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Wang Y, Lin Y, Wu S, Sun J, Meng Y, Jin E, Kong D, Duan G, Bei S, Fan Z, Wu G, Hao L, Song S, Tang B, Zhao W. BioKA: a curated and integrated biomarker knowledgebase for animals. Nucleic Acids Res 2024; 52:D1121-D1130. [PMID: 37843156 PMCID: PMC10767812 DOI: 10.1093/nar/gkad873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/19/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023] Open
Abstract
Biomarkers play an important role in various area such as personalized medicine, drug development, clinical care, and molecule breeding. However, existing animals' biomarker resources predominantly focus on human diseases, leaving a significant gap in non-human animal disease understanding and breeding research. To address this limitation, we present BioKA (Biomarker Knowledgebase for Animals, https://ngdc.cncb.ac.cn/bioka), a curated and integrated knowledgebase encompassing multiple animal species, diseases/traits, and annotated resources. Currently, BioKA houses 16 296 biomarkers associated with 951 mapped diseases/traits across 31 species from 4747 references, including 11 925 gene/protein biomarkers, 1784 miRNA biomarkers, 1043 mutation biomarkers, 773 metabolic biomarkers, 357 circRNA biomarkers and 127 lncRNA biomarkers. Furthermore, BioKA integrates various annotations such as GOs, protein structures, protein-protein interaction networks, miRNA targets and so on, and constructs an interactive knowledge network of biomarkers including circRNA-miRNA-mRNA associations, lncRNA-miRNA associations and protein-protein associations, which is convenient for efficient data exploration. Moreover, BioKA provides detailed information on 308 breeds/strains of 13 species, and homologous annotations for 8784 biomarkers across 16 species, and offers three online application tools. The comprehensive knowledge provided by BioKA not only advances human disease research but also contributes to a deeper understanding of animal diseases and supports livestock breeding.
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Affiliation(s)
- Yibo Wang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yihao Lin
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sicheng Wu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiani Sun
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuyan Meng
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Enhui Jin
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Demian Kong
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangya Duan
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shaoqi Bei
- Qilu University of Technology (Shandong Academy of Sciences), Shandong 250353, China
| | - Zhuojing Fan
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Gangao Wu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Lili Hao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Shuhui Song
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Bixia Tang
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Wenming Zhao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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2
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Spector C, De Sanctis CM, Panettieri RA, Koziol-White CJ. Rhinovirus induces airway remodeling: what are the physiological consequences? Respir Res 2023; 24:238. [PMID: 37773065 PMCID: PMC10540383 DOI: 10.1186/s12931-023-02529-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/01/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Rhinovirus infections commonly evoke asthma exacerbations in children and adults. Recurrent asthma exacerbations are associated with injury-repair responses in the airways that collectively contribute to airway remodeling. The physiological consequences of airway remodeling can manifest as irreversible airway obstruction and diminished responsiveness to bronchodilators. Structural cells of the airway, including epithelial cells, smooth muscle, fibroblasts, myofibroblasts, and adjacent lung vascular endothelial cells represent an understudied and emerging source of cellular and extracellular soluble mediators and matrix components that contribute to airway remodeling in a rhinovirus-evoked inflammatory environment. MAIN BODY While mechanistic pathways associated with rhinovirus-induced airway remodeling are still not fully characterized, infected airway epithelial cells robustly produce type 2 cytokines and chemokines, as well as pro-angiogenic and fibroblast activating factors that act in a paracrine manner on neighboring airway cells to stimulate remodeling responses. Morphological transformation of structural cells in response to rhinovirus promotes remodeling phenotypes including induction of mucus hypersecretion, epithelial-to-mesenchymal transition, and fibroblast-to-myofibroblast transdifferentiation. Rhinovirus exposure elicits airway hyperresponsiveness contributing to irreversible airway obstruction. This obstruction can occur as a consequence of sub-epithelial thickening mediated by smooth muscle migration and myofibroblast activity, or through independent mechanisms mediated by modulation of the β2 agonist receptor activation and its responsiveness to bronchodilators. Differential cellular responses emerge in response to rhinovirus infection that predispose asthmatic individuals to persistent signatures of airway remodeling, including exaggerated type 2 inflammation, enhanced extracellular matrix deposition, and robust production of pro-angiogenic mediators. CONCLUSIONS Few therapies address symptoms of rhinovirus-induced airway remodeling, though understanding the contribution of structural cells to these processes may elucidate future translational targets to alleviate symptoms of rhinovirus-induced exacerbations.
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Affiliation(s)
- Cassandra Spector
- Rutgers Institute for Translation Medicine and Science, New Brunswick, NJ, USA
| | - Camden M De Sanctis
- Rutgers Institute for Translation Medicine and Science, New Brunswick, NJ, USA
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3
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Radzikowska U, Eljaszewicz A, Tan G, Stocker N, Heider A, Westermann P, Steiner S, Dreher A, Wawrzyniak P, Rückert B, Rodriguez-Coira J, Zhakparov D, Huang M, Jakiela B, Sanak M, Moniuszko M, O'Mahony L, Jutel M, Kebadze T, Jackson JD, Edwards RM, Thiel V, Johnston LS, Akdis AC, Sokolowska M. Rhinovirus-induced epithelial RIG-I inflammasome suppresses antiviral immunity and promotes inflammation in asthma and COVID-19. Nat Commun 2023; 14:2329. [PMID: 37087523 PMCID: PMC10122208 DOI: 10.1038/s41467-023-37470-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/16/2023] [Indexed: 04/24/2023] Open
Abstract
Rhinoviruses and allergens, such as house dust mite are major agents responsible for asthma exacerbations. The influence of pre-existing airway inflammation on the infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is largely unknown. We analyse mechanisms of response to viral infection in experimental in vivo rhinovirus infection in healthy controls and patients with asthma, and in in vitro experiments with house dust mite, rhinovirus and SARS-CoV-2 in human primary airway epithelium. Here, we show that rhinovirus infection in patients with asthma leads to an excessive RIG-I inflammasome activation, which diminishes its accessibility for type I/III interferon responses, leading to their early functional impairment, delayed resolution, prolonged viral clearance and unresolved inflammation in vitro and in vivo. Pre-exposure to house dust mite augments this phenomenon by inflammasome priming and auxiliary inhibition of early type I/III interferon responses. Prior infection with rhinovirus followed by SARS-CoV-2 infection augments RIG-I inflammasome activation and epithelial inflammation. Timely inhibition of the epithelial RIG-I inflammasome may lead to more efficient viral clearance and lower the burden of rhinovirus and SARS-CoV-2 infections.
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Affiliation(s)
- Urszula Radzikowska
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
- Christine Kühne - Center for Allergy Research and Education (CK-CARE), Herman-Burchard-Strasse 1, 7265, Davos Wolfgang, Switzerland
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, Waszyngtona 13 Str., 15-269, Bialystok, Poland
| | - Andrzej Eljaszewicz
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
- Christine Kühne - Center for Allergy Research and Education (CK-CARE), Herman-Burchard-Strasse 1, 7265, Davos Wolfgang, Switzerland
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, Waszyngtona 13 Str., 15-269, Bialystok, Poland
| | - Ge Tan
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Nino Stocker
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
| | - Anja Heider
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
| | - Patrick Westermann
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
| | - Silvio Steiner
- Institute of Virology and Immunology (IVI), Laenggassstrasse 122, 3012, Bern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Laenggassstrasse 122, 3012, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Mittelstrasse 43, 3012, Bern, Switzerland
| | - Anita Dreher
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
- Christine Kühne - Center for Allergy Research and Education (CK-CARE), Herman-Burchard-Strasse 1, 7265, Davos Wolfgang, Switzerland
| | - Paulina Wawrzyniak
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
- Christine Kühne - Center for Allergy Research and Education (CK-CARE), Herman-Burchard-Strasse 1, 7265, Davos Wolfgang, Switzerland
- Division of Clinical Chemistry and Biochemistry, University Children's Hospital Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
- Children's Research Center, University Children's Hospital Zurich, Raemistrasse 100, 8091, Zurich, Switzerland
| | - Beate Rückert
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
| | - Juan Rodriguez-Coira
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
- IMMA, Department of Basic Medical Sciences, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities Madrid, C. de Julian Romea 23, 28003, Madrid, Spain
- Centre for Metabolomics and Bioanalysis (CEMBIO), Department of Chemistry and Biochemistry, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities Madrid, Urb. Monteprincipe 28925, Alcorcon, Madrid, Spain
| | - Damir Zhakparov
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
| | - Mengting Huang
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
| | - Bogdan Jakiela
- Department of Internal Medicine, Jagiellonian University Medical College, M. Skawinska 8 Str., 31-066, Krakow, Poland
| | - Marek Sanak
- Department of Internal Medicine, Jagiellonian University Medical College, M. Skawinska 8 Str., 31-066, Krakow, Poland
| | - Marcin Moniuszko
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, Waszyngtona 13 Str., 15-269, Bialystok, Poland
- Department of Allergology and Internal Medicine, Medical University of Bialystok, M. Sklodowskiej-Curie 24A Str., 15-276, Bialystok, Poland
| | - Liam O'Mahony
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
- Department of Medicine and School of Microbiology, APC Microbiome Ireland, University College Cork, College Rd, T12 E138, Cork, Ireland
| | - Marek Jutel
- Department of Clinical Immunology, Wroclaw Medical University, wyb. Lidwika Pasteura 1 Str, 50-367, Wroclaw, Poland
- ALL-MED Medical Research Institute, Gen. Jozefa Hallera 95 Str., 53-201, Wroclaw, Poland
| | - Tatiana Kebadze
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Cale Street, London, SW3 6LY, UK
- Department of Infectious Diseases, Imperial College London, School of Medicine, St Mary's Hospital, Praed Street, London, W21NY, UK
| | - J David Jackson
- Guy's Severe Asthma Centre, School of Immunology & Microbial Sciences, King's College London, Strand, London, WC2R 2LS, UK
- Guy's & St Thomas' NHS Trust, St Thomas' Hospital, Westminster Bridge Rd, London, SE1 7EH, UK
| | - R Michael Edwards
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Cale Street, London, SW3 6LY, UK
- Asthma UK Centre in Allergic Mechanisms of Asthma, Norfolk Place, London, W2 1PG, UK
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Laenggassstrasse 122, 3012, Bern, Switzerland
- Multidisciplinary Center for Infectious Diseases, University of Bern, Hallerstrasse 6, 3012, Bern, Switzerland
| | - L Sebastian Johnston
- National Heart and Lung Institute, Imperial College London, Guy Scadding Building, Cale Street, London, SW3 6LY, UK
- Asthma UK Centre in Allergic Mechanisms of Asthma, Norfolk Place, London, W2 1PG, UK
- Imperial College Healthcare HNS Trust, The Bays, S Wharf Rd, London, W2 1NY, UK
| | - A Cezmi Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland
- Christine Kühne - Center for Allergy Research and Education (CK-CARE), Herman-Burchard-Strasse 1, 7265, Davos Wolfgang, Switzerland
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Herman-Burchard-Strasse 9, 7265, Davos Wolfgang, Switzerland.
- Christine Kühne - Center for Allergy Research and Education (CK-CARE), Herman-Burchard-Strasse 1, 7265, Davos Wolfgang, Switzerland.
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Liebhoff AM, Menden K, Laschtowitz A, Franke A, Schramm C, Bonn S. Pathogen detection in RNA-seq data with Pathonoia. BMC Bioinformatics 2023; 24:53. [PMID: 36803415 PMCID: PMC9938591 DOI: 10.1186/s12859-023-05144-z] [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: 08/29/2022] [Accepted: 01/10/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND Bacterial and viral infections may cause or exacerbate various human diseases and to detect microbes in tissue, one method of choice is RNA sequencing. The detection of specific microbes using RNA sequencing offers good sensitivity and specificity, but untargeted approaches suffer from high false positive rates and a lack of sensitivity for lowly abundant organisms. RESULTS We introduce Pathonoia, an algorithm that detects viruses and bacteria in RNA sequencing data with high precision and recall. Pathonoia first applies an established k-mer based method for species identification and then aggregates this evidence over all reads in a sample. In addition, we provide an easy-to-use analysis framework that highlights potential microbe-host interactions by correlating the microbial to the host gene expression. Pathonoia outperforms state-of-the-art methods in microbial detection specificity, both on in silico and real datasets. CONCLUSION Two case studies in human liver and brain show how Pathonoia can support novel hypotheses on microbial infection exacerbating disease. The Python package for Pathonoia sample analysis and a guided analysis Jupyter notebook for bulk RNAseq datasets are available on GitHub.
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Affiliation(s)
- Anna-Maria Liebhoff
- Institute for Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. .,Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, USA.
| | - Kevin Menden
- grid.424247.30000 0004 0438 0426Department of Genome Biology of Neurodegenerative Diseases, DZNE, Tübingen, Germany
| | - Alena Laschtowitz
- grid.13648.380000 0001 2180 3484I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Andre Franke
- grid.9764.c0000 0001 2153 9986Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Christoph Schramm
- grid.13648.380000 0001 2180 3484I. Department of Medicine, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany ,grid.13648.380000 0001 2180 3484Martin Zeitz Center for Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany ,grid.13648.380000 0001 2180 3484Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Bonn
- grid.13648.380000 0001 2180 3484Institute for Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Stocker N, Radzikowska U, Wawrzyniak P, Tan G, Huang M, Ding M, Akdis CA, Sokolowska M. Regulation of angiotensin-converting enzyme 2 isoforms by type 2 inflammation and viral infection in human airway epithelium. Mucosal Immunol 2023; 16:5-16. [PMID: 36642382 PMCID: PMC9836991 DOI: 10.1016/j.mucimm.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 12/06/2022] [Indexed: 01/15/2023]
Abstract
SARS-CoV-2 enters human cells through its main receptor, angiotensin-converting enzyme 2 (ACE2), which constitutes a limiting factor of infection. Recent findings demonstrating novel ACE2 isoforms implicate that this receptor is regulated in a more complex way than previously anticipated. However, it remains unknown how various inflammatory conditions influence the abundance of these ACE2 variants. Hence, we studied expression of ACE2 messenger RNA (mRNA) and protein isoforms, together with its glycosylation and spatial localization in primary human airway epithelium upon allergic inflammation and viral infection. We found that interleukin-13, the main type 2 cytokine, decreased expression of long ACE2 mRNA and reduced glycosylation of full-length ACE2 protein via alteration of N-linked glycosylation process, limiting its availability on the apical side of ciliated cells. House dust mite allergen did not affect the expression of ACE2. Rhinovirus infection increased short ACE2 mRNA, but it did not influence its protein expression. In addition, by screening other SARS-CoV-2 related host molecules, we found that interleukin-13 and rhinovirus significantly regulated mRNA, but not protein of transmembrane serine protease 2 and neuropilin 1. Regulation of ACE2 and other host proteins was comparable in healthy and asthmatic epithelium, underlining the lack of intrinsic differences but dependence on the inflammatory milieu in the airways.
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Affiliation(s)
- Nino Stocker
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
| | - Urszula Radzikowska
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland; Christine Kühne - Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - Paulina Wawrzyniak
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland; Department of Gastroenterology and Hepatology, University Hospital Zürich, University of Zürich, Zürich, Switzerland
| | - Ge Tan
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
| | - Mengting Huang
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
| | - Mei Ding
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland; Christine Kühne - Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland; Christine Kühne - Center for Allergy Research and Education (CK-CARE), Davos, Switzerland.
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6
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Ong HH, Andiappan AK, Duan K, Lum J, Liu J, Tan KS, Howland S, Lee B, Ong YK, Thong M, Chow VT, Wang DY. Transcriptomics of rhinovirus persistence reveals sustained expression of RIG-I and interferon-stimulated genes in nasal epithelial cells in vitro. Allergy 2022; 77:2778-2793. [PMID: 35274302 DOI: 10.1111/all.15280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 02/19/2022] [Accepted: 02/21/2022] [Indexed: 01/27/2023]
Abstract
BACKGROUND Human rhinoviruses (HRVs) are frequently associated with asthma exacerbations, and have been found in the airways of asthmatic patients. While HRV-induced acute infection is well-documented, it is less clear whether the nasal epithelium sustains prolonged HRV infections along with the associated activation of host immune responses. OBJECTIVE To investigate sustainably regulated host responses of human nasal epithelial cells (hNECs) during HRV persistence. METHODS Using a time-course study, HRV16 persistence and viral replication dynamics were established using an in vitro infection model of hNECs. RNA sequencing was performed on hNECs in the early and late stages of infection at 3 and 14 days post-infection (dpi), respectively. The functional enrichment of differentially expressed genes (DEGs) was evaluated using gene ontology (GO) and Ingenuity pathway analysis. RESULTS HRV RNA and protein expression persisted throughout prolonged infections, even after decreased production of infectious virus progeny. GO analysis of unique DEGs indicated altered regulation of pathways related to ciliary function and airway remodeling at 3 dpi and serine-type endopeptidase activity at 14 dpi. The functional enrichment of shared DEGs between the two time-points was related to interferon (IFN) and cytoplasmic pattern recognition receptor (PRR) signaling pathways. Validation of the sustained regulation of candidate genes confirmed the persistent expression of RIG-I and revealed its close co-regulation with interferon-stimulated genes (ISGs) during HRV persistence. CONCLUSIONS The persistence of HRV RNA does not necessarily indicate an active infection during prolonged infection. The sustained expression of RIG-I and ISGs in response to viral RNA persistence highlights the importance of assessing how immune-activating host factors can change during active HRV infection and the immune regulation that persists thereafter.
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Affiliation(s)
- Hsiao Hui Ong
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Anand Kumar Andiappan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Kaibo Duan
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Josephine Lum
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jing Liu
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Kai Sen Tan
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Biosafety level 3 Core Facility, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore, Singapore
| | - Shanshan Howland
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Bernett Lee
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yew Kwang Ong
- Department of Otolaryngology - Head & Neck Surgery, National University Health System, Singapore, Singapore
| | - Mark Thong
- Department of Otolaryngology - Head & Neck Surgery, National University Health System, Singapore, Singapore
| | - Vincent T Chow
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - De-Yun Wang
- Department of Otolaryngology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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7
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Privitera GF, Alaimo S, Ferro A, Pulvirenti A. Virus finding tools: current solutions and limitations. Brief Bioinform 2022; 23:6618234. [PMID: 35753694 DOI: 10.1093/bib/bbac235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/02/2022] [Accepted: 05/20/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION The study of the Human Virome remains challenging nowadays. Viral metagenomics, through high-throughput sequencing data, is the best choice for virus discovery. The metagenomics approach is culture-independent and sequence-independent, helping search for either known or novel viruses. Though it is estimated that more than 40% of the viruses found in metagenomics analysis are not recognizable, we decided to analyze several tools to identify and discover viruses in RNA-seq samples. RESULTS We have analyzed eight Virus Tools for the identification of viruses in RNA-seq data. These tools were compared using a synthetic dataset of 30 viruses and a real one. Our analysis shows that no tool succeeds in recognizing all the viruses in the datasets. So we can conclude that each of these tools has pros and cons, and their choice depends on the application domain. AVAILABILITY Synthetic data used through the review and raw results of their analysis can be found at https://zenodo.org/record/6426147. FASTQ files of real data can be found in GEO (https://www.ncbi.nlm.nih.gov/gds) or ENA (https://www.ebi.ac.uk/ena/browser/home). Raw results of their analysis can be downloaded from https://zenodo.org/record/6425917.
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Affiliation(s)
- Grete Francesca Privitera
- Department of Physics and Astronomy, University of Catania, Viale A. Doria, 6, 95125, Catania, Italy
| | - Salvatore Alaimo
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dept. of Math. and Comp. Science Viale A. Doria, 6, 95125, Catania, Italy
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dept. of Math. and Comp. Science Viale A. Doria, 6, 95125, Catania, Italy
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, University of Catania, c/o Dept. of Math. and Comp. Science Viale A. Doria, 6, 95125, Catania, Italy
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8
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Wang Z, Wu J, Jiang J, Ma Q, Song M, Xu T, Liu Y, Chen Z, Bao Y, Huang M, Zhang M, Ji N. KIF2A decreases IL-33 production and attenuates allergic asthmatic inflammation. ALLERGY, ASTHMA, AND CLINICAL IMMUNOLOGY : OFFICIAL JOURNAL OF THE CANADIAN SOCIETY OF ALLERGY AND CLINICAL IMMUNOLOGY 2022; 18:55. [PMID: 35718777 PMCID: PMC9208156 DOI: 10.1186/s13223-022-00697-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 06/05/2022] [Indexed: 11/21/2022]
Abstract
Background The microtubule-dependent molecular motor protein Kinesin Family Member 2A (KIF2A) is down-regulated in asthmatic human airway epithelium. However, little is known about the roles of KIF2A as well as the possible underlying mechanisms in asthma. Methods House dust mite (HDM) extract was administered to establish a murine model of asthma. The expression of KIF2A, IL-33 and the autophagy pathways were detected. The plasmid pCMV-KIF2A was used to overexpress KIF2A in the airway epithelial cells in vitro and in vivo. IL-4, IL-5, IL-33 and other cytokines in bronchoalveolar lavage fluid (BALF) and lung tissues homogenates were measured. Results In response to the challenge of house dust mite (HDM) in vitro and in vivo, airway epithelial cells displayed decreased production of KIF2A. Meanwhile, autophagy and IL-33 were increased in HMD-treated epithelial cells. Mechanistically, KIF2A decreased autophagy via suppressing mTORC1 pathway in HDM-treated epithelial cells, which contributed to the reduced production of IL-33. Moreover, in vivo KIF2A transfection reduced IL-33 and autophagy in the lung, leading to the attenuation of allergic asthma. Conclusion KIF2A suppressed mTORC1-mediated autophagy and decreased the production of epithelial-derived cytokine IL-33 in allergic airway inflammation. These data indicate that KIF2A may be a novel target in allergic asthma. Supplementary Information The online version contains supplementary material available at 10.1186/s13223-022-00697-9.
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Affiliation(s)
- Zhengxia Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jingjing Wu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jingxian Jiang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qiyun Ma
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Meijuan Song
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Tingting Xu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yanan Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhongqi Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yanmin Bao
- Department of Respiratory Medicine, Shenzhen Children's Hospital, Shenzhen, China
| | - Mao Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mingshun Zhang
- Jiangsu Province Engineering Research Center of Antibody Drug, NHC Key Laboratory of Antibody Technique, Department of Immunology, Nanjing Medical University, Nanjing, China.
| | - Ningfei Ji
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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9
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Liew KY, Koh SK, Hooi SL, Ng MKL, Chee HY, Harith HH, Israf DA, Tham CL. Rhinovirus-Induced Cytokine Alterations With Potential Implications in Asthma Exacerbations: A Systematic Review and Meta-Analysis. Front Immunol 2022; 13:782936. [PMID: 35242128 PMCID: PMC8886024 DOI: 10.3389/fimmu.2022.782936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Accepted: 01/13/2022] [Indexed: 12/01/2022] Open
Abstract
Background Rhinovirus (RV) infections are a major cause of asthma exacerbations. Unlike other respiratory viruses, RV causes minimal cytotoxic effects on airway epithelial cells and cytokines play a critical role in its pathogenesis. However, previous findings on RV-induced cytokine responses were largely inconsistent. Thus, this study sought to identify the cytokine/chemokine profiles induced by RV infection and their correlations with airway inflammatory responses and/or respiratory symptoms using systematic review, and to determine whether a quantitative difference exists in cytokine levels between asthmatic and healthy individuals via meta-analysis. Methods Relevant articles were obtained from PubMed, Scopus, and ScienceDirect databases. Studies that compared RV-induced cytokine responses between asthmatic and healthy individuals were included in the systematic review, and their findings were categorized based on the study designs, which were ex vivo primary bronchial epithelial cells (PBECs), ex vivo peripheral blood mononuclear cells (PBMCs), and human experimental studies. Data on cytokine levels were also extracted and analyzed using Review Manager 5.4. Results Thirty-four articles were included in the systematic review, with 18 of these further subjected to meta-analysis. Several studies reported the correlations between the levels of cytokines, such as IL-8, IL-4, IL-5, and IL-13, and respiratory symptoms. Evidence suggests that IL-25 and IL-33 may be the cytokines that promote type 2 inflammation in asthmatics after RV infection. Besides that, a meta-analysis revealed that PBECs from children with atopic asthma produced significantly lower levels of IFN-β [Effect size (ES): -0.84, p = 0.030] and IFN-λ (ES: -1.00, p = 0.002), and PBECs from adult atopic asthmatics produced significantly lower levels of IFN-β (ES: -0.68, p = 0.009), compared to healthy subjects after RV infection. A trend towards a deficient production of IFN-γ (ES: -0.56, p = 0.060) in PBMCs from adult atopic asthmatics was observed. In lower airways, asthmatics also had significantly lower baseline IL-15 (ES: -0.69, p = 0.020) levels. Conclusion Overall, RV-induced asthma exacerbations are potentially caused by an imbalance between Th1 and Th2 cytokines, which may be contributed by defective innate immune responses at cellular levels. Exogenous IFNs delivery may be beneficial as a prophylactic approach for RV-induced asthma exacerbations. Systematic Review Registration https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=184119, identifier CRD42020184119.
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Affiliation(s)
- Kong Yen Liew
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Sue Kie Koh
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Suet Li Hooi
- School of Science, Monash University Malaysia, Subang Jaya, Malaysia
| | | | - Hui-Yee Chee
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Hanis Hazeera Harith
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Daud Ahmad Israf
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Chau Ling Tham
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Malaysia
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10
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Targeting intercellular adhesion molecule-1 (ICAM-1) to reduce rhinovirus-induced acute exacerbations in chronic respiratory diseases. Inflammopharmacology 2022; 30:725-735. [PMID: 35316427 PMCID: PMC8938636 DOI: 10.1007/s10787-022-00968-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 02/24/2022] [Indexed: 01/21/2023]
Abstract
The chronic respiratory non-communicable diseases, asthma and chronic obstructive pulmonary disease (COPD) are among the leading causes of global mortality and morbidity. Individuals suffering from these diseases are particularly susceptible to respiratory infections caused by bacterial and/or viral pathogens, which frequently result in exacerbation of symptoms, lung function decline, frequent hospital emergency visits and increased socioeconomic burden. Human rhinoviruses (HRV) remain the major viral pathogen group implicated in exacerbations of both asthma and COPD. The rhinoviral entry into the host lung epithelium is facilitated primarily by the adhesion site (“receptor”) intercellular adhesion molecule-1 (ICAM-1), coincidentally expressed on the respiratory epithelium in these conditions. Multiple observations of increased airway ICAM-1 protein in asthmatics, smokers and smoking-related COPD have been recorded in the literature. However, the lack of robust therapies for COPD in particular has triggered a renewed interest in assessing receptor antagonism-based anti-viral strategies for treatment of intercurrent viral infections in those with pre-existing chronic lung diseases. Given the crucial role ICAM-1 plays in facilitating HRV adhesion and, thus, transmissibility to the host respiratory system, as well as the up-regulation of ICAM-1 by smoking, we summarize the role of HRV in smoking-induced COPD and especially highlight the role of ICAM-1 in epithelial viral adhesion and chronic lung disease progression. Further, the review also sheds light specifically on evolving precision therapeutic strategies in blocking ICAM-1 for preventing viral adhesion and exacerbations of COPD.
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11
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Balázs A, Millar-Büchner P, Mülleder M, Farztdinov V, Szyrwiel L, Addante A, Kuppe A, Rubil T, Drescher M, Seidel K, Stricker S, Eils R, Lehmann I, Sawitzki B, Röhmel J, Ralser M, Mall MA. Age-Related Differences in Structure and Function of Nasal Epithelial Cultures From Healthy Children and Elderly People. Front Immunol 2022; 13:822437. [PMID: 35296085 PMCID: PMC8918506 DOI: 10.3389/fimmu.2022.822437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/28/2022] [Indexed: 11/13/2022] Open
Abstract
The nasal epithelium represents the first line of defense against inhaled pathogens, allergens, and irritants and plays a key role in the pathogenesis of a spectrum of acute and chronic airways diseases. Despite age-dependent clinical phenotypes triggered by these noxious stimuli, little is known about how aging affects the structure and function of the airway epithelium that is crucial for lung homeostasis and host defense. The aim of this study was therefore to determine age-related differences in structural and functional properties of primary nasal epithelial cultures from healthy children and non-smoking elderly people. To achieve this goal, highly differentiated nasal epithelial cultures were established from nasal brushes at air–liquid interface and used to study epithelial cell type composition, mucin (MUC5AC and MUC5B) expression, and ion transport properties. Furthermore, we determined age-dependent molecular signatures using global proteomic analysis. We found lower numeric densities of ciliated cells and higher levels of MUC5AC expression in cultures from children vs. elderly people. Bioelectric studies showed no differences in basal ion transport properties, ENaC-mediated sodium absorption, or CFTR-mediated chloride transport, but detected decreased calcium-activated TMEM16A-mediated chloride secretory responses in cultures from children vs. elderly people. Proteome analysis identified distinct age-dependent molecular signatures associated with ciliation and mucin biosynthesis, as well as other pathways implicated in aging. Our data identified intrinsic, age-related differences in structure and function of the nasal epithelium and provide a basis for further studies on the role of these findings in age-dependent airways disease phenotypes observed with a spectrum of respiratory infections and other noxious stimuli.
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Affiliation(s)
- Anita Balázs
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Chariteí - Universitaätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany
- *Correspondence: Anita Balázs, ; Marcus A. Mall,
| | - Pamela Millar-Büchner
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Chariteí - Universitaätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany
| | - Michael Mülleder
- Charité - Universitätsmedizin Berlin, Core Facility - High-Throughput Mass Spectrometry, Berlin, Germany
| | - Vadim Farztdinov
- Charité - Universitätsmedizin Berlin, Core Facility - High-Throughput Mass Spectrometry, Berlin, Germany
| | - Lukasz Szyrwiel
- Charité - Universitätsmedizin Berlin, Core Facility - High-Throughput Mass Spectrometry, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
| | - Annalisa Addante
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Chariteí - Universitaätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany
| | - Aditi Kuppe
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Chariteí - Universitaätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany
| | - Tihomir Rubil
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Chariteí - Universitaätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany
| | - Marika Drescher
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Chariteí - Universitaätsmedizin Berlin, Berlin, Germany
| | - Kathrin Seidel
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Chariteí - Universitaätsmedizin Berlin, Berlin, Germany
| | - Sebastian Stricker
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Chariteí - Universitaätsmedizin Berlin, Berlin, Germany
| | - Roland Eils
- German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany
- Center for Digital Health, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Irina Lehmann
- German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany
- Molecular Epidemiology Unit, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Birgit Sawitzki
- Institute of Medical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jobst Röhmel
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Chariteí - Universitaätsmedizin Berlin, Berlin, Germany
| | - Markus Ralser
- Charité - Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
- The Francis Crick Institute, Molecular Biology of Metabolism Laboratory, London, United Kingdom
| | - Marcus A. Mall
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Chariteí - Universitaätsmedizin Berlin, Berlin, Germany
- German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité, Berlin, Germany
- *Correspondence: Anita Balázs, ; Marcus A. Mall,
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12
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Costa-Martins AG, Mane K, Lindsey BB, Ogava RL, Castro Í, Jagne YJ, Sallah HJ, Armitage EP, Jarju S, Ahadzie B, Ellis-Watson R, Tregoning JS, Bingle CD, Bogaert D, Clarke E, Ordovas-Montanes J, Jeffries D, Kampmann B, Nakaya HI, de Silva TI. Prior upregulation of interferon pathways in the nasopharynx impacts viral shedding following live attenuated influenza vaccine challenge in children. Cell Rep Med 2021; 2:100465. [PMID: 35028607 PMCID: PMC8714852 DOI: 10.1016/j.xcrm.2021.100465] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/28/2021] [Accepted: 11/12/2021] [Indexed: 02/06/2023]
Abstract
In children lacking influenza-specific adaptive immunity, upper respiratory tract innate immune responses may influence viral replication and disease outcome. We use trivalent live attenuated influenza vaccine (LAIV) as a surrogate challenge model in children aged 24-59 months to identify pre-infection mucosal transcriptomic signatures associated with subsequent viral shedding. Upregulation of interferon signaling pathways prior to LAIV is significantly associated with lower strain-specific viral loads (VLs) at days 2 and 7. Several interferon-stimulated genes are differentially expressed in children with pre-LAIV asymptomatic respiratory viral infections and negatively correlated with LAIV VLs. Upregulation of genes enriched in macrophages, neutrophils, and eosinophils is associated with lower VLs and found more commonly in children with asymptomatic viral infections. Variability in pre-infection mucosal interferon gene expression in children may impact the course of subsequent influenza infections. This variability may be due to frequent respiratory viral infections, demonstrating the potential importance of mucosal virus-virus interactions in children.
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Affiliation(s)
- André G. Costa-Martins
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Scientific Platform Pasteur, University of São Paulo, São Paulo, Brazil
| | - Karim Mane
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Benjamin B. Lindsey
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK
| | - Rodrigo L.T. Ogava
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ícaro Castro
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ya Jankey Jagne
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Hadijatou J. Sallah
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Edwin P. Armitage
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Sheikh Jarju
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Bankole Ahadzie
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Rebecca Ellis-Watson
- The University of Edinburgh/MRC Centre for Inflammation Research, The Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - John S. Tregoning
- Department of Infectious Disease, Imperial College London, London W2 1NY, UK
| | - Colin D. Bingle
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK
| | - Debby Bogaert
- The University of Edinburgh/MRC Centre for Inflammation Research, The Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK
| | - Ed Clarke
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital, Boston, MA 02115, USA
- Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - David Jeffries
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
| | - Beate Kampmann
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
- The Vaccine Centre, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Helder I. Nakaya
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Scientific Platform Pasteur, University of São Paulo, São Paulo, Brazil
- Corresponding author
| | - Thushan I. de Silva
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, P.O. Box 273, Fajara, The Gambia
- The Florey Institute for Host-Pathogen Interactions and Department of Infection, Immunity and Cardiovascular Disease, The University of Sheffield, Sheffield S10 2RX, UK
- Corresponding author
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13
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Menzel M, Akbarshahi H, Mahmutovic Persson I, Andersson C, Puthia M, Uller L. NFκB1 Dichotomously Regulates Pro-Inflammatory and Antiviral Responses in Asthma. J Innate Immun 2021; 14:182-191. [PMID: 34350857 DOI: 10.1159/000517847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/13/2021] [Indexed: 11/19/2022] Open
Abstract
Asthma exacerbations are commonly triggered by rhinovirus infections. Viruses can activate the NFκB pathway resulting in airway inflammation and increased Th2 cytokine expression. NFκB signaling is also involved in early activation of IFNβ, which is a central mediator of antiviral responses to rhinovirus infection. Using a mouse model, this study tests our hypothesis that NFκB signaling is involved in impaired IFNβ production at viral-induced asthma exacerbations. C57BL/6 wild-type and NFκB1-/- mice were challenged with house dust mite for 3 weeks and were subsequently stimulated with the rhinoviral mimic poly(I:C). General lung inflammatory parameters and levels of the Th2 upstream cytokine IL-33 were measured after allergen challenge. At exacerbation, production of IFNβ and antiviral proteins as well as gene expression of pattern recognition receptors and IRF3/IRF7 was assessed. In the asthma exacerbation mouse model, lack of NFκB1 resulted in lower levels of IL-33 after allergen challenge alone and was associated with reduced eosinophilia. At exacerbation, mice deficient in NFκB1 exhibited enhanced expression of IFNβ and antiviral proteins. This was accompanied by increased IRF3/IRF7 expression and induction of pattern recognition receptor expression. In a human asthma dataset, a negative correlation between IRF3 and NFκB1 expression was observed. NFκB may impair antiviral responses at exacerbation, possibly by reducing expression of the transcription factors IRF3/IRF7. These findings suggest a therapeutic potential for targeting NFκB pathways at viral infection-induced exacerbations.
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Affiliation(s)
- Mandy Menzel
- Respiratory Immunopharmacology, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Hamid Akbarshahi
- Respiratory Immunopharmacology, Department of Experimental Medical Sciences, Lund University, Lund, Sweden.,Respiratory Medicine and Allergology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Irma Mahmutovic Persson
- Respiratory Immunopharmacology, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Cecilia Andersson
- Respiratory Cell Biology, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
| | - Manoj Puthia
- Division of Dermatology and Venerology, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Lena Uller
- Respiratory Immunopharmacology, Department of Experimental Medical Sciences, Lund University, Lund, Sweden
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14
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Jakiela B, Rebane A, Soja J, Bazan-Socha S, Laanesoo A, Plutecka H, Surmiak M, Sanak M, Sladek K, Bochenek G. Remodeling of bronchial epithelium caused by asthmatic inflammation affects its response to rhinovirus infection. Sci Rep 2021; 11:12821. [PMID: 34140575 PMCID: PMC8211645 DOI: 10.1038/s41598-021-92252-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/08/2021] [Indexed: 02/05/2023] Open
Abstract
Human rhinoviruses (HRV) are frequent cause of asthma exacerbations, however the influence of airway inflammation on the severity of viral infection is poorly understood. Here, we investigated how cytokine-induced remodeling of airway epithelium modulates antiviral response. We analyzed gene expression response in in vitro differentiated bronchial epithelium exposed to cytokines and next infected with HRV16. IL-13-induced mucous cell metaplasia (MCM) was associated with impaired ciliogenesis and induction of antiviral genes, resulting in lower susceptibility to HRV. Epithelial-mesenchymal transition caused by TGF-β was associated with increased virus replication and boosted innate response. Moreover, HRV infection per se caused transient upregulation of MCM markers and growth factors, followed by low-level virus replication and shedding. Our data suggest that the outcome of HRV infection depends on the type of lower airway inflammation and the extent of epithelial damage. Type-2 inflammation (eosinophilic asthma) may induce antiviral state of epithelium and decrease virus sensitivity, while growth factor exposure during epithelial repair may facilitate virus replication and inflammatory response. Additionally, responses to HRV were similar in cells obtained from asthma patients and control subjects, which implicates that antiviral mechanisms are not intrinsically impaired in asthma, but may develop in the presence of uncontrolled airway inflammation.
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Affiliation(s)
- Bogdan Jakiela
- grid.5522.00000 0001 2162 9631Department of Internal Medicine, Faculty of Medicine, Jagiellonian University Medical College, Skawinska 8, 31-066 Kraków, Poland
| | - Ana Rebane
- grid.10939.320000 0001 0943 7661Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Jerzy Soja
- grid.5522.00000 0001 2162 9631Department of Internal Medicine, Faculty of Medicine, Jagiellonian University Medical College, Skawinska 8, 31-066 Kraków, Poland
| | - Stanislawa Bazan-Socha
- grid.5522.00000 0001 2162 9631Department of Internal Medicine, Faculty of Medicine, Jagiellonian University Medical College, Skawinska 8, 31-066 Kraków, Poland
| | - Anet Laanesoo
- grid.10939.320000 0001 0943 7661Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Hanna Plutecka
- grid.5522.00000 0001 2162 9631Department of Internal Medicine, Faculty of Medicine, Jagiellonian University Medical College, Skawinska 8, 31-066 Kraków, Poland
| | - Marcin Surmiak
- grid.5522.00000 0001 2162 9631Department of Internal Medicine, Faculty of Medicine, Jagiellonian University Medical College, Skawinska 8, 31-066 Kraków, Poland
| | - Marek Sanak
- grid.5522.00000 0001 2162 9631Department of Internal Medicine, Faculty of Medicine, Jagiellonian University Medical College, Skawinska 8, 31-066 Kraków, Poland
| | - Krzysztof Sladek
- grid.5522.00000 0001 2162 9631Department of Internal Medicine, Faculty of Medicine, Jagiellonian University Medical College, Skawinska 8, 31-066 Kraków, Poland
| | - Grazyna Bochenek
- grid.5522.00000 0001 2162 9631Department of Internal Medicine, Faculty of Medicine, Jagiellonian University Medical College, Skawinska 8, 31-066 Kraków, Poland
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15
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Plante JA, Liu Y, Liu J, Xia H, Johnson BA, Lokugamage KG, Zhang X, Muruato AE, Zou J, Fontes-Garfias CR, Mirchandani D, Scharton D, Bilello JP, Ku Z, An Z, Kalveram B, Freiberg AN, Menachery VD, Xie X, Plante KS, Weaver SC, Shi PY. Spike mutation D614G alters SARS-CoV-2 fitness. Nature 2021; 592:116-121. [PMID: 33106671 PMCID: PMC8158177 DOI: 10.1038/s41586-020-2895-3] [Citation(s) in RCA: 1071] [Impact Index Per Article: 357.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/20/2020] [Indexed: 11/09/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein substitution D614G became dominant during the coronavirus disease 2019 (COVID-19) pandemic1,2. However, the effect of this variant on viral spread and vaccine efficacy remains to be defined. Here we engineered the spike D614G substitution in the USA-WA1/2020 SARS-CoV-2 strain, and found that it enhances viral replication in human lung epithelial cells and primary human airway tissues by increasing the infectivity and stability of virions. Hamsters infected with SARS-CoV-2 expressing spike(D614G) (G614 virus) produced higher infectious titres in nasal washes and the trachea, but not in the lungs, supporting clinical evidence showing that the mutation enhances viral loads in the upper respiratory tract of COVID-19 patients and may increase transmission. Sera from hamsters infected with D614 virus exhibit modestly higher neutralization titres against G614 virus than against D614 virus, suggesting that the mutation is unlikely to reduce the ability of vaccines in clinical trials to protect against COVID-19, and that therapeutic antibodies should be tested against the circulating G614 virus. Together with clinical findings, our work underscores the importance of this variant in viral spread and its implications for vaccine efficacy and antibody therapy.
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Affiliation(s)
- Jessica A Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jianying Liu
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Bryan A Johnson
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Kumari G Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xianwen Zhang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Antonio E Muruato
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Camila R Fontes-Garfias
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Divya Mirchandani
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Dionna Scharton
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Birte Kalveram
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Alexander N Freiberg
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D Menachery
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Kenneth S Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Scott C Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
| | - Pei-Yong Shi
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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16
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Sridhar A, Simmini S, Ribeiro CMS, Tapparel C, Evers MM, Pajkrt D, Wolthers K. A Perspective on Organoids for Virology Research. Viruses 2020; 12:v12111341. [PMID: 33238561 PMCID: PMC7700289 DOI: 10.3390/v12111341] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/12/2020] [Accepted: 11/22/2020] [Indexed: 12/27/2022] Open
Abstract
Animal models and cell lines are invaluable for virology research and host-pathogen interaction studies. However, it is increasingly evident that these models are not sufficient to fully understand human viral diseases. With the advent of three-dimensional organotypic cultures, it is now possible to study viral infections in the human context. This perspective explores the potential of these organotypic cultures, also known as organoids, for virology research, antiviral testing, and shaping the virology landscape.
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Affiliation(s)
- Adithya Sridhar
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, 1100 AZ Amsterdam, The Netherlands; (A.S.); (D.P.)
- Department of Pediatric Infectious Diseases, Emma Children’s Hospital, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, 1100 AZ Amsterdam, The Netherlands
| | - Salvatore Simmini
- Gastrointestinal Biology Group, STEMCELL Technologies UK Ltd., Cambridge CB28 9TL, UK;
| | - Carla M. S. Ribeiro
- Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam UMC, University of Amsterdam, 1100 AZ Amsterdam, The Netherlands;
| | - Caroline Tapparel
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland;
- Division of Infectious Diseases, Geneva University Hospital, 1205 Geneva, Switzerland
| | - Melvin M. Evers
- Department of Research and Development, uniQure Biopharma B.V., 1105 BE Amsterdam, The Netherlands;
| | - Dasja Pajkrt
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, 1100 AZ Amsterdam, The Netherlands; (A.S.); (D.P.)
- Department of Pediatric Infectious Diseases, Emma Children’s Hospital, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, 1100 AZ Amsterdam, The Netherlands
| | - Katja Wolthers
- OrganoVIR Labs, Department of Medical Microbiology, Amsterdam UMC, Location Academic Medical Center, University of Amsterdam, 1100 AZ Amsterdam, The Netherlands; (A.S.); (D.P.)
- Correspondence:
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17
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Michi AN, Love ME, Proud D. Rhinovirus-Induced Modulation of Epithelial Phenotype: Role in Asthma. Viruses 2020; 12:v12111328. [PMID: 33227953 PMCID: PMC7699223 DOI: 10.3390/v12111328] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/17/2020] [Accepted: 11/17/2020] [Indexed: 12/15/2022] Open
Abstract
Human rhinoviruses have been linked both to the susceptibility of asthma development and to the triggering of acute exacerbations. Given that the human airway epithelial cell is the primary site of human rhinovirus (HRV) infection and replication, the current review focuses on how HRV-induced modulation of several aspects of epithelial cell phenotype could contribute to the development of asthma or to the induction of exacerbations. Modification of epithelial proinflammatory and antiviral responses are considered, as are alterations in an epithelial barrier function and cell phenotype. The contributions of the epithelium to airway remodeling and to the potential modulation of immune responses are also considered. The potential interactions of each type of HRV-induced epithelial phenotypic changes with allergic sensitization and allergic phenotype are also considered in the context of asthma development and of acute exacerbations.
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18
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Cao X, Coyle JP, Xiong R, Wang Y, Heflich RH, Ren B, Gwinn WM, Hayden P, Rojanasakul L. Invited review: human air-liquid-interface organotypic airway tissue models derived from primary tracheobronchial epithelial cells-overview and perspectives. In Vitro Cell Dev Biol Anim 2020; 57:104-132. [PMID: 33175307 PMCID: PMC7657088 DOI: 10.1007/s11626-020-00517-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/29/2020] [Indexed: 02/07/2023]
Abstract
The lung is an organ that is directly exposed to the external environment. Given the large surface area and extensive ventilation of the lung, it is prone to exposure to airborne substances, such as pathogens, allergens, chemicals, and particulate matter. Highly elaborate and effective mechanisms have evolved to protect and maintain homeostasis in the lung. Despite these sophisticated defense mechanisms, the respiratory system remains highly susceptible to environmental challenges. Because of the impact of respiratory exposure on human health and disease, there has been considerable interest in developing reliable and predictive in vitro model systems for respiratory toxicology and basic research. Human air-liquid-interface (ALI) organotypic airway tissue models derived from primary tracheobronchial epithelial cells have in vivo–like structure and functions when they are fully differentiated. The presence of the air-facing surface allows conducting in vitro exposures that mimic human respiratory exposures. Exposures can be conducted using particulates, aerosols, gases, vapors generated from volatile and semi-volatile substances, and respiratory pathogens. Toxicity data have been generated using nanomaterials, cigarette smoke, e-cigarette vapors, environmental airborne chemicals, drugs given by inhalation, and respiratory viruses and bacteria. Although toxicity evaluations using human airway ALI models require further standardization and validation, this approach shows promise in supplementing or replacing in vivo animal models for conducting research on respiratory toxicants and pathogens.
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Affiliation(s)
- Xuefei Cao
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., AR, Jefferson, USA.
| | - Jayme P Coyle
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
| | - Rui Xiong
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., AR, Jefferson, USA
| | - Yiying Wang
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., AR, Jefferson, USA
| | - Robert H Heflich
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., AR, Jefferson, USA
| | - Baiping Ren
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd., AR, Jefferson, USA
| | - William M Gwinn
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Durham, NC, USA
| | | | - Liying Rojanasakul
- Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, WV, USA
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19
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Affiliation(s)
- Ricardo Wesley Alberca
- Laboratorio de Dermatologia e Imunodeficiencias (LIM-56), Departamento de Dermatologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, Brazil
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20
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Branco ACCC, Sato MN, Alberca RW. The Possible Dual Role of the ACE2 Receptor in Asthma and Coronavirus (SARS-CoV2) Infection. Front Cell Infect Microbiol 2020; 10:550571. [PMID: 33072624 PMCID: PMC7538685 DOI: 10.3389/fcimb.2020.550571] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/26/2020] [Indexed: 01/08/2023] Open
Affiliation(s)
- Anna Cláudia Calvielli Castelo Branco
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, School of Medicine and Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, Brazil
| | - Maria Notomi Sato
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, School of Medicine and Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, Brazil
| | - Ricardo Wesley Alberca
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, School of Medicine and Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, Brazil
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21
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Shi PY, Plante J, Liu Y, Liu J, Xia H, Johnson B, Lokugamage K, Zhang X, Muruato A, Zou J, Fontes-Garfias C, Mirchandani D, Scharton D, Kalveram B, Bilello J, Ku Z, An Z, Freiberg A, Menachery V, Xie X, Plante K, Weaver S. Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. RESEARCH SQUARE 2020:rs.3.rs-70482. [PMID: 32935091 PMCID: PMC7491579 DOI: 10.21203/rs.3.rs-70482/v1] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A spike protein mutation D614G became dominant in SARS-CoV-2 during the COVID-19 pandemic. However, the mutational impact on viral spread and vaccine efficacy remains to be defined. Here we engineer the D614G mutation in the SARS-CoV-2 USA-WA1/2020 strain and characterize its effect on viral replication, pathogenesis, and antibody neutralization. The D614G mutation significantly enhances SARS-CoV-2 replication on human lung epithelial cells and primary human airway tissues, through an improved infectivity of virions with the spike receptor-binding domain in an "up" conformation for binding to ACE2 receptor. Hamsters infected with D614 or G614 variants developed similar levels of weight loss. However, the G614 virus produced higher infectious titers in the nasal washes and trachea, but not lungs, than the D614 virus. The hamster results confirm clinical evidence that the D614G mutation enhances viral loads in the upper respiratory tract of COVID-19 patients and may increases transmission. For antibody neutralization, sera from D614 virus-infected hamsters consistently exhibit higher neutralization titers against G614 virus than those against D614 virus, indicating that (i) the mutation may not reduce the ability of vaccines in clinical trials to protect against COVID-19 and (ii) therapeutic antibodies should be tested against the circulating G614 virus before clinical development.
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Affiliation(s)
- Pei-Yong Shi
- The University of Texas Medical Branch at Galveston
| | | | - Yang Liu
- University of Texas Medical Branch
| | | | | | | | | | | | | | | | | | | | | | | | | | - Zhiqiang Ku
- The University of Texas Health Science Center at Houston
| | - Zhiqiang An
- University of Texas Health Science Center at Houston
| | | | | | | | | | - Scott Weaver
- The University of Texas Medical Branch at Galveston
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22
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Plante JA, Liu Y, Liu J, Xia H, Johnson BA, Lokugamage KG, Zhang X, Muruato AE, Zou J, Fontes-Garfias CR, Mirchandani D, Scharton D, Bilello JP, Ku Z, An Z, Kalveram B, Freiberg AN, Menachery VD, Xie X, Plante KS, Weaver SC, Shi PY. Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.09.01.278689. [PMID: 32908978 PMCID: PMC7480025 DOI: 10.1101/2020.09.01.278689] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A spike protein mutation D614G became dominant in SARS-CoV-2 during the COVID-19 pandemic. However, the mutational impact on viral spread and vaccine efficacy remains to be defined. Here we engineer the D614G mutation in the SARS-CoV-2 USA-WA1/2020 strain and characterize its effect on viral replication, pathogenesis, and antibody neutralization. The D614G mutation significantly enhances SARS-CoV-2 replication on human lung epithelial cells and primary human airway tissues, through an improved infectivity of virions with the spike receptor-binding domain in an "up" conformation for binding to ACE2 receptor. Hamsters infected with D614 or G614 variants developed similar levels of weight loss. However, the G614 virus produced higher infectious titers in the nasal washes and trachea, but not lungs, than the D614 virus. The hamster results confirm clinical evidence that the D614G mutation enhances viral loads in the upper respiratory tract of COVID-19 patients and may increases transmission. For antibody neutralization, sera from D614 virus-infected hamsters consistently exhibit higher neutralization titers against G614 virus than those against D614 virus, indicating that (i) the mutation may not reduce the ability of vaccines in clinical trials to protect against COVID-19 and (ii) therapeutic antibodies should be tested against the circulating G614 virus before clinical development.
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Affiliation(s)
- Jessica A. Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
| | - Jianying Liu
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
| | - Bryan A. Johnson
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
| | - Kumari G. Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Xianwen Zhang
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
| | - Antonio E. Muruato
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
| | - Camila R. Fontes-Garfias
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
| | - Divya Mirchandani
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Dionna Scharton
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | | | - Zhiqiang Ku
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, USA
| | - Birte Kalveram
- Department of Pathology, University of Texas Medical Branch, Galveston TX, USA
| | - Alexander N. Freiberg
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston TX, USA
- Center for Biodefense & Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Vineet D. Menachery
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
| | - Kenneth S. Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
| | - Scott C. Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston TX, USA
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston TX, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA
- Center for Biodefense & Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA
- Center for Biodefense & Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
- Lead Contact
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23
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Nakagome K, Shimizu T, Bochkov YA, Noguchi T, Kobayashi T, Soma T, Ueki S, Gern JE, Nagata M. Cadherin-related family member 3 upregulates the effector functions of eosinophils. Allergy 2020; 75:1805-1809. [PMID: 32056219 DOI: 10.1111/all.14229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/03/2020] [Accepted: 02/11/2020] [Indexed: 01/07/2023]
Affiliation(s)
- Kazuyuki Nakagome
- Department of Respiratory Medicine Saitama Medical University Saitama Japan
- Allergy Center Saitama Medical University Saitama Japan
| | - Toshiaki Shimizu
- Department of Respiratory Medicine Saitama Medical University Saitama Japan
- Allergy Center Saitama Medical University Saitama Japan
| | - Yury A. Bochkov
- Department of Pediatrics School of Medicine and Public Health University of Wisconsin Madison WI USA
| | - Toru Noguchi
- Department of Respiratory Medicine Saitama Medical University Saitama Japan
- Allergy Center Saitama Medical University Saitama Japan
| | - Takehito Kobayashi
- Department of Respiratory Medicine Saitama Medical University Saitama Japan
- Allergy Center Saitama Medical University Saitama Japan
| | - Tomoyuki Soma
- Department of Respiratory Medicine Saitama Medical University Saitama Japan
- Allergy Center Saitama Medical University Saitama Japan
| | - Shigeharu Ueki
- Department of General Internal Medicine and Clinical Laboratory Medicine Akita University Graduate School of Medicine Akita Japan
| | - James E. Gern
- Department of Pediatrics School of Medicine and Public Health University of Wisconsin Madison WI USA
- Department of Medicine School of Medicine and Public Health University of Wisconsin Madison WI USA
| | - Makoto Nagata
- Department of Respiratory Medicine Saitama Medical University Saitama Japan
- Allergy Center Saitama Medical University Saitama Japan
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24
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Ganjian H, Rajput C, Elzoheiry M, Sajjan U. Rhinovirus and Innate Immune Function of Airway Epithelium. Front Cell Infect Microbiol 2020; 10:277. [PMID: 32637363 PMCID: PMC7316886 DOI: 10.3389/fcimb.2020.00277] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
Airway epithelial cells, which lines the respiratory mucosa is in direct contact with the environment. Airway epithelial cells are the primary target for rhinovirus and other inhaled pathogens. In response to rhinovirus infection, airway epithelial cells mount both pro-inflammatory responses and antiviral innate immune responses to clear the virus efficiently. Some of the antiviral responses include the expression of IFNs, endoplasmic reticulum stress induced unfolded protein response and autophagy. Airway epithelial cells also recruits other innate immune cells to establish antiviral state and resolve the inflammation in the lungs. In patients with chronic lung disease, these responses may be either defective or induced in excess leading to deficient clearing of virus and sustained inflammation. In this review, we will discuss the mechanisms underlying antiviral innate immunity and the dysregulation of some of these mechanisms in patients with chronic lung diseases.
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Affiliation(s)
- Haleh Ganjian
- Department of Thoracic Medicine and Surgery, Lewis Katz Medical School, Temple University, Philadelphia, PA, United States
| | - Charu Rajput
- Department of Thoracic Medicine and Surgery, Lewis Katz Medical School, Temple University, Philadelphia, PA, United States
| | - Manal Elzoheiry
- Department of Thoracic Medicine and Surgery, Lewis Katz Medical School, Temple University, Philadelphia, PA, United States
| | - Umadevi Sajjan
- Department of Thoracic Medicine and Surgery, Lewis Katz Medical School, Temple University, Philadelphia, PA, United States
- Department of Physiology, Lewis Katz Medical School, Temple University, Philadelphia, PA, United States
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Veerati PC, Troy NM, Reid AT, Li NF, Nichol KS, Kaur P, Maltby S, Wark PAB, Knight DA, Bosco A, Grainge CL, Bartlett NW. Airway Epithelial Cell Immunity Is Delayed During Rhinovirus Infection in Asthma and COPD. Front Immunol 2020; 11:974. [PMID: 32499788 PMCID: PMC7243842 DOI: 10.3389/fimmu.2020.00974] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/24/2020] [Indexed: 12/31/2022] Open
Abstract
Respiratory viral infections, particularly those caused by rhinovirus, exacerbate chronic respiratory inflammatory diseases, such as asthma and chronic obstructive pulmonary disease (COPD). Airway epithelial cells are the primary site of rhinovirus replication and responsible of initiating the host immune response to infection. Numerous studies have reported that the anti-viral innate immune response (including type I and type III interferon) in asthma is less effective or deficient leading to the conclusion that epithelial innate immunity is a key determinant of disease severity during a rhinovirus induced exacerbation. However, deficient rhinovirus-induced epithelial interferon production in asthma has not always been observed. We hypothesized that disparate in vitro airway epithelial infection models using high multiplicity of infection (MOI) and lacking genome-wide, time course analyses have obscured the role of epithelial innate anti-viral immunity in asthma and COPD. To address this, we developed a low MOI rhinovirus model of differentiated primary epithelial cells obtained from healthy, asthma and COPD donors. Using genome-wide gene expression following infection, we demonstrated that gene expression patterns are similar across patient groups, but that the kinetics of induction are delayed in cells obtained from asthma and COPD donors. Rhinovirus-induced innate immune responses were defined by interferons (type-I, II, and III), interferon response factors (IRF1, IRF3, and IRF7), TLR signaling and NF-κB and STAT1 activation. Induced gene expression was evident at 24 h and peaked at 48 h post-infection in cells from healthy subjects. In contrast, in cells from donors with asthma or COPD induction was maximal at or beyond 72–96 h post-infection. Thus, we propose that propensity for viral exacerbations of asthma and COPD relate to delayed (rather than deficient) expression of epithelial cell innate anti-viral immune genes which in turns leads to a delayed and ultimately more inflammatory host immune response.
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Affiliation(s)
- Punnam Chander Veerati
- School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, Australia.,Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, NSW, Australia
| | - Niamh M Troy
- Systems Immunology, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Andrew T Reid
- School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, Australia.,Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, NSW, Australia
| | - Ngan Fung Li
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, NSW, Australia.,School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
| | - Kristy S Nichol
- School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, Australia.,Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, NSW, Australia
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, Faculty of Science, The University of Western Australia, Perth, WA, Australia
| | - Steven Maltby
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, NSW, Australia.,School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
| | - Peter A B Wark
- School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, Australia.,Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, NSW, Australia.,Department of Respiratory and Sleep Medicine, John Hunter Hospital, New Lambton Heights, NSW, Australia
| | - Darryl A Knight
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, NSW, Australia.,School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia.,Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, BC, Canada.,Research and Academic Affairs, Providence Health Care Research Institute, Vancouver, BC, Canada
| | - Anthony Bosco
- Systems Immunology, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Chris L Grainge
- School of Medicine and Public Health, University of Newcastle, Callaghan, NSW, Australia.,Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, NSW, Australia.,Department of Respiratory and Sleep Medicine, John Hunter Hospital, New Lambton Heights, NSW, Australia
| | - Nathan W Bartlett
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, University of Newcastle, New Lambton Heights, NSW, Australia.,School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia
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Differential asthma odds following respiratory infection in children from three minority populations. PLoS One 2020; 15:e0231782. [PMID: 32369487 PMCID: PMC7199930 DOI: 10.1371/journal.pone.0231782] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/31/2020] [Indexed: 01/01/2023] Open
Abstract
RATIONALE Severe early-life respiratory illnesses, particularly those caused by respiratory syncytial virus (RSV) and human rhinovirus (HRV), are strongly associated with the development of asthma in children. Puerto Rican children in particular have a strikingly high asthma burden. However, prior studies of the potential associations between early-life respiratory illnesses and asthma in Puerto Rican and other minority populations have been limited. OBJECTIVES We sought to determine whether early-life respiratory illness was associated with asthma in Puerto Rican, Mexican American, and African American children. METHODS Using a logistic regression analysis, we examined the association between early-life respiratory illnesses (report of upper respiratory infection (URI), pneumonia, bronchitis, and bronchiolitis/RSV) within the first two years of life and physician-diagnosed asthma after the age of two in a large cohort of Puerto Rican, Mexican American, and African American children. MEASUREMENTS AND MAIN RESULTS While early-life respiratory illnesses were associated with greater asthma odds in Puerto Ricans, Mexican Americans, and African Americans, these associations were stronger among Puerto Rican children. Specifically, in Puerto Ricans, the odds was 6.15 (95% CI: 4.21-9.05) if the child reported at least one of the following respiratory illness: URI, pneumonia, bronchitis or bronchiolitis. The odds were also higher in Puerto Ricans when considering these conditions separately. CONCLUSIONS We observed population-specific associations between early-life respiratory illnesses and asthma, which were especially significant and stronger in Puerto Ricans. Taken together with the known high burden of RSV in Puerto Rico, our results may help explain the high burden of asthma in Puerto Ricans.
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Duclos GE, Teixeira VH, Autissier P, Gesthalter YB, Reinders-Luinge MA, Terrano R, Dumas YM, Liu G, Mazzilli SA, Brandsma CA, van den Berge M, Janes SM, Timens W, Lenburg ME, Spira A, Campbell JD, Beane J. Characterizing smoking-induced transcriptional heterogeneity in the human bronchial epithelium at single-cell resolution. SCIENCE ADVANCES 2019; 5:eaaw3413. [PMID: 31844660 PMCID: PMC6905872 DOI: 10.1126/sciadv.aaw3413] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 10/15/2019] [Indexed: 06/10/2023]
Abstract
The human bronchial epithelium is composed of multiple distinct cell types that cooperate to defend against environmental insults. While studies have shown that smoking alters bronchial epithelial function and morphology, its precise effects on specific cell types and overall tissue composition are unclear. We used single-cell RNA sequencing to profile bronchial epithelial cells from six never and six current smokers. Unsupervised analyses led to the characterization of a set of toxin metabolism genes that localized to smoker ciliated cells, tissue remodeling associated with a loss of club cells and extensive goblet cell hyperplasia, and a previously unidentified peri-goblet epithelial subpopulation in smokers who expressed a marker of bronchial premalignant lesions. Our data demonstrate that smoke exposure drives a complex landscape of cellular alterations that may prime the human bronchial epithelium for disease.
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Affiliation(s)
- Grant E. Duclos
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Vitor H. Teixeira
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Patrick Autissier
- Boston University Flow Cytometry Core Facility, Boston University School of Medicine, Boston, MA, USA
| | - Yaron B. Gesthalter
- Department of Medicine, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Marjan A. Reinders-Luinge
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, Netherlands
| | - Robert Terrano
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Yves M. Dumas
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Gang Liu
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Sarah A. Mazzilli
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, Netherlands
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, Netherlands
| | - Sam M. Janes
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
- Department of Thoracic Medicine, University College London Hospital, London, UK
| | - Wim Timens
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, Netherlands
| | - Marc E. Lenburg
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Avrum Spira
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Johnson & Johnson Innovation, Cambridge, MA, USA
| | - Joshua D. Campbell
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Jennifer Beane
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
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28
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Yang Z, Bochkov YA, Voelker DR, Foster MW, Que LG. Identification of a Novel Inhibitor of Human Rhinovirus Replication and Inflammation in Airway Epithelial Cells. Am J Respir Cell Mol Biol 2019; 60:58-67. [PMID: 30156431 DOI: 10.1165/rcmb.2018-0058oc] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Human rhinovirus (RV), the major cause of the common cold, triggers the majority of acute airway exacerbations in patients with asthma and chronic obstructive pulmonary disease. Nitric oxide, and the related metabolite S-nitrosoglutathione, are produced in the airway epithelium via nitric oxide synthase (NOS) 2 and have been shown to function in host defense against RV infection. We hypothesized that inhibitors of the S-nitrosoglutathione-metabolizing enzyme, S-nitrosoglutathione reductase (GSNOR), might potentiate the antiviral properties of airway-derived NOS2. Using in vitro models of RV-A serotype 16 (RV-A16) and mNeonGreen-H1N1pr8 infection of human airway epithelial cells, we found that treatment with a previously characterized GSNOR inhibitor (4-[[2-[[(3-cyanophenyl)methyl]thio]-4-oxothieno-[3,2-d]pyrimidin-3(4H)-yl]methyl]-benzoic acid; referred to as C3m) decreased RV-A16 replication and expression of downstream proinflammatory and antiviral mediators (e.g., RANTES [regulated upon activation, normal T cell expressed and secreted], CXCL10, and Mx1), and increased Nrf2 (nuclear factor erythroid 2-related factor 2)-dependent genes (e.g., SQSTM1 and TrxR1). In contrast, C3m had no effect on influenza virus H1N1pr8 replication. Moreover, a structurally dissimilar GSNOR inhibitor (N6022) did not alter RV replication, suggesting that the properties of C3m may be specific to rhinovirus owing to an off-target effect. Consistent with this, C3m antiviral effects were not blocked by either NOS inhibition or GSNOR knockdown but appeared to be mediated by reduced intercellular adhesion molecule 1 transcription and increased shedding of soluble intercellular adhesion molecule 1 protein. Collectively these data show that C3m has novel antirhinoviral properties that may synergize with, but are unrelated to, its GSNOR inhibitor activity.
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Affiliation(s)
- Zhonghui Yang
- 1 Department of Medicine, Duke University Health System, Durham, North Carolina
| | - Yury A Bochkov
- 2 Department of Pediatrics, University of Wisconsin, Madison, Madison, Wisconsin; and
| | - Dennis R Voelker
- 3 Department of Medicine, National Jewish Health, Denver, Colorado
| | - Matthew W Foster
- 1 Department of Medicine, Duke University Health System, Durham, North Carolina
| | - Loretta G Que
- 1 Department of Medicine, Duke University Health System, Durham, North Carolina
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29
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Warner SM, Wiehler S, Michi AN, Proud D. Rhinovirus replication and innate immunity in highly differentiated human airway epithelial cells. Respir Res 2019; 20:150. [PMID: 31299975 PMCID: PMC6626354 DOI: 10.1186/s12931-019-1120-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/01/2019] [Indexed: 12/23/2022] Open
Abstract
Background Human rhinovirus (HRV) infections are the primary cause of the common cold and are a major trigger for exacerbations of lower airway diseases, such as asthma and chronic obstructive pulmonary diseases. Although human bronchial epithelial cells (HBE) are the natural host for HRV infections, much of our understanding of how HRV replicates and induces host antiviral responses is based on studies using non-airway cell lines (e.g. HeLa cells). The current study examines the replication cycle of HRV, and host cell responses, in highly differentiated cultures of HBE. Methods Highly differentiated cultures of HBE were exposed to initial infectious doses ranging from 104 to 101 50% tissue culture-infective dose (TCID50) of purified HRV-16, and responses were monitored up to 144 h after infection. Viral genomic RNA and negative strand RNA template levels were monitored, along with levels of type I and II interferons and selected antivirals. Results Regardless of initial infectious dose, relatively constant levels of both genomic and negative strand RNA are generated during replication, with negative strand copy numbers being10,000-fold lower than those of genomic strands. Infections were limited to a small percentage of ciliated cells and did not result in any overt signs of epithelial death. Importantly, regardless of infectious dose, HRV-16 infections were cleared by HBE in the absence of immune cells. Levels of type I and type III interferons (IFNs) varied with initial infectious dose, implying that factors other than levels of double-stranded RNA regulate IFN induction, but the time-course of HRV-16 clearance HBE was the same regardless of levels of IFNs produced. Patterns of antiviral viperin and ISG15 expression suggest they may be generated in an IFN-independent manner during HRV-16 infections. Conclusions These data challenge a number of aspects of dogma generated from studies in HeLa cells and emphasize the importance of appropriate cell context when studying HRV infections.
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Affiliation(s)
- Stephanie M Warner
- Department of Physiology & Pharmacology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Shahina Wiehler
- Department of Physiology & Pharmacology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - Aubrey N Michi
- Department of Physiology & Pharmacology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada
| | - David Proud
- Department of Physiology & Pharmacology and Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, 3280 Hospital Drive NW, Calgary, AB, T2N 4Z6, Canada.
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30
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A host gene expression approach for identifying triggers of asthma exacerbations. PLoS One 2019; 14:e0214871. [PMID: 30958855 PMCID: PMC6453459 DOI: 10.1371/journal.pone.0214871] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/21/2019] [Indexed: 11/19/2022] Open
Abstract
Rationale Asthma exacerbations often occur due to infectious triggers, but determining whether infection is present and whether it is bacterial or viral remains clinically challenging. A diagnostic strategy that clarifies these uncertainties could enable personalized asthma treatment and mitigate antibiotic overuse. Objectives To explore the performance of validated peripheral blood gene expression signatures in discriminating bacterial, viral, and noninfectious triggers in subjects with asthma exacerbations. Methods Subjects with suspected asthma exacerbations of various etiologies were retrospectively selected for peripheral blood gene expression analysis from a pool of subjects previously enrolled in emergency departments with acute respiratory illness. RT-PCR quantified 87 gene targets, selected from microarray-based studies, followed by logistic regression modeling to define bacterial, viral, or noninfectious class. The model-predicted class was compared to clinical adjudication and procalcitonin. Results Of 46 subjects enrolled, 7 were clinically adjudicated as bacterial, 18 as viral, and 21 as noninfectious. Model prediction was congruent with clinical adjudication in 15/18 viral and 13/21 noninfectious cases, but only 1/7 bacterial cases. None of the adjudicated bacterial cases had confirmatory microbiology; the precise etiology in this group was uncertain. Procalcitonin classified only one subject in the cohort as bacterial. 47.8% of subjects received antibiotics. Conclusions Our model classified asthma exacerbations by the underlying bacterial, viral, and noninfectious host response. Compared to clinical adjudication, the majority of discordances occurred in the bacterial group, due to either imperfect adjudication or model misclassification. Bacterial infection was identified infrequently by all classification schemes, but nearly half of subjects were prescribed antibiotics. A gene expression-based approach may offer useful diagnostic information in this population and guide appropriate antibiotic use.
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31
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Bolmarcich J, Wilbert S, Jackson GR, Oldach J, Bachelor M, Kenney T, Wright CD, Hayden PJ. In VitroHuman Airway Models for Study of Goblet Cell Hyperplasia and Mucus Production: Effects of Th2 Cytokines, Double-Stranded RNA, and Tobacco Smoke. ACTA ACUST UNITED AC 2018. [DOI: 10.1089/aivt.2017.0001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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32
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Simon LM, Karg S, Westermann AJ, Engel M, Elbehery AHA, Hense B, Heinig M, Deng L, Theis FJ. MetaMap: an atlas of metatranscriptomic reads in human disease-related RNA-seq data. Gigascience 2018; 7:5036539. [PMID: 29901703 PMCID: PMC6025204 DOI: 10.1093/gigascience/giy070] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Background With the advent of the age of big data in bioinformatics, large volumes of data and high-performance computing power enable researchers to perform re-analyses of publicly available datasets at an unprecedented scale. Ever more studies imply the microbiome in both normal human physiology and a wide range of diseases. RNA sequencing technology (RNA-seq) is commonly used to infer global eukaryotic gene expression patterns under defined conditions, including human disease-related contexts; however, its generic nature also enables the detection of microbial and viral transcripts. Findings We developed a bioinformatic pipeline to screen existing human RNA-seq datasets for the presence of microbial and viral reads by re-inspecting the non-human-mapping read fraction. We validated this approach by recapitulating outcomes from six independent, controlled infection experiments of cell line models and compared them with an alternative metatranscriptomic mapping strategy. We then applied the pipeline to close to 150 terabytes of publicly available raw RNA-seq data from more than 17,000 samples from more than 400 studies relevant to human disease using state-of-the-art high-performance computing systems. The resulting data from this large-scale re-analysis are made available in the presented MetaMap resource. Conclusions Our results demonstrate that common human RNA-seq data, including those archived in public repositories, might contain valuable information to correlate microbial and viral detection patterns with diverse diseases. The presented MetaMap database thus provides a rich resource for hypothesis generation toward the role of the microbiome in human disease. Additionally, codes to process new datasets and perform statistical analyses are made available.
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Affiliation(s)
- L M Simon
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | - S Karg
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | - A J Westermann
- Institute of Molecular Infection Biology, University of Würzburg, Würzburg, Germany.,Helmholtz Institute for RNA-Based Infection Research, Würzburg, Germany
| | - M Engel
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,Helmholtz Zentrum München, German Research Center for Environmental Health, Scientific Computing Research Unit, Neuherberg, Germany
| | - A H A Elbehery
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Virology, Neuherberg, Germany
| | - B Hense
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | - M Heinig
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany
| | - L Deng
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Virology, Neuherberg, Germany
| | - F J Theis
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.,Department of Mathematics, Technische Universität München, Munich, Germany
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Gelfand EW, Schedel M. Molecular Endotypes Contribute to the Heterogeneity of Asthma. Immunol Allergy Clin North Am 2018; 38:655-665. [PMID: 30342586 DOI: 10.1016/j.iac.2018.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Diagnosis and management of asthma is commonly implemented based on clinical assessment. Although these nonmolecular biomarkers have been useful, limited resolution of the heterogeneity among asthmatic patients and little information regarding the underlying pathobiology of disease in individuals have been provided. Molecular endotying using global transcriptome expression profiling associated with clinical features of asthma has improved our understanding of disease mechanisms, risk assessment of asthma exacerbations, and treatment responses, especially in patients with type 2 inflammation. Further advances in establishing pathobiological subgroups, bioactive pathways, and true disease endotypes hold potential for a more personalized medical approach in asthmatic patients.
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Affiliation(s)
- Erwin W Gelfand
- Division of Cell Biology, Department of Pediatrics, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA
| | - Michaela Schedel
- Division of Cell Biology, Department of Pediatrics, National Jewish Health, 1400 Jackson Street, Denver, CO 80206, USA.
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34
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Howell C, Smith JR, Shute JK. Targeting matrix metalloproteinase-13 in bronchial epithelial repair. Clin Exp Allergy 2018; 48:1214-1221. [PMID: 29924890 DOI: 10.1111/cea.13215] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/15/2018] [Accepted: 06/17/2018] [Indexed: 02/05/2023]
Abstract
BACKGROUND Viral infection of the bronchial epithelium disrupts the barrier properties of the epithelium in healthy individuals and those with lung disease. Repair of the bronchial epithelium is dependent of the formation of a provisional fibrin matrix and migration of epithelial cells to cover denuded areas, followed by proliferation and differentiation. OBJECTIVE The objective was to test the hypothesis that poly I:C, a model of viral infection, limits epithelial repair through the stimulated release of matrix metalloproteinase-13 (MMP-13). METHODS Confluent layers of cultured normal human primary bronchial epithelial cells (NHBE) and SV-40 virus-transformed 16HBE14o- bronchial epithelial cells were mechanically wounded, and video microscopy used to measure the rate of wound closure over 2 hours, in the absence and presence of poly I:C (1-20 μg/mL). MMP-13, tissue factor and endothelin release were measured by ELISA. The effect of inhibitors of MMP-13 activity and expression and a nonspecific endothelin receptor antagonist, bosentan, on the rate of epithelial repair was investigated. RESULTS Poly I:C limited the rate of epithelial repair, and NHBE were significantly more sensitive to poly I:C effects than 16HBE14o- cells. NHBE, but not 16HBE14o-, released MMP-13 in response to poly I:C. Inhibitors of MMP-13 activity (WAY 170523) and expression (dimethyl fumarate) significantly enhanced the rate of repair. Bosentan enhanced the rate of bronchial epithelial repair by a mechanism that was independent of MMP-13. CONCLUSIONS AND CLINICAL RELEVANCE Bronchial epithelial repair is limited by endothelin and by MMP-13, a protease that degrades coagulation factors, such as fibrinogen, and matrix proteins essential for epithelial repair. Further studies with primary cells from patients are needed to confirm whether repurposing bosentan and inhibitors of MMP-13 expression or activity, for inhalation may be a useful therapeutic strategy in diseases where repeated cycles of epithelial injury and repair occur, such as asthma and COPD.
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Affiliation(s)
- Christopher Howell
- School of Pharmacy and Biomedical Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - James R Smith
- School of Pharmacy and Biomedical Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
| | - Janis K Shute
- School of Pharmacy and Biomedical Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, UK
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35
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Jackson GR, Maione AG, Klausner M, Hayden PJ. Prevalidation of an Acute Inhalation Toxicity Test Using the EpiAirway In Vitro Human Airway Model. ACTA ACUST UNITED AC 2018; 4:149-158. [PMID: 29904643 PMCID: PMC5994905 DOI: 10.1089/aivt.2018.0004] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Introduction: Knowledge of acute inhalation toxicity potential is important for establishing safe use of chemicals and consumer products. Inhalation toxicity testing and classification procedures currently accepted within worldwide government regulatory systems rely primarily on tests conducted in animals. The goal of the current work was to develop and prevalidate a nonanimal (in vitro) test for determining acute inhalation toxicity using the EpiAirway™ in vitro human airway model as a potential alternative for currently accepted animal tests. Materials and Methods: The in vitro test method exposes EpiAirway tissues to test chemicals for 3 hours, followed by measurement of tissue viability as the test endpoint. Fifty-nine chemicals covering a broad range of toxicity classes, chemical structures, and physical properties were evaluated. The in vitro toxicity data were utilized to establish a prediction model to classify the chemicals into categories corresponding to the currently accepted Globally Harmonized System (GHS) and the Environmental Protection Agency (EPA) system. Results: The EpiAirway prediction model identified in vivo rat-based GHS Acute Inhalation Toxicity Category 1–2 and EPA Acute Inhalation Toxicity Category I–II chemicals with 100% sensitivity and specificity of 43.1% and 50.0%, for GHS and EPA acute inhalation toxicity systems, respectively. The sensitivity and specificity of the EpiAirway prediction model for identifying GHS specific target organ toxicity-single exposure (STOT-SE) Category 1 human toxicants were 75.0% and 56.5%, respectively. Corrosivity and electrophilic and oxidative reactivity appear to be the predominant mechanisms of toxicity for the most highly toxic chemicals. Conclusions: These results indicate that the EpiAirway test is a promising alternative to the currently accepted animal tests for acute inhalation toxicity.
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Loxham M, Smart DE, Bedke NJ, Smithers NP, Filippi I, Blume C, Swindle EJ, Tariq K, Howarth PH, Holgate ST, Davies DE. Allergenic proteases cleave the chemokine CX3CL1 directly from the surface of airway epithelium and augment the effect of rhinovirus. Mucosal Immunol 2018; 11:404-414. [PMID: 28677664 DOI: 10.1038/mi.2017.63] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 05/29/2017] [Indexed: 02/04/2023]
Abstract
CX3CL1 has been implicated in allergen-induced airway CD4+ T-lymphocyte recruitment in asthma. As epidemiological evidence supports a viral infection-allergen synergy in asthma exacerbations, we postulated that rhinovirus (RV) infection in the presence of allergen augments epithelial CX3CL1 release. Fully differentiated primary bronchial epithelial cultures were pretreated apically with house dust mite (HDM) extract and infected with rhinovirus-16 (RV16). CX3CL1 was measured by enzyme-linked immunosorbent assay and western blotting, and shedding mechanisms assessed using inhibitors, protease-activated receptor-2 (PAR-2) agonist, and recombinant CX3CL1-expressing HEK293T cells. Basolateral CX3CL1 release was unaffected by HDM but stimulated by RV16; inhibition by fluticasone or GM6001 implicated nuclear factor-κB and ADAM (A Disintegrin and Metalloproteinase) sheddases. Conversely, apical CX3CL1 shedding was stimulated by HDM and augmented by RV16. Although fluticasone or GM6001 reduced RV16+HDM-induced apical CX3CL1 release, heat inactivation or cysteine protease inhibition completely blocked CX3CL1 shedding. The HDM effect was via enzymatic cleavage of CX3CL1, not PAR-2 activation, yielding a product mitogenic for smooth muscle cells. Extracts of Alternaria fungus caused similar CX3CL1 shedding. We have identified a novel mechanism whereby allergenic proteases cleave CX3CL1 from the apical epithelial surface to yield a biologically active product. RV16 infection augmented HDM-induced CX3CL1 shedding-this may contribute to synergy between allergen exposure and RV infection in triggering asthma exacerbations and airway remodeling.
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Affiliation(s)
- M Loxham
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK.,Institute for Life Sciences, Highfield Campus, University of Southampton, Southampton, UK
| | - D E Smart
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK
| | - N J Bedke
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK
| | - N P Smithers
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK
| | - I Filippi
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK.,Cellular and Molecular Physiology Unit, Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - C Blume
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK
| | - E J Swindle
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK.,Institute for Life Sciences, Highfield Campus, University of Southampton, Southampton, UK
| | - K Tariq
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK.,NIHR Southampton Respiratory Biomedical Research Unit, University Hospital Southampton, Southampton, UK
| | - P H Howarth
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK.,NIHR Southampton Respiratory Biomedical Research Unit, University Hospital Southampton, Southampton, UK
| | - S T Holgate
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK
| | - D E Davies
- Academic Unit of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, University Hospital Southampton, Southampton, UK.,Institute for Life Sciences, Highfield Campus, University of Southampton, Southampton, UK.,NIHR Southampton Respiratory Biomedical Research Unit, University Hospital Southampton, Southampton, UK
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37
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Stenberg Hammar K, Niespodziana K, van Hage M, Kere J, Valenta R, Hedlin G, Söderhäll C. Reduced CDHR3 expression in children wheezing with rhinovirus. Pediatr Allergy Immunol 2018; 29:200-206. [PMID: 29314338 DOI: 10.1111/pai.12858] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/15/2017] [Indexed: 01/12/2023]
Abstract
BACKGROUND Rhinovirus-induced wheezing in young children has been associated with increased asthma risk at school age. Recently, the transmembrane protein cadherin-related family member 3 (CDHR3) was identified as the RV-C receptor and the genetic variant rs6967330 (p.Cys529Tyr) was reported to be associated with enhanced RV-C binding and increased replication in vitro. The aim of this study was to examine rs6967330 genotypes and mRNA expression of CDHR3 in relation to presence of rhinovirus and clinical symptoms in children with acute wheezing and compare to a group of age-matched healthy children. METHODS rs6967330;G>A was genotyped (n = 216), and CDHR3 mRNA expression was measured in peripheral blood leukocytes (n = 69) from a subgroup of children wheezing with RV infection acute and at a follow-up visit 2-3 months later, and in healthy controls. Standardized TaqMan assays were used. RESULTS The risk allele rs6967330-A was over-represented in the wheezing group (P < .001). Reduced mRNA levels of CDHR3 were found in children with acute wheezing as compared to the control group (P = .001). Children with the rs6967330 genotypes AA/AG showed the largest differences in CDHR3 expression between acute and follow-up visit (P < .04). CONCLUSIONS Preschool children with RV-induced wheezing were shown to have reduced CDHR3 mRNA levels, which might result in an increased permeability of the epithelial layers of the airways and thereby an increased vulnerability. Thus, measuring CDHR3 mRNA levels might help to identify a more severe phenotype of wheezing preschool children.
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Affiliation(s)
- Katarina Stenberg Hammar
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Centre of Allergy Research, Karolinska Institutet, Stockholm, Sweden
| | - Katarzyna Niespodziana
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Marianne van Hage
- Immunology and Allergy Unit, Department of Medicine, Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Rudolf Valenta
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Gunilla Hedlin
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Centre of Allergy Research, Karolinska Institutet, Stockholm, Sweden
| | - Cilla Söderhäll
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Centre of Allergy Research, Karolinska Institutet, Stockholm, Sweden.,Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
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38
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Gon Y, Hashimoto S. Role of airway epithelial barrier dysfunction in pathogenesis of asthma. Allergol Int 2018; 67:12-17. [PMID: 28941636 DOI: 10.1016/j.alit.2017.08.011] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 08/02/2017] [Accepted: 08/07/2017] [Indexed: 12/20/2022] Open
Abstract
Bronchial asthma is characterized by persistent cough, increased sputum, and repeated wheezing. The pathophysiology underlying these symptoms is the hyper-responsiveness of the airway along with chronic airway inflammation. Repeated injury, repair, and regeneration of the airway epithelium following exposure to environmental factors and inflammation results in histological changes and functional abnormalities in the airway mucosal epithelium; such changes are believed to have a significant association with the pathophysiology of asthma. Damage to the barrier functions of the airway epithelium enhances mucosal permeability of foreign substances in the airway epithelium of patients with asthma. Thus, epithelial barrier fragility is closely involved in releasing epithelial cytokines (e.g., TSLP, IL-25, and IL-33) because of the activation of airway epithelial cells, dendritic cells, and innate group 2 innate lymphoid cells (ILC2). Functional abnormalities of the airway epithelial cells along with the activation of dendritic cells, Th2 cells, and ILC2 form a single immunopathological unit that is considered to cause allergic airway inflammation. Here we use the latest published literature to discuss the potential pathological mechanisms regarding the onset and progressive severity of asthma with regard to the disruption of the airway epithelial function.
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Martinovich KM, Iosifidis T, Buckley AG, Looi K, Ling KM, Sutanto EN, Kicic-Starcevich E, Garratt LW, Shaw NC, Montgomery S, Lannigan FJ, Knight DA, Kicic A, Stick SM. Conditionally reprogrammed primary airway epithelial cells maintain morphology, lineage and disease specific functional characteristics. Sci Rep 2017; 7:17971. [PMID: 29269735 PMCID: PMC5740081 DOI: 10.1038/s41598-017-17952-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/04/2017] [Indexed: 01/19/2023] Open
Abstract
Current limitations to primary cell expansion led us to test whether airway epithelial cells derived from healthy children and those with asthma and cystic fibrosis (CF), co-cultured with an irradiated fibroblast feeder cell in F-medium containing 10 µM ROCK inhibitor could maintain their lineage during expansion and whether this is influenced by underlying disease status. Here, we show that conditionally reprogrammed airway epithelial cells (CRAECs) can be established from both healthy and diseased phenotypes. CRAECs can be expanded, cryopreserved and maintain phenotypes over at least 5 passages. Population doublings of CRAEC cultures were significantly greater than standard cultures, but maintained their lineage characteristics. CRAECs from all phenotypes were also capable of fully differentiating at air-liquid interface (ALI) and maintained disease specific characteristics including; defective CFTR channel function cultures and the inability to repair wounds. Our findings indicate that CRAECs derived from children maintain lineage, phenotypic and importantly disease-specific functional characteristics over a specified passage range.
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Affiliation(s)
- Kelly M Martinovich
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Crawley, Western Australia, Australia
| | - Thomas Iosifidis
- School of Paediatrics and Child Health, The University of Western Australia, Crawley, Western Australia, Australia.,Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Alysia G Buckley
- Centre of Microscopy, Characterisation and Analysis, The University of Western Australia, Crawley, Western Australia, Australia
| | - Kevin Looi
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Crawley, Western Australia, Australia
| | - Kak-Ming Ling
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Crawley, Western Australia, Australia
| | - Erika N Sutanto
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Crawley, Western Australia, Australia
| | - Elizabeth Kicic-Starcevich
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Crawley, Western Australia, Australia
| | - Luke W Garratt
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Crawley, Western Australia, Australia
| | - Nicole C Shaw
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Crawley, Western Australia, Australia
| | - Samuel Montgomery
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Crawley, Western Australia, Australia
| | - Francis J Lannigan
- School of Paediatrics and Child Health, The University of Western Australia, Crawley, Western Australia, Australia
| | - Darryl A Knight
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, New South Wales, Australia.,Priority Research Centre for Asthma and Respiratory Disease, Hunter Medical Research Institute, Newcastle, New South Wales, Australia.,Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Anthony Kicic
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Crawley, Western Australia, Australia. .,School of Paediatrics and Child Health, The University of Western Australia, Crawley, Western Australia, Australia. .,Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia, Nedlands, Western Australia, Australia. .,Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, Western Australia, Australia. .,Occupation and Environment, School of Public Health, Curtin University, Perth, Western Australia, Australia.
| | - Stephen M Stick
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Crawley, Western Australia, Australia.,School of Paediatrics and Child Health, The University of Western Australia, Crawley, Western Australia, Australia.,Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia, Nedlands, Western Australia, Australia.,Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, Western Australia, Australia
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40
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Upton N, Jackson DJ, Nikonova AA, Hingley-Wilson S, Khaitov M, del Rosario A, Traub S, Trujillo-Torralbo MB, Habibi M, Elkin SL, Kon OM, Edwards MR, Mallia P, Footitt J, Macintyre J, Stanciu LA, Johnston SL, Sykes A. Rhinovirus induction of fractalkine (CX3CL1) in airway and peripheral blood mononuclear cells in asthma. PLoS One 2017; 12:e0183864. [PMID: 28859129 PMCID: PMC5578648 DOI: 10.1371/journal.pone.0183864] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 08/12/2017] [Indexed: 12/21/2022] Open
Abstract
Rhinovirus infection is associated with the majority of asthma exacerbations. The role of fractalkine in anti-viral (type 1) and pathogenic (type 2) responses to rhinovirus infection in allergic asthma is unknown. To determine whether (1) fractalkine is produced in airway cells and in peripheral blood leucocytes, (2) rhinovirus infection increases production of fractalkine and (3) levels of fractalkine differ in asthmatic compared to non-asthmatic subjects. Fractalkine protein and mRNA levels were measured in bronchoalveolar lavage (BAL) cells and peripheral blood mononuclear cells (PBMCs) from non-asthmatic controls (n = 15) and mild allergic asthmatic (n = 15) subjects. Protein levels of fractalkine were also measured in macrophages polarised ex vivo to give M1 (type 1) and M2 (type 2) macrophages and in BAL fluid obtained from mild (n = 11) and moderate (n = 14) allergic asthmatic and non-asthmatic control (n = 10) subjects pre and post in vivo rhinovirus infection. BAL cells produced significantly greater levels of fractalkine than PBMCs. Rhinovirus infection increased production of fractalkine by BAL cells from non-asthmatic controls (P<0.01) and in M1-polarised macrophages (P<0.05), but not in BAL cells from mild asthmatics or in M2 polarised macrophages. Rhinovirus induced fractalkine in PBMCs from asthmatic (P<0.001) and healthy control subjects (P<0.05). Trends towards induction of fractalkine in moderate asthmatic subjects during in vivo rhinovirus infection failed to reach statistical significance. Fractalkine may be involved in both immunopathological and anti-viral immune responses to rhinovirus infection. Further investigation into how fractalkine is regulated across different cell types and into the effect of stimulation including rhinovirus infection is warranted to better understand the precise role of this unique dual adhesion factor and chemokine in immune cell recruitment.
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Affiliation(s)
- Nadine Upton
- Airway Disease Infection Section, National Heart & Lung Institute, Imperial College London, London, United Kingdom
- MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, London, United Kingdom
- Randall Division of Cell and Molecular Biophysics, Kings College London, London, United Kingdom
| | - David J. Jackson
- Airway Disease Infection Section, National Heart & Lung Institute, Imperial College London, London, United Kingdom
- MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, London, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Alexandra A. Nikonova
- NRC institute of Immunology FMBA, Moscow, Russian Federation
- Mechnikov Research Institute for Vaccines and Sera, Moscow, Russian Federation
- * E-mail:
| | - Suzie Hingley-Wilson
- Respiratory Infection Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Musa Khaitov
- NRC institute of Immunology FMBA, Moscow, Russian Federation
| | - Ajerico del Rosario
- Airway Disease Infection Section, National Heart & Lung Institute, Imperial College London, London, United Kingdom
- MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, London, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Stephanie Traub
- Airway Disease Infection Section, National Heart & Lung Institute, Imperial College London, London, United Kingdom
- MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, London, United Kingdom
| | - Maria-Belen Trujillo-Torralbo
- Airway Disease Infection Section, National Heart & Lung Institute, Imperial College London, London, United Kingdom
- MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, London, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Max Habibi
- Airway Disease Infection Section, National Heart & Lung Institute, Imperial College London, London, United Kingdom
- MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, London, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
- Respiratory Infection Section, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Sarah L. Elkin
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Onn M. Kon
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Michael R. Edwards
- Airway Disease Infection Section, National Heart & Lung Institute, Imperial College London, London, United Kingdom
- MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, London, United Kingdom
| | - Patrick Mallia
- Airway Disease Infection Section, National Heart & Lung Institute, Imperial College London, London, United Kingdom
- MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, London, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Joseph Footitt
- Airway Disease Infection Section, National Heart & Lung Institute, Imperial College London, London, United Kingdom
- MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, London, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Jonathan Macintyre
- Airway Disease Infection Section, National Heart & Lung Institute, Imperial College London, London, United Kingdom
- MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, London, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Luminita A. Stanciu
- Airway Disease Infection Section, National Heart & Lung Institute, Imperial College London, London, United Kingdom
- MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, London, United Kingdom
| | - Sebastian L. Johnston
- Airway Disease Infection Section, National Heart & Lung Institute, Imperial College London, London, United Kingdom
- MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, London, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Annemarie Sykes
- Airway Disease Infection Section, National Heart & Lung Institute, Imperial College London, London, United Kingdom
- MRC & Asthma UK Centre in Allergic Mechanisms of Asthma, London, United Kingdom
- Imperial College Healthcare NHS Trust, London, United Kingdom
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Shariff S, Shelfoon C, Holden NS, Traves SL, Wiehler S, Kooi C, Proud D, Leigh R. Human Rhinovirus Infection of Epithelial Cells Modulates Airway Smooth Muscle Migration. Am J Respir Cell Mol Biol 2017; 56:796-803. [PMID: 28257236 DOI: 10.1165/rcmb.2016-0252oc] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Airway remodeling, a characteristic feature of asthma, begins in early life. Recurrent human rhinovirus (HRV) infections are a potential inciting stimulus for remodeling. One component of airway remodeling is an increase in airway smooth muscle cell (ASMC) mass with a greater proximity of the ASMCs to the airway epithelium. We asked whether human bronchial epithelial cells infected with HRV produced mediators that are chemotactic for ASMCs. ASMC migration was investigated using the modified Boyden Chamber and the xCELLigence Real-Time Cell Analyzer (ACEA Biosciences Inc., San Diego, CA). Multiplex bead analysis was used to measure HRV-induced epithelial chemokine release. The chemotactic effects of CCL5, CXCL8, and CXCL10 were also examined. Supernatants from HRV-infected epithelial cells caused ASMC chemotaxis. Pretreatment of ASMCs with pertussis toxin abrogated chemotaxis, as did treatment with formoterol, forskolin, or 8-bromo-cAMP. CCL5, CXCL8, and CXCL10 were the most up-regulated chemokines produced by HRV-infected airway epithelial cells. When recombinant CCL5, CXCL8, and CXCL10 were used at levels found in epithelial supernatants, they induced ASMC chemotaxis similar to that seen with epithelial cell supernatants. When examined individually, CCL5 was the most effective chemokine in causing ASMC migration, and treatment of supernatant from HRV-infected epithelial cells with anti-CCL5 antibodies significantly attenuated ASMC migration. These findings suggest that HRV-induced CCL5 can induce ASMC chemotaxis and thus may contribute to the pathogenesis of airway remodeling in patients with asthma.
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Affiliation(s)
- Sami Shariff
- 1 Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Christopher Shelfoon
- 1 Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Neil S Holden
- 2 School of Life Sciences, University of Lincoln, Lincoln, United Kingdom; and
| | - Suzanne L Traves
- 1 Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Shahina Wiehler
- 1 Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Cora Kooi
- 1 Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - David Proud
- 1 Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Richard Leigh
- 1 Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada.,3 Department of Medicine, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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42
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Mertens TCJ, Karmouty-Quintana H, Taube C, Hiemstra PS. Use of airway epithelial cell culture to unravel the pathogenesis and study treatment in obstructive airway diseases. Pulm Pharmacol Ther 2017; 45:101-113. [PMID: 28502841 DOI: 10.1016/j.pupt.2017.05.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 04/19/2017] [Accepted: 05/10/2017] [Indexed: 12/12/2022]
Abstract
Asthma and chronic obstructive pulmonary disease (COPD) are considered as two distinct obstructive diseases. Both chronic diseases share a component of airway epithelial dysfunction. The airway epithelium is localized to deal with inhaled substances, and functions as a barrier preventing penetration of such substances into the body. In addition, the epithelium is involved in the regulation of both innate and adaptive immune responses following inhalation of particles, allergens and pathogens. Through triggering and inducing immune responses, airway epithelial cells contribute to the pathogenesis of both asthma and COPD. Various in vitro research models have been described to study airway epithelial cell dysfunction in asthma and COPD. However, various considerations and cautions have to be taken into account when designing such in vitro experiments. Epithelial features of asthma and COPD can be modelled by using a variety of disease-related invoking substances either alone or in combination, and by the use of primary cells isolated from patients. Differentiation is a hallmark of airway epithelial cells, and therefore models should include the ability of cells to differentiate, as can be achieved in air-liquid interface models. More recently developed in vitro models, including precision cut lung slices, lung-on-a-chip, organoids and human induced pluripotent stem cells derived cultures, provide novel state-of-the-art alternatives to the conventional in vitro models. Furthermore, advanced models in which cells are exposed to respiratory pathogens, aerosolized medications and inhaled toxic substances such as cigarette smoke and air pollution are increasingly used to model e.g. acute exacerbations. These exposure models are relevant to study how epithelial features of asthma and COPD are affected and provide a useful tool to study the effect of drugs used in treatment of asthma and COPD. These new developments are expected to contribute to a better understanding of the complex gene-environment interactions that contribute to development and progression of asthma and COPD.
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Affiliation(s)
- Tinne C J Mertens
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands; Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA.
| | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Christian Taube
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Pieter S Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
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43
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Wesolowska-Andersen A, Everman JL, Davidson R, Rios C, Herrin R, Eng C, Janssen WJ, Liu AH, Oh SS, Kumar R, Fingerlin TE, Rodriguez-Santana J, Burchard EG, Seibold MA. Dual RNA-seq reveals viral infections in asthmatic children without respiratory illness which are associated with changes in the airway transcriptome. Genome Biol 2017; 18:12. [PMID: 28103897 PMCID: PMC5244706 DOI: 10.1186/s13059-016-1140-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/16/2016] [Indexed: 12/01/2022] Open
Abstract
Background Respiratory illness caused by viral infection is associated with the development and exacerbation of childhood asthma. Little is known about the effects of respiratory viral infections in the absence of illness. Using quantitative PCR (qPCR) for common respiratory viruses and for two genes known to be highly upregulated in viral infections (CCL8/CXCL11), we screened 92 asthmatic and 69 healthy children without illness for respiratory virus infections. Results We found 21 viral qPCR-positive and 2 suspected virus-infected subjects with high expression of CCL8/CXCL11. We applied a dual RNA-seq workflow to these subjects, together with 25 viral qPCR-negative subjects, to compare qPCR with sequencing-based virus detection and to generate the airway transcriptome for analysis. RNA-seq virus detection achieved 86% sensitivity when compared to qPCR-based screening. We detected additional respiratory viruses in the two CCL8/CXCL11-high subjects and in two of the qPCR-negative subjects. Viral read counts varied widely and were used to stratify subjects into Virus-High and Virus-Low groups. Examination of the host airway transcriptome found that the Virus-High group was characterized by immune cell airway infiltration, downregulation of cilia genes, and dampening of type 2 inflammation. Even the Virus-Low group was differentiated from the No-Virus group by 100 genes, some involved in eIF2 signaling. Conclusions Respiratory virus infection without illness is not innocuous but may determine the airway function of these subjects by driving immune cell airway infiltration, cellular remodeling, and alteration of asthmogenic gene expression. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1140-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Jamie L Everman
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Rebecca Davidson
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Cydney Rios
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Rachelle Herrin
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, CA, USA
| | | | - Andrew H Liu
- Department of Pediatrics, National Jewish Health, 1400 Jackson St, Denver, CO, 80206, USA.,Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Sam S Oh
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Rajesh Kumar
- Department of Pediatrics, The Ann and Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Tasha E Fingerlin
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA.,Department of Biomedical Research, National Jewish Health, Denver, CO, USA
| | | | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, CA, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Max A Seibold
- Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, USA. .,Department of Pediatrics, National Jewish Health, 1400 Jackson St, Denver, CO, 80206, USA. .,Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, USA.
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Wawrzyniak P, Wawrzyniak M, Wanke K, Sokolowska M, Bendelja K, Rückert B, Globinska A, Jakiela B, Kast JI, Idzko M, Akdis M, Sanak M, Akdis CA. Regulation of bronchial epithelial barrier integrity by type 2 cytokines and histone deacetylases in asthmatic patients. J Allergy Clin Immunol 2017; 139:93-103. [DOI: 10.1016/j.jaci.2016.03.050] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 03/04/2016] [Accepted: 03/16/2016] [Indexed: 12/11/2022]
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Immunodominant T-Cell Epitopes in the VP1 Capsid Protein of Rhinovirus Species A and C. J Virol 2016; 90:10459-10471. [PMID: 27630239 DOI: 10.1128/jvi.01701-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 09/04/2016] [Indexed: 01/15/2023] Open
Abstract
Rhinovirus (RV) species A and C are the most frequent cause of respiratory viral illness worldwide, and RV-C has been linked to more severe exacerbations of asthma in young children. Little is known about the immune responses to the different RV species, although studies comparing IgG1 antibody titers found impaired antibody responses to RV-C. Therefore, the aim of this study was to assess whether T-cell immunity to RV-C is similarly impaired. We measured T-cell proliferation to overlapping synthetic peptides covering the entire VP1 capsid protein of an RV-A and RV-C genotype for 20 healthy adult donors. Human leukocyte antigen (HLA) was typed in all the donors in order to investigate possible associations between the HLA type and RV peptide recognition. Total and specific IgG1 antibody titers to the VP1 proteins of both RV-A and RV-C were also measured to examine associations between the antibody and T-cell responses. We identified T-cell epitopes that are specific to and representative of each RV-A and RV-C species. These epitopes stimulated CD4+-specific T-cell proliferation, with similar magnitudes of response for both RV species. All the donors, independent of their HLA-DR or -DQ type, were able to recognize the immunodominant RV-A and -C regions of VP1. Furthermore, the presence or absence of specific antibody titers was not related to changes in T-cell recognition. Our results indicate a dissociation between the antibody and T-cell responses to rhinoviruses. The species-representative T-cell epitopes identified in this study are valuable tools for future studies investigating T-cell responses to the different RV species. IMPORTANCE Rhinoviruses (RVs) are mostly associated with the common cold and asthma exacerbations, although their contributions to most upper and lower respiratory tract diseases have increasingly been reported. Species C (RV-C) has been associated with more frequent and severe asthma exacerbations in young children and, along with RV-A, is the most clinically relevant species. Little is known about how our immune system responds to rhinoviruses, and there are limited tools to study specific adaptive immunity against each rhinovirus species. In this study, we identified immunodominant T-cell epitopes of the VP1 proteins of RV-A and RV-C, which are representative of each species. The study found that T-cell responses to RV-A and RV-C were of similar magnitudes, in contrast with previous findings showing RV-C-specific antibody responses were low. These findings will provide the basis for future studies on the immune response to rhinoviruses and can help elucidate the mechanisms of severity of rhinovirus-induced infections.
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Inhibition of Human Metapneumovirus Binding to Heparan Sulfate Blocks Infection in Human Lung Cells and Airway Tissues. J Virol 2016; 90:9237-50. [PMID: 27489270 DOI: 10.1128/jvi.01362-16] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 07/27/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Human metapneumovirus (HMPV), a recently discovered paramyxovirus, infects nearly 100% of the world population and causes severe respiratory disease in infants, the elderly, and immunocompromised patients. We previously showed that HMPV binds heparan sulfate proteoglycans (HSPGs) and that HMPV binding requires only the viral fusion (F) protein. To characterize the features of this interaction critical for HMPV binding and the role of this interaction in infection in relevant models, we utilized sulfated polysaccharides, heparan sulfate mimetics, and occluding compounds. Iota-carrageenan demonstrated potent anti-HMPV activity by inhibiting binding to lung cells mediated by the F protein. Furthermore, analysis of a minilibrary of variably sulfated derivatives of Escherichia coli K5 polysaccharide mimicking the HS structure revealed that the highly O-sulfated K5 polysaccharides inhibited HMPV infection, identifying a potential feature of HS critical for HMPV binding. The peptide dendrimer SB105-A10, which binds HS, reduced binding and infection in an F-dependent manner, suggesting that occlusion of HS at the target cell surface is sufficient to prevent infection. HMPV infection was also inhibited by these compounds during apical infection of polarized airway tissues, suggesting that these interactions take place during HMPV infection in a physiologically relevant model. These results reveal key features of the interaction between HMPV and HS, supporting the hypothesis that apical HS in the airway serves as a binding factor during infection, and HS modulating compounds may serve as a platform for potential antiviral development. IMPORTANCE Human metapneumovirus (HMPV) is a paramyxovirus that causes respiratory disease worldwide. It has been previously shown that HMPV requires binding to heparan sulfate on the surfaces of target cells for attachment and infection. In this study, we characterize the key features of this binding interaction using heparan sulfate mimetics, identify an important sulfate modification, and demonstrate that these interactions occur at the apical surface of polarized airway tissues. These findings provide insights into the initial binding step of HMPV infection that has potential for antiviral development.
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Moheimani F, Hsu ACY, Reid AT, Williams T, Kicic A, Stick SM, Hansbro PM, Wark PAB, Knight DA. The genetic and epigenetic landscapes of the epithelium in asthma. Respir Res 2016; 17:119. [PMID: 27658857 PMCID: PMC5034566 DOI: 10.1186/s12931-016-0434-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 09/17/2016] [Indexed: 12/24/2022] Open
Abstract
Asthma is a global health problem with increasing prevalence. The airway epithelium is the initial barrier against inhaled noxious agents or aeroallergens. In asthma, the airway epithelium suffers from structural and functional abnormalities and as such, is more susceptible to normally innocuous environmental stimuli. The epithelial structural and functional impairments are now recognised as a significant contributing factor to asthma pathogenesis. Both genetic and environmental risk factors play important roles in the development of asthma with an increasing number of genes associated with asthma susceptibility being expressed in airway epithelium. Epigenetic factors that regulate airway epithelial structure and function are also an attractive area for assessment of susceptibility to asthma. In this review we provide a comprehensive discussion on genetic factors; from using linkage designs and candidate gene association studies to genome-wide association studies and whole genome sequencing, and epigenetic factors; DNA methylation, histone modifications, and non-coding RNAs (especially microRNAs), in airway epithelial cells that are functionally associated with asthma pathogenesis. Our aims were to introduce potential predictors or therapeutic targets for asthma in airway epithelium. Overall, we found very small overlap in asthma susceptibility genes identified with different technologies. Some potential biomarkers are IRAKM, PCDH1, ORMDL3/GSDMB, IL-33, CDHR3 and CST1 in airway epithelial cells. Recent studies on epigenetic regulatory factors have further provided novel insights to the field, particularly their effect on regulation of some of the asthma susceptibility genes (e.g. methylation of ADAM33). Among the epigenetic regulatory mechanisms, microRNA networks have been shown to regulate a major portion of post-transcriptional gene regulation. Particularly, miR-19a may have some therapeutic potential.
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Affiliation(s)
- Fatemeh Moheimani
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, HMRI building, The University of Newcastle, Callaghan, NSW, 2308, Australia. .,Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, New South Wales, Australia.
| | - Alan C-Y Hsu
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, HMRI building, The University of Newcastle, Callaghan, NSW, 2308, Australia.,Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, New South Wales, Australia
| | - Andrew T Reid
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, HMRI building, The University of Newcastle, Callaghan, NSW, 2308, Australia.,Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, New South Wales, Australia
| | - Teresa Williams
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, HMRI building, The University of Newcastle, Callaghan, NSW, 2308, Australia.,Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, New South Wales, Australia.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, Canada
| | - Anthony Kicic
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, 6009, Western Australia, Australia.,Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, 6001, Western Australia, Australia.,School of Paediatrics and Child Health, The University of Western Australia, Nedlands, 6009, Western Australia, Australia.,Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia, Nedlands, 6009, Western Australia, Australia
| | - Stephen M Stick
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, 6009, Western Australia, Australia.,Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, 6001, Western Australia, Australia.,School of Paediatrics and Child Health, The University of Western Australia, Nedlands, 6009, Western Australia, Australia.,Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia, Nedlands, 6009, Western Australia, Australia
| | - Philip M Hansbro
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, HMRI building, The University of Newcastle, Callaghan, NSW, 2308, Australia.,Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, New South Wales, Australia
| | - Peter A B Wark
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, New South Wales, Australia.,Department of Respiratory and Sleep Medicine, John Hunter Hospital, New South Wales, Australia
| | - Darryl A Knight
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, HMRI building, The University of Newcastle, Callaghan, NSW, 2308, Australia.,Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, New South Wales, Australia.,Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, Canada
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Bochkov YA, Gern JE. Rhinoviruses and Their Receptors: Implications for Allergic Disease. Curr Allergy Asthma Rep 2016; 16:30. [PMID: 26960297 DOI: 10.1007/s11882-016-0608-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Human rhinoviruses (RVs) are picornaviruses that can cause a variety of illnesses including the common cold, lower respiratory tract illnesses such as bronchitis and pneumonia, and exacerbations of asthma. RVs are classified into three species, RV-A, B, and C, which include over 160 types. They utilize three major types of cellular membrane glycoproteins to gain entry into the host cell: intercellular adhesion molecule 1 (ICAM-1) (the majority of RV-A and all RV-B), low-density lipoprotein receptor (LDLR) family members (12 RV-A types), and cadherin-related family member 3 (CDHR3) (RV-C). CDHR3 is a member of cadherin superfamily of transmembrane proteins with yet unknown biological function, and there is relatively little information available about the mechanisms of RV-C interaction with CDHR3. A coding single nucleotide polymorphism (rs6967330) in CDHR3 could promote RV-C infections and illnesses in infancy, which could in turn adversely affect the developing lung to increase the risk of asthma. Further studies are needed to determine how RV infections contribute to pathogenesis of asthma and to develop the optimal treatment approach to control asthma exacerbations.
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Affiliation(s)
- Yury A Bochkov
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, 600 Highland Ave, Madison, WI, 53792, USA.
| | - James E Gern
- Department of Pediatrics, School of Medicine and Public Health, University of Wisconsin-Madison, 600 Highland Ave, Madison, WI, 53792, USA.,Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, 600 Highland Ave, Madison, WI, 53792, USA
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Jamieson KC, Warner SM, Leigh R, Proud D. Rhinovirus in the Pathogenesis and Clinical Course of Asthma. Chest 2016; 148:1508-1516. [PMID: 26270739 DOI: 10.1378/chest.15-1335] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
In healthy individuals, human rhinovirus (HRV) infections are the major cause of the common cold. These are generally uncomplicated infections except for occasional cases of otitis media or sinusitis. In individuals with asthma, however, HRV infections can have a major impact on disease development and progression. HRV-induced wheezing illnesses in early life are a significant risk factor for subsequent development of asthma, and growing evidence supports a role of recurrent HRV infections in the development and progression of several aspects of airway remodeling in asthma. In addition, HRV infections are one of the most common triggers for acute exacerbations of asthma, which represent a major burden to health-care systems around the world. None of the currently prescribed medications for asthma are effective in preventing or reversing asthma development and airway remodeling or are ideal for treating HRV-induced exacerbations of asthma. Thus, a better understanding of the role of HRV in asthma is important if we are to develop more effective therapies. In the past decade, we have gained new insights into the role of HRV infections in the development and progression of airway remodeling as well as a new appreciation for the proinflammatory and host defense responses to HRV infections that may help to regulate susceptibility to asthma exacerbations. This article reviews the current understanding of the role HRV infections play in the pathogenesis of asthma and identifies possible avenues to new therapeutic strategies for limiting the effects of HRV infections in asthma.
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Affiliation(s)
- Kyla C Jamieson
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Stephanie M Warner
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Richard Leigh
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Medicine, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - David Proud
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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Vacchini A, Locati M, Borroni EM. Overview and potential unifying themes of the atypical chemokine receptor family. J Leukoc Biol 2016; 99:883-92. [PMID: 26740381 DOI: 10.1189/jlb.2mr1015-477r] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 12/12/2015] [Indexed: 12/17/2022] Open
Abstract
Chemokines modulate immune responses through their ability to orchestrate the migration of target cells. Chemokines directly induce cell migration through a distinct set of 7 transmembrane domain G protein-coupled receptors but are also recognized by a small subfamily of atypical chemokine receptors, characterized by their inability to support chemotactic activity. Atypical chemokine receptors are now emerging as crucial regulatory components of chemokine networks in a wide range of physiologic and pathologic contexts. Although a new nomenclature has been approved recently to reflect their functional distinction from their conventional counterparts, a systematic view of this subfamily is still missing. This review discusses their biochemical and immunologic properties to identify potential unifying themes in this emerging family.
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Affiliation(s)
- Alessandro Vacchini
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, and Humanitas Clinical and Research Center, Milan, Italy
| | - Massimo Locati
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, and Humanitas Clinical and Research Center, Milan, Italy
| | - Elena Monica Borroni
- Department of Medical Biotechnologies and Translational Medicine, University of Milan, and Humanitas Clinical and Research Center, Milan, Italy
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