pharmacy and Biomedical Sciences, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth, UK -
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5
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Yang Y, Jia M, Ou Y, Adcock IM, Yao X. Mechanisms and biomarkers of airway epithelial cell damage in asthma: A review. CLINICAL RESPIRATORY JOURNAL 2021; 15:1027-1045. [PMID: 34097803 DOI: 10.1111/crj.13407] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 05/17/2021] [Accepted: 06/03/2021] [Indexed: 12/15/2022]
Abstract
Bronchial asthma is a heterogeneous disease with complex pathological mechanisms representing different phenotypes, including severe asthma. The airway epithelium is a major site of complex pathological changes in severe asthma due, in part, to activation of inflammatory and immune mechanisms in response to noxious agents. Current imaging procedures are unable to accurately measure epithelial and airway remodeling. Damage of airway epithelial cells occurs is linked to specific phenotypes and endotypes which provides an opportunity for the identification of biomarkers reflecting epithelial, and airway, remodeling. Identification of patients with more severe epithelial disruption using biomarkers may also provide personalised therapeutic opportunities and/or markers of successful therapeutic intervention. Here, we review the evidence for ongoing epithelial cell dysregulation in the pathogenesis of asthma, the sentinel role of the airway epithelium and how understanding these molecular mechanisms provides the basis for the identification of candidate biomarkers for asthma prediction, prevention, diagnosis, treatment and monitoring.
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Affiliation(s)
- Yuemei Yang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Man Jia
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yingwei Ou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Department of Emergency Medical, Zhejiang Province People's Hospital, Zhejiang, China
| | - Ian M Adcock
- Airway Disease Section, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, UK
| | - Xin Yao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Srinivasan A, Sundar IK. Recent updates on the role of extracellular vesicles in the pathogenesis of allergic asthma. EXTRACELLULAR VESICLES AND CIRCULATING NUCLEIC ACIDS 2021; 2:127-147. [PMID: 34414402 PMCID: PMC8372030 DOI: 10.20517/evcna.2021.03] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Asthma is a chronic inflammatory disease of the airway diagnosed with different endotypes and phenotypes, characterized by airway obstruction in response to allergens, bacterial/viral infections, or pollutants. Several cell types such as the airway epithelial cells, mesenchymal stem cells and different immune cells including dendritic cells (DCs), T and B cells and mast cells play an essential role during the pathobiology of asthma. Extracellular vesicles (EVs) are membranous nanovesicles produced by every cell type that facilitates intercellular communications. EVs contain heterogeneous cargos that primarily depend on the composition or cell type of origin and they can alter the physiological state of the target cells. EVs encompass a wide variety of proteins including Tetraspanins, MHC classes I and II, co-stimulatory molecules, nucleic acids such as RNA, miRNA, piRNA, circRNA, and lipids like ceramides and sphingolipids. Recent literature indicates that EVs play a pivotal role in the pathophysiology of allergic asthma and may potentially be used as a novel biomarker to determine endotypes and phenotypes in severe asthmatics. Based on the prior reports, we speculate that regulation of EVs biogenesis and release might be under the control of circadian rhythms. Thus, circadian rhythms may influence the composition of the EVs, which alter the microenvironment that results in the induction of an immune-inflammatory response to various environmental insults or allergens such as air pollutants, ozone, diesel exhaust particles, pollens, outdoor molds, environmental tobacco smoke, etc. In this mini-review, we summarize the recent updates on the novel role of EVs in the pathogenesis of asthma, and highlight the link between circadian rhythms and EVs that may be important to identify molecular mechanisms to target during the pathogenesis of chronic inflammatory lung disease such as asthma.
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Affiliation(s)
- Ashokkumar Srinivasan
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas Medical Center, Lawrence, KS 66160, USA
| | - Isaac Kirubakaran Sundar
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas Medical Center, Lawrence, KS 66160, USA
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7
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Tang S, Jiang J, Zhang N, Sun J, Sun G. Tumor necrosis factor-α requires Ezrin to regulate the cytoskeleton and cause pulmonary microvascular endothelial barrier damage. Microvasc Res 2021; 133:104093. [PMID: 33007316 PMCID: PMC7525657 DOI: 10.1016/j.mvr.2020.104093] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/25/2020] [Accepted: 09/25/2020] [Indexed: 02/09/2023]
Abstract
Acute respiratory distress syndrome (ARDS) is a rapidly progressive disease with unknown pathogenesis. Damage of pulmonary microvascular endothelial cells (PMVECs) caused by inflammatory storm caused by cytokines such as TNF-α is the potential pathogenesis of ARDS. In this study, we examined the role of ezrin and Rac1 in TNF-α-related pathways, which regulates the permeability of PMVECs. Primary rat pulmonary microvascular endothelial cells (RPMVECs) were isolated and cultured. RPMVECs were treated with rat TNF-α (0, 1, 10, 100 ng/ml), and the cell activity of each group was measured using a CCK8 kit. The integrity of endothelial barrier was measured by transendothelial resistance (TEER) and FITC-BSA flux across RPMVECs membranes. Pulldown assay and Western blot was used to detect the activity of RAS-associated C3 botulinum toxin substrate 1 (Rac1) and Ezrin phosphorylation. Short hairpin RNA (shRNA) targeting ezrin and Rac1 was utilized to evaluate the effect of RPMVECs permeability and related pathway. The effects of ezrin and Rac1 on cytoskeleton were confirmed by immunofluorescence. Our results revealed that active Rac1 was essential for protecting the RPMVEC barrier stimulated by TNF-α, while active ezrin could partially destroy the PMVEC barrier by reducing Rac1 activity and regulating the subcellular structure of the cytoskeleton. These findings may be used to create new therapeutic strategies for targeting Rac1 in the treatment of ARDS.
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Affiliation(s)
- Sihui Tang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, PR China
| | - Jianjun Jiang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, PR China
| | - Na Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, PR China
| | - Juan Sun
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, PR China
| | - Gengyun Sun
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, PR China.
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Saglani S, Wisnivesky JP, Charokopos A, Pascoe CD, Halayko AJ, Custovic A. Update in Asthma 2019. Am J Respir Crit Care Med 2020; 202:184-192. [PMID: 32338992 DOI: 10.1164/rccm.202003-0596up] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Sejal Saglani
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Juan P Wisnivesky
- Division of General Internal Medicine and.,Division of Pulmonary and Critical Care Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Antonios Charokopos
- Division of Pulmonary and Critical Care Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Christopher D Pascoe
- Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada; and.,Biology of Breathing Group, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Andrew J Halayko
- Department of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada; and.,Biology of Breathing Group, Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Adnan Custovic
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
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Kalinauskaite-Zukauske V, Janulaityte I, Januskevicius A, Malakauskas K. Serum levels of epithelial-derived mediators and interleukin-4/interleukin-13 signaling after bronchial challenge with Dermatophagoides pteronyssinus in patients with allergic asthma. Scand J Immunol 2019; 90:e12820. [PMID: 31486098 DOI: 10.1111/sji.12820] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/14/2019] [Accepted: 08/26/2019] [Indexed: 01/21/2023]
Abstract
Allergens are the main trigger that enhances airway type 2 inflammation, and the epithelium is the first line of defense that reacts to its exposure. Therefore, epithelial-derived mediators, such as interleukin (IL)-25, IL-33, thymic stromal lymphopoietin (TSLP) and ezrin, may play a role as alarmins in IL-4/IL-13 signaling in allergic asthma (AA). We investigated the serum levels of IL-25, IL-33, TSLP, ezrin, IL-4 and IL-13, after bronchial challenge with Dermatophagoides pteronyssinus in patients with AA. We examined 18 subjects: nine steroid-free stable patients with AA sensitized to D. pteronyssinus and nine non-atopic healthy subjects (HS). Bronchial allergen challenge was performed using inhaled D. pteronyssinus allergen. IL-4, IL-13, IL-25, IL-33, TSLP and ezrin levels in serum were measured by ELISA at two time points - before and 24 hours after bronchial allergen challenge. The serum levels of IL-25, TSLP and ezrin did not differ between AA and HS groups at baseline. However, after allergen exposure, significant increases in serum levels of IL-25, TSLP and ezrin were observed only in patients with AA. The serum level of IL-33 at baseline was significantly higher in the AA group compared with HS, but the allergen challenge did not provoke an increase of this cytokine in any group. IL-4 and IL-13 levels were significantly higher at baseline in the AA group compared with HS and, after allergen exposure, were significantly increased in the AA group, with no effect on HS. Thus, the epithelial-derived mediators IL-25, TSLP and ezrin, via IL4/IL13 signaling, enhance type 2 inflammation after bronchial challenge with D. pteronyssinus in AA.
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Affiliation(s)
| | - Ieva Janulaityte
- Laboratory of Pulmonology, Department of Pulmonology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Andrius Januskevicius
- Laboratory of Pulmonology, Department of Pulmonology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Kestutis Malakauskas
- Department of Pulmonology, Lithuanian University of Health Sciences, Kaunas, Lithuania.,Laboratory of Pulmonology, Department of Pulmonology, Lithuanian University of Health Sciences, Kaunas, Lithuania
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