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An Q, Cao Y, Guo W, Jiang Z, Luo H, Liu H, Zhan X. Identification of common genes of rhinovirus single/double‑stranded RNA‑induced asthma deterioration by bioinformatics analysis. Exp Ther Med 2024; 27:210. [PMID: 38590566 PMCID: PMC11000450 DOI: 10.3892/etm.2024.12498] [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: 08/28/2023] [Accepted: 01/29/2024] [Indexed: 04/10/2024] Open
Abstract
Rhinovirus (RV) is the most common respiratory virus affecting humans. The majority of asthma deteriorations are triggered by RV infections. However, whether the effects of RV single- and double-stranded RNA on asthma deterioration have common target genes needs to be further studied. In the present study, two datasets (GSE51392 and GSE30326) were used to screen for common differentially expressed genes (cDEGs). The molecular function, signaling pathways, interaction networks, hub genes, key modules and regulatory molecules of cDEGs were systematically analyzed using online tools such as Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, STRING and NetworkAnalyst. Finally, the hub genes STAT1 and IFIH1 were verified in clinical samples using reverse transcription-quantitative PCR (RT-qPCR). A total of 85 cDEGs were identified. Function analysis revealed that cDEGs served an important role in the innate immune response to viruses and its regulation. Signal transducer and activator of transcription 1 (STAT1), interferon induced with helicase C domain 1 (IFIH1), interferon regulatory factor 7 (IRF7), DExD/H box helicase 58 (DDX58) and interferon-stimulating gene 15 (ISG15) were detected to be hub genes based on the protein-protein interactions and six topological algorithms. A key module involved in influenza A, the Toll-like receptor signaling pathway, was identified using Cytoscape software. The hub genes were regulated by GATA-binding factor 2 and microRNA-146a-5p. In addition, RT-qPCR indicated that the expression levels of the hub genes STAT1 and IFIH1 were low during asthma deterioration compared with post-treatment recovery samples. The present study enhanced the understanding of the mechanism of RV-induced asthma deterioration.
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Affiliation(s)
- Qian An
- Department of Respiratory and Critical Care Medicine, Wuhu Hospital of Traditional Chinese Medicine, Wuhu, Anhui 241000, P.R. China
| | - Yi Cao
- Department of Medical Parasitology, School of Basic Medicine, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Wei Guo
- Department of Medical Parasitology, School of Basic Medicine, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Ziyun Jiang
- Department of Medical Parasitology, School of Basic Medicine, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Hui Luo
- Department of Medical Parasitology, School of Basic Medicine, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Hui Liu
- Department of Medical Parasitology, School of Basic Medicine, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
| | - Xiaodong Zhan
- Department of Medical Parasitology, School of Basic Medicine, Wannan Medical College, Wuhu, Anhui 241002, P.R. China
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Zhu H, Shi J, Li W. Bioinformatics analysis of ceRNA network of autophagy-related genes in pediatric asthma. Medicine (Baltimore) 2023; 102:e36343. [PMID: 38050261 PMCID: PMC10695615 DOI: 10.1097/md.0000000000036343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/06/2023] [Indexed: 12/06/2023] Open
Abstract
The molecular underpinnings of pediatric asthma present avenues for targeted therapies. A deeper exploration into the significance of differentially expressed autophagy-related genes (DE-ARGs) and their interactions with the long noncoding RNA (lncRNA)-microRNA (miRNA)-mRNA network may offer insights into the pathogenesis of pediatric asthma. DE-ARGs were retrieved from the Gene Expression Omnibus and the Human Autophagy Database. These DE-ARGs were subjected to comprehensive analyses, including Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway, Gene Set Enrichment Analysis, and protein-protein interaction networks. The identified DE-ARGs were further verified for core gene expression. The miRDB and ENCORI databases were used for inverse miRNA predictions. Furthermore, miRNA-lncRNA interactions were predicted using LncBase and ENCORI platforms. Following the exclusion of lncRNAs exclusively localized in the nucleus and extracellular space, a competitive endogenous RNA (ceRNA) network was established and subsequently subjected to detailed analysis. The mRNA expression patterns in the ceRNA network were validated using quantitative real-time PCR. In total, 31 DE-ARGs were obtained, of which 29 were up-regulated and 2 were down-regulated. Notably, the autophagy, regulation of apoptotic signaling pathways, interferon-α/β signaling, interferon γ signaling, autophagy-animal, and apoptosis pathways were predominantly enriched in pediatric asthma. Five hub genes (VEGFA, CFLAR, RELA, FAS, and ATF6) were further analyzed using the Gene Expression Omnibus dataset to verify their expression patterns and diagnostic efficacy. Four hub genes (VEGFA, CFLAR, RELA, and FAS) were obtained. Finally, a ceRNA network of 4 mRNAs (VEGFA, CFLAR, RELA, and FAS), 3 miRNAs (hsa-miR-320b, hsa-miR-22-3p, and hsa-miR-625-5p), and 35 lncRNAs was constructed by integrating data from literature review and analyzing the predicted miRNAs and lncRNAs. Moreover, the quantitative real-time PCR data revealed a pronounced upregulation of Fas cell surface death receptor. The identification of 4 DE-ARGs, especially Fas cell surface death receptor, has shed light on their potential pivotal role in the pathogenesis of pediatric asthma. The established ceRNA network provides novel insights into the autophagy mechanism in asthma and suggests promising avenues for the development of potential therapeutic strategies.
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Affiliation(s)
- Hao Zhu
- Department of Pediatrics, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xianning, China
| | - Jiao Shi
- Clinical Laboratory, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xianning, China
| | - Wen Li
- Department of Pediatrics, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xianning, China
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Holmdahl I, Chakraborty S, Hoyer A, Filiou A, Asarnoj A, Sjölander A, Borres MP, van Hage M, Hedlin G, Konradsen JR, Söderhäll C. Inflammatory related plasma proteins involved in acute preschool wheeze. Clin Transl Allergy 2023; 13:e12308. [PMID: 38006384 PMCID: PMC10618892 DOI: 10.1002/clt2.12308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 10/01/2023] [Accepted: 10/16/2023] [Indexed: 11/27/2023] Open
Abstract
BACKGROUND Preschool wheeze is a risk factor for asthma development. However, the molecular mechanism behind a wheezing episode is not well understood. OBJECTIVE Our aims were to assess the association of plasma proteins with acute preschool wheeze and to study the proteins with differential expression at the acute phase at revisit after 3 months. Additionally, to investigate the relationship between protein expression and clinical parameters. METHOD We measured 92 inflammatory proteins in plasma and clinical parameters from 145 children during an episode of preschool wheeze (PW) and at the revisit after 3 months (PW-R, n = 113/145) and 101 healthy controls (HC) aged 6-48 months in the GEWAC cohort using the antibody-mediated proximity extension-based assay (Olink Proteomics, Uppsala). RESULTS Of the 74 analysed proteins, 52 were differentially expressed between PW and HC. The expression profiles of the top 10 proteins, Oncostatin M (OSM), IL-10, IL-6, Fibroblast growth factor 21 (FGF21), AXIN1, CXCL10, SIRT2, TNFSF11, Tumour necrosis factor β (TNF-β) and CASP8, could almost entirely separate PW from HC. Five out of 10 proteins were associated with intake of oral corticosteroids (OCS) 24 h preceding blood sampling (OSM, CASP8, IL-10, TNF-β and CXCL10). No differences in protein expression were seen between PWs with or without OCS in comparison to HC. At the revisit after 3 months, differential protein expressions were still seen between PW-R and HC for three (IL-10, SIRT2 and FGF21) of the 10 proteins. CONCLUSION Our results contribute to unravelling potential immunopathological pathways shared between preschool wheeze and asthma.
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Affiliation(s)
- Idun Holmdahl
- Department of Women's and Children's HealthKarolinska InstitutetStockholmSweden
- Astrid Lindgren's Children's HospitalKarolinska University HospitalStockholmSweden
| | - Sandip Chakraborty
- Department of Women's and Children's HealthKarolinska InstitutetStockholmSweden
- Astrid Lindgren's Children's HospitalKarolinska University HospitalStockholmSweden
| | - Angela Hoyer
- Department of Women's and Children's HealthKarolinska InstitutetStockholmSweden
- Astrid Lindgren's Children's HospitalKarolinska University HospitalStockholmSweden
| | - Anastasia Filiou
- Department of Women's and Children's HealthKarolinska InstitutetStockholmSweden
- Astrid Lindgren's Children's HospitalKarolinska University HospitalStockholmSweden
| | - Anna Asarnoj
- Department of Women's and Children's HealthKarolinska InstitutetStockholmSweden
- Astrid Lindgren's Children's HospitalKarolinska University HospitalStockholmSweden
| | | | - Magnus P. Borres
- Thermo Fisher ScientificUppsalaSweden
- Department of Women's and Children's HealthUppsala UniversityUppsalaSweden
| | - Marianne van Hage
- Division of Immunology and AllergyDepartment of Medicine SolnaKarolinska Institutet and Karolinska University HospitalStockholmSweden
| | - Gunilla Hedlin
- Department of Women's and Children's HealthKarolinska InstitutetStockholmSweden
| | - Jon R. Konradsen
- Department of Women's and Children's HealthKarolinska InstitutetStockholmSweden
- Astrid Lindgren's Children's HospitalKarolinska University HospitalStockholmSweden
| | - Cilla Söderhäll
- Department of Women's and Children's HealthKarolinska InstitutetStockholmSweden
- Astrid Lindgren's Children's HospitalKarolinska University HospitalStockholmSweden
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Volpe S, Irish J, Palumbo S, Lee E, Herbert J, Ramadan I, Chang EH. Viral infections and chronic rhinosinusitis. J Allergy Clin Immunol 2023; 152:819-826. [PMID: 37574080 PMCID: PMC10592176 DOI: 10.1016/j.jaci.2023.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/15/2023]
Abstract
Viral infections are the most common cause of upper respiratory infections; they frequently infect adults once or twice and children 6 to 8 times annually. In most cases, these infections are self-limiting and resolve. However, many patients with chronic rhinosinusitis (CRS) relay that their initiating event began with an upper respiratory infection that progressed in both symptom severity and duration. Viruses bind to sinonasal epithelia through specific receptors, thereby entering cells and replicating within them. Viral infections stimulate interferon-mediated innate immune responses. Recent studies suggest that viral infections may also induce type 2 immune responses and stimulate the aberrant production of cytokines that can result in loss of barrier function, which is a hallmark in CRS. The main purpose of this review will be to highlight common viruses and their associated binding receptors and highlight pathophysiologic mechanisms associated with alterations in mucociliary clearance, epithelial barrier function, and dysfunctional immune responses that might lead to a further understanding of the pathogenesis of CRS.
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Affiliation(s)
- Sophia Volpe
- Department of Otolaryngology-Head and Neck Surgery, College of Medicine, University of Arizona, Tucson, Ariz
| | - Joseph Irish
- Department of Otolaryngology-Head and Neck Surgery, College of Medicine, University of Arizona, Tucson, Ariz
| | - Sunny Palumbo
- Department of Otolaryngology-Head and Neck Surgery, College of Medicine, University of Arizona, Tucson, Ariz
| | - Eric Lee
- Department of Otolaryngology-Head and Neck Surgery, College of Medicine, University of Arizona, Tucson, Ariz
| | - Jacob Herbert
- Department of Otolaryngology-Head and Neck Surgery, College of Medicine, University of Arizona, Tucson, Ariz
| | - Ibrahim Ramadan
- Department of Otolaryngology-Head and Neck Surgery, College of Medicine, University of Arizona, Tucson, Ariz
| | - Eugene H Chang
- Department of Otolaryngology-Head and Neck Surgery, College of Medicine, University of Arizona, Tucson, Ariz.
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5
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Lombardi C, Berti A, Cottini M, Roca E, Ventura L. Using the 6-min walk test to assess the clinical response to mepolizumab and conventional therapy in severe eosinophilic asthma. ERJ Open Res 2023; 9:00114-2023. [PMID: 37868145 PMCID: PMC10588793 DOI: 10.1183/23120541.00114-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 06/21/2023] [Indexed: 10/24/2023] Open
Abstract
Background Severe asthma limits exercise to avoid respiratory symptoms. The objective of the present study was to investigate the role of the 6-min walk test (6MWT) in severe asthma. Methods Consecutive patients with severe eosinophilic asthma were enrolled. A 6MWT was performed before and after 12 months. Inhaled therapy dose, oral corticosteroids dose, pulmonary function tests, eosinophil blood count, fractional exhaled nitric oxide (FeNO), Asthma Control Test (ACT) score and responses to the Asthma Quality of Life Questionnaire (AQLQ) were also recorded. Results Of the 22 patients enrolled, 13 were treated with mepolizumab 100 mg every 4 weeks in addition to conventional therapy and nine with conventional therapy only. The majority of the patients were treated with high-dose inhaled corticosteroids/long-acting β-agonists/long-acting muscarinic receptor antagonists, while approximately half were on continuous oral corticosteroids. After 12 months, the mepolizumab group only showed a significant improvement in pulmonary function tests (percentage forced expiratory volume in 1 s and percentage forced expiratory flow at 25-75% forced vital capacity (FEF25-75%), both p<0.001; percentage forced vital capacity, p<0.01) and clinical laboratory parameters (eosinophil count, FeNO measured at a flow rate of 50 mL·s-1, ACT and AQLQ, p<0.001). No significant changes in the proportion of patients using continuous oral corticosteroids and high-dose inhaled corticosteroids/long-acting β-agonists/long-acting muscarinic receptor antagonists were observed in either group (p>0.05). By paired comparisons, statistically significant improvements of the mean 6-min walk distance (6MWD) were observed in the mepolizumab (p<0.001) and conventional therapy (p<0.01) groups, while no improvement was seen in dyspnoea Borg scale, heart rate, percentage oxygen saturation or systolic and diastolic blood pressure. 6MWD showed significant direct correlations with ACT (r=0.5998, p<0.001), AQLQ (r=0.3978, p=0.009) and FEF25-75% (r=0.3589, p=0.017). Conclusions The 6MWT could complement severe asthma assessment and be relevant in evaluating the objective response to treatment, including biological therapies like mepolizumab.
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Affiliation(s)
- Carlo Lombardi
- Departmental Unit of Allergology, Immunology and Pulmonary Diseases, Fondazione Poliambulanza, Brescia, Italy
| | - Alvise Berti
- Center for Medical Sciences (CISMed), Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
- Santa Chiara Hospital, APSS Trento, Trento, Italy
| | | | - Elena Roca
- Departmental Unit of Allergology, Immunology and Pulmonary Diseases, Fondazione Poliambulanza, Brescia, Italy
| | - Laura Ventura
- Allergy and Pneumology Outpatient Clinic, Bergamo, Italy
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6
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Abstract
Allergic diseases typically begin in early life and can impose a heavy burden on children and their families. Effective preventive measures are currently unavailable but may be ushered in by studies on the "farm effect", the strong protection from asthma and allergy found in children born and raised on traditional farms. Two decades of epidemiologic and immunologic research have demonstrated that this protection is provided by early and intense exposure to farm-associated microbes that target primarily innate immune pathways. Farm exposure also promotes timely maturation of the gut microbiome, which mediates a proportion of the protection conferred by the farm effect. Current research seeks to identify allergy-protective compounds from traditional farm environments, but standardization and regulation of such substances will likely prove challenging. On the other hand, studies in mouse models show that administration of standardized, pharmacological-grade lysates of human airway bacteria abrogates allergic lung inflammation by acting on multiple innate immune targets, including the airway epithelium/IL-33/ILC2 axis and dendritic cells whose Myd88/Trif-dependent tolerogenic reprogramming is sufficient for asthma protection in adoptive transfer models. To the extent that these bacterial lysates mimic the protective effects of natural exposure to microbe-rich environments, these agents might provide an effective tool for prevention of allergic disease.
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Affiliation(s)
- Donata Vercelli
- Department of Cellular and Molecular Medicine, Asthma & Airway Disease Research Center, The BIO5 Institute, and The Arizona Center for the Biology of Complex Diseases, The University of Arizona, Tucson, AZ, USA.
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7
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Bosco A. Emerging role for interferons in respiratory viral infections and childhood asthma. Front Immunol 2023; 14:1109001. [PMID: 36895568 PMCID: PMC9989033 DOI: 10.3389/fimmu.2023.1109001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 02/02/2023] [Indexed: 02/23/2023] Open
Abstract
Respiratory syncytial virus (RSV) and Rhinovirus (RV) infections are major triggers of severe lower respiratory illnesses (sLRI) in infants and children and are strongly associated with the subsequent development of asthma. Decades of research has focused on the role of type I interferons in antiviral immunity and ensuing airway diseases, however, recent findings have highlighted several novel aspects of the interferon response that merit further investigation. In this perspective, we discuss emerging roles of type I interferons in the pathogenesis of sLRI in children. We propose that variations in interferon response patterns exist as discrete endotypes, which operate locally in the airways and systemically through a lung-blood-bone marrow axis. We discuss new insights into the role of interferons in immune training, bacterial lysate immunotherapy, and allergen-specific immunotherapy. Interferons play complex and diverse roles in the pathogenesis of sLRI and later asthma, providing new directions for mechanistic studies and drug development.
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Affiliation(s)
- Anthony Bosco
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States.,Department of Immunobiology, The University of Arizona College of Medicine, Tucson, AZ, United States
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8
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Tu X, Gomez HM, Kim RY, Brown AC, de Jong E, Galvao I, Faiz A, Bosco A, Horvat JC, Hansbro P, Donovan C. Airway and parenchyma transcriptomics in a house dust mite model of experimental asthma. Respir Res 2023; 24:32. [PMID: 36698141 PMCID: PMC9878882 DOI: 10.1186/s12931-022-02298-x] [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: 07/18/2022] [Accepted: 12/15/2022] [Indexed: 01/26/2023] Open
Abstract
Lung transcriptomics studies in asthma have provided valuable information in the whole lung context, however, deciphering the individual contributions of the airway and parenchyma in disease pathogenesis may expedite the development of novel targeted treatment strategies. In this study, we performed transcriptomics on the airway and parenchyma using a house dust mite (HDM)-induced model of experimental asthma that replicates key features of the human disease. HDM exposure increased the expression of 3,255 genes, of which 212 were uniquely increased in the airways, 856 uniquely increased in the parenchyma, and 2187 commonly increased in both compartments. Further interrogation of these genes using a combination of network and transcription factor enrichment analyses identified several transcription factors that regulate airway and/or parenchymal gene expression, including transcription factor EC (TFEC), transcription factor PU.1 (SPI1), H2.0-like homeobox (HLX), metal response element binding transcription factor-1 (MTF1) and E74-like factor 4 (ets domain transcription factor, ELF4) involved in controlling innate immune responses. We next assessed the effects of inhibiting lung SPI1 responses using commercially available DB1976 and DB2313 on key disease outcomes. We found that both compounds had no protective effects on airway inflammation, however DB2313 (8 mg/kg) decreased mucus secreting cell number, and both DB2313 (1 mg/kg) and DB1976 (2.5 mg/kg and 1 mg/kg) reduced small airway collagen deposition. Significantly, both compounds decreased airway hyperresponsiveness. This study demonstrates that SPI1 is important in HDM-induced experimental asthma and that its pharmacological inhibition reduces HDM-induced airway collagen deposition and hyperresponsiveness.
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Affiliation(s)
- Xiaofan Tu
- grid.266842.c0000 0000 8831 109XPriority Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW Australia
| | - Henry M. Gomez
- grid.266842.c0000 0000 8831 109XPriority Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW Australia
| | - Richard Y. Kim
- grid.266842.c0000 0000 8831 109XPriority Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW Australia ,grid.117476.20000 0004 1936 7611Faculty of Science, School of Life Sciences, University of Technology Sydney, Sydney, NSW Australia
| | - Alexandra C. Brown
- grid.266842.c0000 0000 8831 109XPriority Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW Australia
| | - Emma de Jong
- Centre for Health Research, Telethon Kids Institute, The University of Western Australia, Nedlands, WA Australia
| | - Izabela Galvao
- grid.117476.20000 0004 1936 7611Centre for Inflammation, Faculty of Science, School of Life Sciences, Centenary Institute and University of Technology Sydney, Sydney, NSW Australia
| | - Alen Faiz
- grid.117476.20000 0004 1936 7611Faculty of Science, School of Life Sciences, University of Technology Sydney, Sydney, NSW Australia
| | - Anthony Bosco
- grid.134563.60000 0001 2168 186XAsthma and Airway Disease Research Center, University of Arizona, Arizona, USA
| | - Jay C. Horvat
- grid.266842.c0000 0000 8831 109XPriority Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW Australia
| | - Philip Hansbro
- grid.266842.c0000 0000 8831 109XPriority Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW Australia ,grid.117476.20000 0004 1936 7611Centre for Inflammation, Faculty of Science, School of Life Sciences, Centenary Institute and University of Technology Sydney, Sydney, NSW Australia
| | - Chantal Donovan
- grid.266842.c0000 0000 8831 109XPriority Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW Australia ,grid.117476.20000 0004 1936 7611Faculty of Science, School of Life Sciences, University of Technology Sydney, Sydney, NSW Australia
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9
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McIntyre A, Busse WW. Asthma exacerbations: the Achilles heel of asthma care. Trends Mol Med 2022; 28:1112-1127. [PMID: 36208987 PMCID: PMC10519281 DOI: 10.1016/j.molmed.2022.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/22/2022] [Accepted: 09/01/2022] [Indexed: 01/21/2023]
Abstract
Asthma exacerbations significantly impact millions of patients worldwide to pose large disease burdens on affected patients, families, and health-care systems. Although numerous environmental factors cause asthma exacerbations, viral respiratory infections are the principal triggers. Advances in the pathophysiology of asthma have elucidated dysregulated protective immune responses and upregulated inflammation that create susceptibility and risks for exacerbation. Biologics for the treatment of severe asthma reduce rates of exacerbations and identify specific pathways of inflammation that contribute to altered pathophysiology, novel therapeutic targets, and informative biomarkers. Major steps to prevent exacerbations include the identification of molecular pathways whose blockage will prevent asthma attacks safely, predictably, and effectively.
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Affiliation(s)
- Amanda McIntyre
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - William W Busse
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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10
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Yang T, Shen J. Small nucleolar RNAs and SNHGs in the intestinal mucosal barrier: Emerging insights and current roles. J Adv Res 2022; 46:75-85. [PMID: 35700920 PMCID: PMC10105082 DOI: 10.1016/j.jare.2022.06.004] [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: 03/19/2022] [Revised: 05/23/2022] [Accepted: 06/08/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Previous studies have focused on the involvement of small nucleolar RNAs (snoRNAs) and SNHGs in tumor cell proliferation, apoptosis, invasion, and metastasis via multiple pathways, including phosphatidylinositol-3-kinase/protein kinase B (PI3K/AKT), Wnt/β catenin, and mitogen-activated protein kinase (MAPK). These molecular mechanisms affect the integrity of the intestinal mucosal barrier. AIM OF REVIEW Current evidence regarding snoRNAs and SNHGs in the context of the mucosal barrier and modulation of homeostasis is fragmented. In this review, we collate the established information on snoRNAs and SNHGs as well as discuss the major pathways affecting the mucosal barrier. KEY SCIENTIFIC CONCEPTS OF REVIEW Intestinal mucosal immunity, microflora, and the physical barrier are altered in non-neoplastic diseases such as inflammatory bowel diseases. Dysregulated snoRNAs and SNHGs may impact the intestinal mucosal barrier to promote the pathogenesis and progression of multiple diseases. SnoRNAs or SNHGs has been shown to be associated with poor disease behaviors, indicating that they may be exploited as prognostic biomarkers. Additionally, clarifying the complicated interactions between snoRNAs or SNHGs and the mucosal barrier may provide novel insights for the therapeutic treatment targeting strengthen the intestinal mucosal barrier.
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Affiliation(s)
- Tian Yang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center. Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160# Pu Jian Ave, Shanghai 200127, China; Shanghai Institute of Digestive Disease, China
| | - Jun Shen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center. Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160# Pu Jian Ave, Shanghai 200127, China; Shanghai Institute of Digestive Disease, China.
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11
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Murray LM, Thillaiyampalam G, Xi Y, Cristino AS, Upham JW. Whole transcriptome analysis of high and low IFN-α producers reveals differential response patterns following rhinovirus stimulation. Clin Transl Immunology 2021; 10:e1356. [PMID: 34868584 PMCID: PMC8599968 DOI: 10.1002/cti2.1356] [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: 02/24/2021] [Revised: 09/01/2021] [Accepted: 10/26/2021] [Indexed: 11/29/2022] Open
Abstract
Objectives Viral respiratory infections cause considerable morbidity and economic loss. While rhinoviruses (RV) typically cause little more than the common cold, they can produce severe infections and disease exacerbations in susceptible individuals, such as those with asthma. Variations in the regulation of key antiviral cytokines, particularly type I interferon (IFN‐α and IFN‐β), may contribute to RV susceptibility. To understand this variability, we compared the transcriptomes of high and low type I IFN producers. Methods Blood mononuclear cells from 238 individuals with or without asthma were cultured in the presence or absence of RV. Those samples demonstrating high or low RV‐stimulated IFN‐α production (N = 75) underwent RNA‐sequencing. Results Gene expression patterns were similar in samples from healthy participants and those with asthma. At baseline, the high IFN‐α producer group showed higher expression of genes associated with plasmacytoid dendritic cells, the innate immune response and vitamin D activation, but lower expression of oxidative stress pathways than the low IFN‐α producer group. After RV stimulation, the high IFN‐α producer group showed higher expression of genes found in immune response biological pathways and lower expression of genes linked to developmental and catabolic processes when compared to the low IFN‐α producer group. Conclusions These differences suggest that the high IFN‐α group has a higher level of immune system readiness, resulting in a more intense and perhaps more focussed pathogen‐specific immune response. These results contribute to a better understanding of the variability in type I IFN production between individuals.
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Affiliation(s)
- Liisa M Murray
- Diamantina Institute The University of Queensland Brisbane QLD Australia
| | - Gayathri Thillaiyampalam
- Diamantina Institute The University of Queensland Brisbane QLD Australia.,Griffith Institute for Drug Discovery Griffith University Brisbane QLD Australia
| | - Yang Xi
- Diamantina Institute The University of Queensland Brisbane QLD Australia
| | - Alexandre S Cristino
- Diamantina Institute The University of Queensland Brisbane QLD Australia.,Griffith Institute for Drug Discovery Griffith University Brisbane QLD Australia
| | - John W Upham
- Diamantina Institute The University of Queensland Brisbane QLD Australia.,Respiratory and Sleep Medicine Princess Alexandra Hospital Brisbane QLD Australia
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12
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Coleman LA, Khoo SK, Franks K, Prastanti F, Le Souëf P, Karpievitch YV, Laing IA, Bosco A. Personal Network Inference Unveils Heterogeneous Immune Response Patterns to Viral Infection in Children with Acute Wheezing. J Pers Med 2021; 11:1293. [PMID: 34945765 PMCID: PMC8706513 DOI: 10.3390/jpm11121293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/26/2021] [Accepted: 12/01/2021] [Indexed: 12/01/2022] Open
Abstract
Human rhinovirus (RV)-induced exacerbations of asthma and wheeze are a major cause of emergency room presentations and hospital admissions among children. Previous studies have shown that immune response patterns during these exacerbations are heterogeneous and are characterized by the presence or absence of robust interferon responses. Molecular phenotypes of asthma are usually identified by cluster analysis of gene expression levels. This approach however is limited, since genes do not exist in isolation, but rather work together in networks. Here, we employed personal network inference to characterize exacerbation response patterns and unveil molecular phenotypes based on variations in network structure. We found that personal gene network patterns were dominated by two major network structures, consisting of interferon-response versus FCER1G-associated networks. Cluster analysis of these structures divided children into subgroups, differing in the prevalence of atopy but not RV species. These network structures were also observed in an independent cohort of children with virus-induced asthma exacerbations sampled over a time course, where we showed that the FCER1G-associated networks were mainly observed at late time points (days four-six) during the acute illness. The ratio of interferon- and FCER1G-associated gene network responses was able to predict recurrence, with low interferon being associated with increased risk of readmission. These findings demonstrate the applicability of personal network inference for biomarker discovery and therapeutic target identification in the context of acute asthma which focuses on variations in network structure.
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Affiliation(s)
- Laura A. Coleman
- Medical School (Paediatrics), University of Western Australia, Perth, WA 6009, Australia; (L.A.C.); (P.L.S.); (I.A.L.)
- Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia; (S.-K.K.); (K.F.); (F.P.); (Y.V.K.)
| | - Siew-Kim Khoo
- Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia; (S.-K.K.); (K.F.); (F.P.); (Y.V.K.)
- School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Kimberley Franks
- Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia; (S.-K.K.); (K.F.); (F.P.); (Y.V.K.)
- School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Franciska Prastanti
- Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia; (S.-K.K.); (K.F.); (F.P.); (Y.V.K.)
- School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Peter Le Souëf
- Medical School (Paediatrics), University of Western Australia, Perth, WA 6009, Australia; (L.A.C.); (P.L.S.); (I.A.L.)
- Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia; (S.-K.K.); (K.F.); (F.P.); (Y.V.K.)
| | - Yuliya V. Karpievitch
- Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia; (S.-K.K.); (K.F.); (F.P.); (Y.V.K.)
- School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Ingrid A. Laing
- Medical School (Paediatrics), University of Western Australia, Perth, WA 6009, Australia; (L.A.C.); (P.L.S.); (I.A.L.)
- Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia; (S.-K.K.); (K.F.); (F.P.); (Y.V.K.)
- School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Anthony Bosco
- Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia; (S.-K.K.); (K.F.); (F.P.); (Y.V.K.)
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13
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Jackson DJ, Bacharier LB. Inhaled corticosteroids for the prevention of asthma exacerbations. Ann Allergy Asthma Immunol 2021; 127:524-529. [PMID: 34400314 DOI: 10.1016/j.anai.2021.08.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 07/27/2021] [Accepted: 08/09/2021] [Indexed: 11/19/2022]
Abstract
OBJECTIVE To provide an overview of the risk factors and mechanisms underlying asthma exacerbations and the role of inhaled corticosteroids (ICSs) in preventing exacerbations. DATA SOURCES Queries for asthma exacerbations and ICSs were conducted using PubMed, searching for primary articles and reviews. STUDY SELECTIONS Studies written in English, with a focus on well-designed randomized controlled clinical trials. RESULTS Asthma exacerbations remain a major source of morbidity, with future exacerbations most likely among patients with previous exacerbations and among those with peripheral blood eosinophilia. Exacerbations are often triggered by viral respiratory tract infections, but recent evidence supports nonviral triggers as well. In terms of exacerbation prevention, several approaches to ICS therapy have been found to be effective, including intermittent high-dose ICS without use of background controller in preschool children with recurrent episodic wheezing, intermittent high-dose ICS without use of background controller in adults with mild asthma, and as-needed ICS dosing whenever rescue treatment is needed among children, adolescents, and adults with mild asthma not receiving daily controller therapy. CONCLUSION ICSs are highly effective in preventing exacerbations of asthma. Multiple dosing strategies have been found to reduce exacerbation risk, allowing for a personalization of approaches based on individual patient phenotypes and preferences.
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Affiliation(s)
- Daniel J Jackson
- Division of Allergy, Immunology and Rheumatology, Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin.
| | - Leonard B Bacharier
- Division of Allergy, Immunology and Pulmonary Medicine, Department of Pediatrics, Monroe Carell Jr. Children's Hospital at Vanderbilt, Nashville, Tennessee
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14
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de Jong E, Lauzon-Joset JF, Leffler J, Serralha M, Larcombe AN, Christophersen CT, Holt PG, Strickland DH, Bosco A. IRF7-Associated Immunophenotypes Have Dichotomous Responses to Virus/Allergen Coexposure and OM-85-Induced Reprogramming. Front Immunol 2021; 12:699633. [PMID: 34367159 PMCID: PMC8339879 DOI: 10.3389/fimmu.2021.699633] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/07/2021] [Indexed: 12/24/2022] Open
Abstract
High risk for virus-induced asthma exacerbations in children is associated with an IRF7lo immunophenotype, but the underlying mechanisms are unclear. Here, we applied a Systems Biology approach to an animal model comprising rat strains manifesting high (BN) versus low susceptibility (PVG) to experimental asthma, induced by virus/allergen coexposure, to elucidate the mechanism(s)-of-action of the high-risk asthma immunophenotype. We also investigated potential risk mitigation via pretreatment with the immune training agent OM-85. Virus/allergen coexposure in low-risk PVG rats resulted in rapid and transient airways inflammation alongside IRF7 gene network formation. In contrast, responses in high-risk BN rats were characterized by severe airways eosinophilia and exaggerated proinflammatory responses that failed to resolve, and complete absence of IRF7 gene networks. OM-85 had more profound effects in high-risk BN rats, inducing immune-related gene expression changes in lung at baseline and reducing exaggerated airway inflammatory responses to virus/allergen coexposure. In low-risk PVG rats, OM-85 boosted IRF7 gene networks in the lung but did not alter baseline gene expression or cellular influx. Distinct IRF7-associated asthma risk immunophenotypes have dichotomous responses to virus/allergen coexposure and respond differentially to OM-85 pretreatment. Extrapolating to humans, our findings suggest that the beneficial effects OM-85 pretreatment may preferentially target those in high-risk subgroups.
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Affiliation(s)
- Emma de Jong
- Telethon Kids Institute, Perth, WA, Australia.,University of Western Australia, Nedlands, WA, Australia
| | - Jean-Francois Lauzon-Joset
- Telethon Kids Institute, Perth, WA, Australia.,Centre de Recherche, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Quebec, QC, Canada
| | - Jonatan Leffler
- Telethon Kids Institute, Perth, WA, Australia.,University of Western Australia, Nedlands, WA, Australia
| | | | - Alexander N Larcombe
- Telethon Kids Institute, Perth, WA, Australia.,School of Public Health, Curtin University, Perth, WA, Australia
| | - Claus T Christophersen
- WA Human Microbiome Collaboration Centre, School of Molecular and Life Sciences, Curtin University, Bentley, WA, Australia.,Centre for Integrative Metabolomics and Computational Biology, School of Medical & Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | | | | | - Anthony Bosco
- Telethon Kids Institute, Perth, WA, Australia.,University of Western Australia, Nedlands, WA, Australia
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15
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Malinczak CA, Parolia A, Fonseca W, Morris S, Rasky AJ, Bawa P, Zhang Y, Mire MM, Ziegler SF, Ptaschinski C, Chinnaiyan AM, Lukacs NW. TSLP-Driven Chromatin Remodeling and Trained Systemic Immunity after Neonatal Respiratory Viral Infection. THE JOURNAL OF IMMUNOLOGY 2021; 206:1315-1328. [PMID: 33514510 DOI: 10.4049/jimmunol.2001205] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/04/2021] [Indexed: 12/26/2022]
Abstract
Our studies have previously shown a role for persistent TSLP production in the lungs of mice after early-life respiratory syncytial virus (RSV) infection that leads to an altered immune phenotype, including accumulation of "inflammatory" dendritic cells (DC). This study investigates the role of TSLP driving systemic trained immunity in DC in early-life RSV-infected mice. Bone marrow-derived DCs (BMDC) from early-life RSV-infected mice at 4 wk postinfection showed enhanced expression of costimulatory molecules and cytokines, including Tslp, that regulate immune cell function. The adoptive transfer of BMDC grown from early-life RSV-infected mice was sufficient to exacerbate allergic disease development. The addition of recombinant TSLP during differentiation of BMDC from naive mice induced a similar altered phenotype as BMDC grown from early-life RSV-infected mice, suggesting a role for TSLP in the phenotypic changes. To assess the role of TSLP in these changes, global transcriptomic characterization of TSLPR-/- BMDC infected with RSV was performed and showed a higher upregulation of type 1 IFN genes and concomitant downregulation of inflammatory genes. Assay for transposase-accessible chromatin using sequencing analysis demonstrated that TSLPR-/- BMDC had a parallel gain in physical chromatin accessibility near type 1 genes and loss in accessibility near genes related to RSV pathology, with IFN regulatory factor 4 (IRF4) and STAT3 predicted as top transcription factors binding within differentially accessible regions in wild-type. Importantly, these studies show that in the absence of TSLP signaling, BMDC are able to mount an appropriate type 1 IFN-associated antiviral response to RSV. In summary, RSV-induced TSLP alters chromatin structure in DC to drive trained innate immunity and activates pathogenic gene programs in mice.
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Affiliation(s)
| | - Abhijit Parolia
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Wendy Fonseca
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Susan Morris
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Andrew J Rasky
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Pushpinder Bawa
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Yuping Zhang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Mohamed M Mire
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Steven F Ziegler
- Department of Immunology, Benaroya Research Institute, Seattle, WA 98101
| | - Catherine Ptaschinski
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109.,Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, MI 48109
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109; and.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI 48109
| | - Nicholas W Lukacs
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109.,Mary H. Weiser Food Allergy Center, University of Michigan, Ann Arbor, MI 48109
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16
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Decoding Susceptibility to Respiratory Viral Infections and Asthma Inception in Children. Int J Mol Sci 2020; 21:ijms21176372. [PMID: 32887352 PMCID: PMC7503410 DOI: 10.3390/ijms21176372] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 01/19/2023] Open
Abstract
Human Respiratory Syncytial Virus and Human Rhinovirus are the most frequent cause of respiratory tract infections in infants and children and are major triggers of acute viral bronchiolitis, wheezing and asthma exacerbations. Here, we will discuss the application of the powerful tools of systems biology to decode the molecular mechanisms that determine risk for infection and subsequent asthma. An important conceptual advance is the understanding that the innate immune system is governed by a Bow-tie architecture, where diverse input signals converge onto a few core pathways (e.g., IRF7), which in turn generate diverse outputs that orchestrate effector and regulatory functions. Molecular profiling studies in children with severe exacerbations of asthma/wheeze have identified two major immunological phenotypes. The IRF7hi phenotype is characterised by robust upregulation of antiviral response networks, and the IRF7lo phenotype is characterised by upregulation of markers of TGFβ signalling and type 2 inflammation. Similar phenotypes have been identified in infants and children with severe viral bronchiolitis. Notably, genome-wide association studies supported by experimental validation have identified key pathways that increase susceptibility to HRV infection (ORMDL3 and CHDR3) and modulate TGFβ signalling (GSDMB, TGFBR1, and SMAD3). Moreover, functional deficiencies in the activation of type I and III interferon responses are already evident at birth in children at risk of developing febrile lower respiratory tract infections and persistent asthma/wheeze, suggesting that the trajectory to asthma begins at birth or in utero. Finally, exposure to microbes and their products reprograms innate immunity and provides protection from the development of allergies and asthma in children, and therefore microbial products are logical candidates for the primary prevention of asthma.
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17
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Lejeune S, Deschildre A, Le Rouzic O, Engelmann I, Dessein R, Pichavant M, Gosset P. Childhood asthma heterogeneity at the era of precision medicine: Modulating the immune response or the microbiota for the management of asthma attack. Biochem Pharmacol 2020; 179:114046. [PMID: 32446884 PMCID: PMC7242211 DOI: 10.1016/j.bcp.2020.114046] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/19/2020] [Indexed: 12/12/2022]
Abstract
Exacerbations are a main characteristic of asthma. In childhood, the risk is increasing with severity. Exacerbations are a strong phenotypic marker, particularly of severe and therapy-resistant asthma. These early-life events may influence the evolution and be involved in lung function decline. In children, asthma attacks are facilitated by exposure to allergens and pollutants, but are mainly triggered by microbial agents. Multiple studies have assessed immune responses to viruses, and to a lesser extend bacteria, during asthma exacerbation. Research has identified impairment of innate immune responses in children, related to altered pathogen recognition, interferon release, or anti-viral response. Influence of this host-microbiota dialog on the adaptive immune response may be crucial, leading to the development of biased T helper (Th)2 inflammation. These dynamic interactions may impact the presentations of asthma attacks, and have long-term consequences. The aim of this review is to synthesize studies exploring immune mechanisms impairment against viruses and bacteria promoting asthma attacks in children. The potential influence of the nature of infectious agents and/or preexisting microbiota on the development of exacerbation is also addressed. We then discuss our understanding of how these diverse host-microbiota interactions in children may account for the heterogeneity of endotypes and clinical presentations. Finally, improving the knowledge of the pathophysiological processes induced by infections has led to offer new opportunities for the development of preventive or curative therapeutics for acute asthma. A better definition of asthma endotypes associated with precision medicine might lead to substantial progress in the management of severe childhood asthma.
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Affiliation(s)
- Stéphanie Lejeune
- CHU Lille, Univ. Lille, Pediatric Pulmonology and Allergy Department, Hôpital Jeanne de Flandre, F-59000 Lille, France; Univ. Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, F-59019 Lille Cedex, France
| | - Antoine Deschildre
- CHU Lille, Univ. Lille, Pediatric Pulmonology and Allergy Department, Hôpital Jeanne de Flandre, F-59000 Lille, France; Univ. Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, F-59019 Lille Cedex, France
| | - Olivier Le Rouzic
- Univ. Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, F-59019 Lille Cedex, France; CHU Lille, Univ. Lille, Department of Respiratory Diseases, F-59000 Lille Cedex, France
| | - Ilka Engelmann
- Univ. Lille, Virology Laboratory, EA3610, Institute of Microbiology, CHU Lille, F-59037 Lille Cedex, France
| | - Rodrigue Dessein
- Univ. Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, F-59019 Lille Cedex, France; Univ. Lille, Bacteriology Department, Institute of Microbiology, CHU Lille, F-59037 Lille Cedex, France
| | - Muriel Pichavant
- Univ. Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, F-59019 Lille Cedex, France
| | - Philippe Gosset
- Univ. Lille, INSERM Unit 1019, CNRS UMR 9017, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, F-59019 Lille Cedex, France.
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18
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Jones AC, Anderson D, Troy NM, Mallon D, Hartmann R, Serralha M, Holt B, Bosco A, Holt PG. Rewiring of gene networks underlying mite allergen-induced CD4 + Th-cell responses during immunotherapy. Allergy 2020; 75:2330-2341. [PMID: 32181882 DOI: 10.1111/all.14265] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 01/23/2020] [Accepted: 02/10/2020] [Indexed: 01/05/2023]
Abstract
BACKGROUND Multiple regulatory mechanisms have been identified employing conventional hypothesis-driven approaches as contributing to allergen-specific immunotherapy outcomes, but understanding of how these integrate to maintain immunological homeostasis is incomplete. OBJECTIVE To explore the potential for unbiased systems-level gene co-expression network analysis to advance understanding of immunotherapy mechanisms. METHODS We profiled genome-wide allergen-induced Th-cell responses prospectively during 24 months subcutaneous immunotherapy (SCIT) in 25 rhinitis, documenting changes in immunoinflammatory pathways and associated co-expression networks and their relationships to symptom scores out to 36 months. RESULTS Prior to immunotherapy, mite-induced Th-cell response networks involved multiple discrete co-expression modules including those related to Th2-, type1 IFN-, inflammation- and FOXP3/IL2-associated signalling. A signature comprising 109 genes correlated with symptom scores, and these mapped to cytokine signalling/T-cell activation-associated pathways, with upstream drivers including hallmark Th1/Th2- and inflammation-associated genes. Reanalysis after 3.5 months SCIT updosing detected minimal changes to pathway/upstream regulator profiles despite 32.5% symptom reduction; however, network analysis revealed underlying merging of FOXP3/IL2-with inflammation-and Th2-associated modules. By 12 months SCIT, symptoms had reduced by 41% without further significant changes to pathway/upstream regulator or network profiles. Continuing SCIT to 24 months stabilized symptoms at 47% of baseline, accompanied by upregulation of the type1 IFN-associated network module and its merging into the Th2/FOXP3/IL2/inflammation module. CONCLUSIONS Subcutaneous immunotherapy stimulates progressive integration of mite-induced Th cell-associated Th2-, FOXP3/IL2-, inflammation- and finally type1 IFN-signalling subnetworks, forming a single highly integrated co-expression network module, maximizing potential for stable homeostatic control of allergen-induced Th2 responses via cross-regulation. Th2-antagonistic type1 IFN signalling may play a key role in stabilizing clinical effects of SCIT.
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Affiliation(s)
- Anya C. Jones
- Telethon Kids Institute The University of Western Australia Perth WA Australia
| | - Denise Anderson
- Telethon Kids Institute The University of Western Australia Perth WA Australia
| | - Niamh M. Troy
- Telethon Kids Institute The University of Western Australia Perth WA Australia
- School of Medicine The University of Western Australia Perth WA Australia
| | - Dominic Mallon
- Department of Clinical Immunology Fiona Stanley Hospital Perth WA Australia
| | - Rochelle Hartmann
- Department of Clinical Immunology Fiona Stanley Hospital Perth WA Australia
| | - Michael Serralha
- Telethon Kids Institute The University of Western Australia Perth WA Australia
| | - Barbara Holt
- Telethon Kids Institute The University of Western Australia Perth WA Australia
| | - Anthony Bosco
- Telethon Kids Institute The University of Western Australia Perth WA Australia
| | - Patrick G. Holt
- Telethon Kids Institute The University of Western Australia Perth WA Australia
- Child Health Research Centre The University of Queensland Brisbane QLD Australia
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19
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Do AN, Chun Y, Grishina G, Grishin A, Rogers AJ, Raby BA, Weiss ST, Vicencio A, Schadt EE, Bunyavanich S. Network study of nasal transcriptome profiles reveals master regulator genes of asthma. J Allergy Clin Immunol 2020; 147:879-893. [PMID: 32828590 DOI: 10.1016/j.jaci.2020.07.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 06/19/2020] [Accepted: 07/01/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Nasal transcriptomics can provide an accessible window into asthma pathobiology. OBJECTIVE Our goal was to move beyond gene signatures of asthma to identify master regulator genes that causally regulate genes associated with asthma phenotypes. METHODS We recruited 156 children with severe persistent asthma and controls for nasal transcriptome profiling and applied network-based and probabilistic causal methods to identify severe asthma genes and their master regulators. We then took the same approach in an independent cohort of 190 adults with mild/moderate asthma and controls to identify mild/moderate asthma genes and their master regulators. Comparative analysis of the master regulator genes followed by validation testing in independent children with severe asthma (n = 21) and mild/moderate asthma (n = 154) was then performed. RESULTS Nasal gene signatures for severe persistent asthma and for mild/moderate persistent asthma were identified; both were found to be enriched in coexpression network modules for ciliary function and inflammatory response. By applying probabilistic causal methods to these gene signatures and validation testing in independent cohorts, we identified (1) a master regulator gene common to asthma across severity and ages (FOXJ1); (2) master regulator genes of severe persistent asthma in children (LRRC23, TMEM231, CAPS, PTPRC, and FYB); and (3) master regulator genes of mild/moderate persistent asthma in children and adults (C1orf38 and FMNL1). The identified master regulators were statistically inferred to causally regulate the expression of downstream genes that modulate ciliary function and inflammatory response to influence asthma. CONCLUSION The identified master regulator genes of asthma provide a novel path forward to further uncovering asthma mechanisms and therapy.
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Affiliation(s)
- Anh N Do
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yoojin Chun
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Galina Grishina
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Alexander Grishin
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Angela J Rogers
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Stanford University School of Medicine, Stanford, Calif
| | - Benjamin A Raby
- Division of Pulmonary Medicine, Children's Hospital Boston, Boston, Mass
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Mass; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Mass
| | - Alfin Vicencio
- Division of Pulmonary Medicine, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Eric E Schadt
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Supinda Bunyavanich
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY.
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20
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Loh Z, Simpson J, Ullah A, Zhang V, Gan WJ, Lynch JP, Werder RB, Sikder AA, Lane K, Sim CB, Porrello E, Mazzone SB, Sly PD, Steptoe RJ, Spann KM, Sukkar MB, Upham JW, Phipps S. HMGB1 amplifies ILC2-induced type-2 inflammation and airway smooth muscle remodelling. PLoS Pathog 2020; 16:e1008651. [PMID: 32658914 PMCID: PMC7377495 DOI: 10.1371/journal.ppat.1008651] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 07/23/2020] [Accepted: 05/24/2020] [Indexed: 12/16/2022] Open
Abstract
Type-2 immunity elicits tissue repair and homeostasis, however dysregulated type-2 responses cause aberrant tissue remodelling, as observed in asthma. Severe respiratory viral infections in infancy predispose to later asthma, however, the processes that mediate tissue damage-induced type-2 inflammation and the origins of airway remodelling remain ill-defined. Here, using a preclinical mouse model of viral bronchiolitis, we find that increased epithelial and mesenchymal high-mobility group box 1 (HMGB1) expression is associated with increased numbers of IL-13-producing type-2 innate lymphoid cell (ILC2s) and the expansion of the airway smooth muscle (ASM) layer. Anti-HMGB1 ablated lung ILC2 numbers and ASM growth in vivo, and inhibited ILC2-mediated ASM cell proliferation in a co-culture model. Furthermore, we identified that HMGB1/RAGE (receptor for advanced glycation endproducts) signalling mediates an ILC2-intrinsic IL-13 auto-amplification loop. In summary, therapeutic targeting of the HMGB1/RAGE signalling axis may act as a novel asthma preventative by dampening ILC2-mediated type-2 inflammation and associated ASM remodelling. Asthma can start at any time in life, although most often begins in early childhood. Wheezy viral bronchiolitis is a major independent risk factor for subsequent asthma. However, key knowledge gaps exist in relation to the sequelae of severe viral bronchiolitis and the pathogenic processes that promote type-2 inflammation and airway wall remodelling, cardinal features of asthma. Our study addresses this gap by identifying high-mobility group box 1 as a pathogenic cytokine that contributes to group 2 innate lymphoid cell-induced airway smooth muscle growth.
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Affiliation(s)
- Zhixuan Loh
- School of Biomedical Sciences, The University of Queensland, Queensland, Australia
- Institute for Molecular Bioscience, The University of Queensland, Queensland, Australia
| | - Jennifer Simpson
- School of Biomedical Sciences, The University of Queensland, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Ashik Ullah
- School of Biomedical Sciences, The University of Queensland, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Vivian Zhang
- QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Wan J. Gan
- School of Biomedical Sciences, The University of Queensland, Queensland, Australia
| | - Jason P. Lynch
- School of Biomedical Sciences, The University of Queensland, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Rhiannon B. Werder
- School of Biomedical Sciences, The University of Queensland, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Al Amin Sikder
- School of Biomedical Sciences, The University of Queensland, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Katie Lane
- School of Biomedical Sciences, The University of Queensland, Queensland, Australia
| | - Choon Boon Sim
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Melbourne, Australia
| | - Enzo Porrello
- Murdoch Children’s Research Institute, The Royal Children’s Hospital, Melbourne, Australia
| | - Stuart B. Mazzone
- School of Biomedical Sciences, The University of Queensland, Queensland, Australia
- Department of Anatomy and Neuroscience, University of Melbourne, Victoria, Australia
| | - Peter D. Sly
- Children’s Health and Environment Program, Child Health Research Centre, University of Queensland, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Queensland, Australia
| | - Raymond J. Steptoe
- UQ Diamantina Institute, The University of Queensland, Queensland, Australia
| | - Kirsten M. Spann
- School of Biomedical Sciences, Queensland University of Technology, Queensland, Australia
| | - Maria B. Sukkar
- Graduate School of Health, Faculty of Health, University of Technology Sydney, Ultimo, NSW, Australia
| | - John W. Upham
- UQ Diamantina Institute, The University of Queensland, Queensland, Australia
| | - Simon Phipps
- School of Biomedical Sciences, The University of Queensland, Queensland, Australia
- QIMR Berghofer Medical Research Institute, Queensland, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, Queensland, Australia
- * E-mail:
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21
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Sokulsky LA, Goggins B, Sherwin S, Eyers F, Kaiko GE, Board PG, Keely S, Yang M, Foster PS. GSTO1-1 is an upstream suppressor of M2 macrophage skewing and HIF-1α-induced eosinophilic airway inflammation. Clin Exp Allergy 2020; 50:609-624. [PMID: 32052502 DOI: 10.1111/cea.13582] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/05/2020] [Accepted: 02/10/2020] [Indexed: 02/04/2023]
Abstract
BACKGROUND Glutathione S-transferases omega class 1 (GSTO1-1) is a unique member of the GST family regulating cellular redox metabolism and innate immunity through the promotion of LPS/TLR4/NLRP3 signalling in macrophages. House dust mite (HDM) triggers asthma by promoting type 2 responses and allergic inflammation via the TLR4 pathway. Although linked to asthma, the role of GSTO1-1 in facilitating type 2 responses and/or HDM-driven allergic inflammation is unknown. OBJECTIVE To determine the role of GSTO1-1 in regulating HDM-induced allergic inflammation in a preclinical model of asthma. METHODS Wild-type and GSTO1-1-deficient mice were sensitized and aeroallergen challenged with HDM to induce allergic inflammation and subsequently hallmark pathophysiological features characterized. RESULTS By contrast to HDM-challenged WT mice, exposed GSTO1-1-deficient mice had increased numbers of eosinophils and macrophages and elevated levels of eotaxin-1 and -2 in their lungs. M1 macrophage-associated factors, such as IL-1β and IL-6, were decreased in GSTO1-1-deficient mice. Conversely, M2 macrophage factors such as Arg-1 and Ym1 were up-regulated. HIF-1α expression was found to be higher in the absence of GSTO1-1 and correlated with the up-regulation of M2 macrophage markers. Furthermore, HIF-1α was shown to bind and activate the eotaxin-2 promotor. Hypoxic conditions induced significant increases in the levels of eotaxin-1 and -2 in GSTO1-deficient BMDMs, providing a potential link between inflammation-induced hypoxia and the regulation of M2 responses in the lung. Collectively, our results suggest that GSTO1-1 deficiency promotes M2-type responses and increased levels of nuclear HIF-1α, which regulates eotaxin (s)-induced eosinophilia and increased disease severity. CONCLUSION & CLINICAL IMPLICATION We propose that GSTO1-1 is a novel negative regulator of TLR4-regulated M2 responses acting as an anti-inflammatory pathway. The discovery of a novel HIF-1α-induced eotaxin pathway identifies an unknown connection between hypoxia and the regulation of the severity of allergic inflammation in asthma.
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Affiliation(s)
- Leon A Sokulsky
- Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Bridie Goggins
- Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Simonne Sherwin
- Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Fiona Eyers
- Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Gerard E Kaiko
- Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Philip G Board
- ACRF Department of Cancer Biology and Therapeutics, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Simon Keely
- Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Ming Yang
- Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Paul S Foster
- Faculty of Health and Medicine, School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia.,Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
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22
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Ning X, Sun L. Gene network analysis reveals a core set of genes involved in the immune response of Japanese flounder (Paralichthys olivaceus) against Vibrio anguillarum infection. FISH & SHELLFISH IMMUNOLOGY 2020; 98:800-809. [PMID: 31743762 DOI: 10.1016/j.fsi.2019.11.033] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/30/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
Japanese flounder (Paralichthys olivaceus) is one of the most economically important marine fish cultured in north Asia. Vibrio anguillarum is a severe bacterial pathogen to Japanese flounder and many other aquaculture species. In order to understand the immune response of flounder during bacterial infection, we systematically examined the transcriptome profiles of flounder spleen at three time points after V. anguillarum challenge. More than one billion high quality reads were obtained, approximately 80.70% of which were successfully mapped to the reference genome of flounder. A total of 6060, 4688 and 4235 differentially expressed genes (DEGs) were captured at 6, 12 and 24-h post-infection, respectively. The DEGs exhibited dynamic changes in expression and were assigned into four different profiles based on expression trend. GO and KEGG analysis showed that the DEGs were enriched in various immune-related terms, including response to stimulation, immune system and pathways of cytokine-cytokine receptor interaction, Jak-STAT signaling and Toll-like receptor signaling. Furthermore, a network of highly interactive DEGs involved in 11 immune-related pathways was detected by utilizing the weighted co-expressing network analysis (WGCNA). Accordingly, 26 hub genes were discovered that constituted an elaborate immune regulatory network and functioned mainly in pathogen recognition, antigen processing, and molecular signaling. The results of this study provided the first systematical transcriptome profile of flounder in association with V. anguillarum infection and can serve as a valuable resource of target genes for future studies on the molecular mechanisms underlying the immune defense of flounder against bacterial infection.
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Affiliation(s)
- Xianhui Ning
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Li Sun
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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23
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Zarei Ghobadi M, Mozhgani SH, Farzanehpour M, Behzadian F. Identifying novel biomarkers of the pediatric influenza infection by weighted co-expression network analysis. Virol J 2019; 16:124. [PMID: 31665046 PMCID: PMC6819563 DOI: 10.1186/s12985-019-1231-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 10/09/2019] [Indexed: 11/18/2022] Open
Abstract
Background Despite the high yearly prevalence of Influenza, the pathogenesis mechanism and involved genes have not been fully known. Finding the patterns and mapping the complex interactions between different genes help us to find the possible biomarkers and treatment targets. Methods Herein, weighted gene co-expression network analysis (WGCNA) was employed to construct a co-expression network among genes identified by microarray analysis of the pediatric influenza-infected samples. Results Three of the 38 modules were found as the most related modules to influenza infection. At a functional level, we found that the genes in these modules regulate the immune responses, protein targeting, and defense to virus. Moreover, the analysis of differentially expressed genes disclosed 719 DEGs between the normal and infected subjects. The comprehensive investigation of genes in the module involved in immune system and viral defense (yellow module) revealed that SP110, HERC5, SAMD9L, RTP4, C19orf66, HELZ2, EPSTI1, and PHF11 which were also identified as DEGs (except C19orf66) have the potential to be as the biomarkers and also drug targeting for the treatment of pediatric influenza. Conclusions The WGCN analysis revealed co-expressed genes which were involved in the innate immune system and defense to virus. The differentially expressed genes in the identified modules can be considered for designing drug targets. Moreover, modules can help to find pathogenesis routes in the future.
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Affiliation(s)
- Mohadeseh Zarei Ghobadi
- Department of Virology, School of Public Health Tehran University of Medical Sciences, Tehran, Iran.,Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Sayed-Hamidreza Mozhgani
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran.,Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mahdieh Farzanehpour
- Department of Virology, School of Public Health Tehran University of Medical Sciences, Tehran, Iran
| | - Farida Behzadian
- Department of Bioscience and Biotechnology, Malek Ashtar University of Technology, Tehran, Iran.
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24
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Martinez FD, Guerra S. Early Origins of Asthma. Role of Microbial Dysbiosis and Metabolic Dysfunction. Am J Respir Crit Care Med 2019; 197:573-579. [PMID: 29048927 DOI: 10.1164/rccm.201706-1091pp] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Fernando D Martinez
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Arizona
| | - Stefano Guerra
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Arizona
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25
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Tang M, Zimmerman KO, Lang JE. Severe childhood asthma exacerbations: Is treatment response variability in the genes? Pediatr Pulmonol 2019; 54:680-682. [PMID: 30868766 PMCID: PMC9460636 DOI: 10.1002/ppul.24309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 01/31/2019] [Accepted: 02/06/2019] [Indexed: 11/12/2022]
Abstract
Worldwide, asthma is one of the most common causes of medical emergency in children. Failed acute management events comprise a large part of the annual healthcare costs of asthma. These severe exacerbations requiring hospitalization likely also contribute to permanent remodeling and impaired lung function in later life. Various studies have uncovered clinical, environmental, and genetic risk factors for severe asthma and exacerbations that cannot be acutely managed and require hospitalization. Tse and colleagues extend their previous work by adding important new insights into the determinants of failed ED management of pediatric asthma. Using a candidate gene approach and stepwise regression, they identified three SNPs in two candidate genes: IL33, rs7037276, rs1342326 and SPATS2L, rs295137, which when aggregated together significantly increased the odds for ED management failure, with each risk allele increasing failure odds by 83% (95% CI, 36–145%). When these genes markers were combined with validated clinical predictors of acute asthma management failure (viral infection, poor baseline pediatric respiratory assessment measure score, oxygen saturation <92%, fever >38.3°C, and presence of symptoms between episodes) the resulting ability to predict acute management failure was significantly improved (ROC curve=0.82). As discussed in this editorial and the discussion by Tse et al, these novel genetic markers provide new avenues of research for management of acute exacerbations. As the syndrome of asthma continues to be better characterized into multiple endo-phenotypes, we are likely to find that personalized treatment is necessary not only for control of asthma but also for acute rescue of exacerbations.
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Affiliation(s)
- Monica Tang
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina
| | - Kanecia O Zimmerman
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina.,Duke Clinical Research Institute, Duke University School of Medicine, Durham, North Carolina
| | - Jason E Lang
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina.,Duke Clinical Research Institute, Duke University School of Medicine, Durham, North Carolina
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26
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Burleson JD, Siniard D, Yadagiri VK, Chen X, Weirauch MT, Ruff BP, Brandt EB, Hershey GKK, Ji H. TET1 contributes to allergic airway inflammation and regulates interferon and aryl hydrocarbon receptor signaling pathways in bronchial epithelial cells. Sci Rep 2019; 9:7361. [PMID: 31089182 PMCID: PMC6517446 DOI: 10.1038/s41598-019-43767-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 05/01/2019] [Indexed: 01/10/2023] Open
Abstract
Previous studies have suggested a role for Tet1 in the pathogenesis of childhood asthma. However, how Tet1 contributes to asthma remains unknown. Here we used mice deficient for Tet1 in a well-established model of allergic airway inflammation and demonstrated that loss of Tet1 increased disease severity including airway hyperresponsiveness and lung eosinophilia. Increased expression of Muc5ac, Il13, Il33, Il17a, Egfr, and Tff2 were observed in HDM-challenged Tet1-deficient mice compared to Tet1+/+ littermates. Further, transcriptomic analysis of lung RNA followed by pathway and protein network analysis showed that the IFN signaling pathway was significantly upregulated and the aryl hydrocarbon receptor (AhR) pathway was significantly downregulated in HDM-challenged Tet1-/- mice. This transcriptional regulation of the IFN and AhR pathways by Tet1 was also present in human bronchial epithelial cells at base line and following HDM challenges. Genes in these pathways were further associated with changes in DNA methylation, predicted binding of transcriptional factors with relevant functions in their promoters, and the presence of histone marks generated by histone enzymes that are known to interact with Tet1. Collectively, our data suggest that Tet1 inhibits HDM-induced allergic airway inflammation by direct regulation of the IFN and AhR pathways.
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Affiliation(s)
- J D Burleson
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Dylan Siniard
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Pyrosequencing lab for genomic and epigenomic research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Veda K Yadagiri
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Brandy P Ruff
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Eric B Brandt
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Gurjit K Khurana Hershey
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Hong Ji
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Pyrosequencing lab for genomic and epigenomic research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA. .,Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, CA, USA. .,California National Primate Research Center, Davis, CA, USA.
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27
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Altman MC, Gill MA, Whalen E, Babineau DC, Shao B, Liu AH, Jepson B, Gruchalla RS, O'Connor GT, Pongracic JA, Kercsmar CM, Khurana Hershey GK, Zoratti EM, Johnson CC, Teach SJ, Kattan M, Bacharier LB, Beigelman A, Sigelman SM, Presnell S, Gern JE, Gergen PJ, Wheatley LM, Togias A, Busse WW, Jackson DJ. Transcriptome networks identify mechanisms of viral and nonviral asthma exacerbations in children. Nat Immunol 2019; 20:637-651. [PMID: 30962590 PMCID: PMC6472965 DOI: 10.1038/s41590-019-0347-8] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 02/11/2019] [Indexed: 12/14/2022]
Abstract
Respiratory infections are common precursors to asthma exacerbations in children, but molecular immune responses that determine whether and how an infection causes an exacerbation are poorly understood. By using systems-scale network analysis, we identify repertoires of cellular transcriptional pathways that lead to and underlie distinct patterns of asthma exacerbation. Specifically, in both virus-associated and nonviral exacerbations, we demonstrate a set of core exacerbation modules, among which epithelial-associated SMAD3 signaling is upregulated and lymphocyte response pathways are downregulated early in exacerbation, followed by later upregulation of effector pathways including epidermal growth factor receptor signaling, extracellular matrix production, mucus hypersecretion, and eosinophil activation. We show an additional set of multiple inflammatory cell pathways involved in virus-associated exacerbations, in contrast to squamous cell pathways associated with nonviral exacerbations. Our work introduces an in vivo molecular platform to investigate, in a clinical setting, both the mechanisms of disease pathogenesis and therapeutic targets to modify exacerbations.
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Affiliation(s)
- Matthew C Altman
- Department of Allergy and Infectious Diseases, University of Washington, Seattle, WA, USA.
- Systems Immunology Program, Benaroya Research Institute, Seattle, WA, USA.
| | - Michelle A Gill
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Elizabeth Whalen
- Systems Immunology Program, Benaroya Research Institute, Seattle, WA, USA
| | | | - Baomei Shao
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andrew H Liu
- Department of Allergy and Immunology, Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Rebecca S Gruchalla
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - George T O'Connor
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | | | | | | | | | | | | | - Meyer Kattan
- Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Leonard B Bacharier
- Division of Allergy, Immunology, and Pulmonary Medicine, Washington University, St. Louis, MO, USA
| | - Avraham Beigelman
- Division of Allergy, Immunology, and Pulmonary Medicine, Washington University, St. Louis, MO, USA
| | - Steve M Sigelman
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Scott Presnell
- Systems Immunology Program, Benaroya Research Institute, Seattle, WA, USA
| | - James E Gern
- University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Peter J Gergen
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Lisa M Wheatley
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Alkis Togias
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - William W Busse
- University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Daniel J Jackson
- University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
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28
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Khoo SK, Read J, Franks K, Zhang G, Bizzintino J, Coleman L, McCrae C, Öberg L, Troy NM, Prastanti F, Everard J, Oo S, Borland ML, Maciewicz RA, Le Souëf PN, Laing IA, Bosco A. Upper Airway Cell Transcriptomics Identify a Major New Immunological Phenotype with Strong Clinical Correlates in Young Children with Acute Wheezing. THE JOURNAL OF IMMUNOLOGY 2019; 202:1845-1858. [PMID: 30745463 DOI: 10.4049/jimmunol.1800178] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 01/08/2019] [Indexed: 01/10/2023]
Abstract
Asthma exacerbations are triggered by rhinovirus infections. We employed a systems biology approach to delineate upper-airway gene network patterns underlying asthma exacerbation phenotypes in children. Cluster analysis unveiled distinct IRF7hi versus IRF7lo molecular phenotypes, the former exhibiting robust upregulation of Th1/type I IFN responses and the latter an alternative signature marked by upregulation of cytokine and growth factor signaling and downregulation of IFN-γ. The two phenotypes also produced distinct clinical phenotypes. For IRF7lo children, symptom duration prior to hospital presentation was more than twice as long from initial symptoms (p = 0.011) and nearly three times as long for cough (p < 0.001), the odds ratio of admission to hospital was increased more than 4-fold (p = 0.018), and time to recurrence was shorter (p = 0.015). In summary, our findings demonstrate that asthma exacerbations in children can be divided into IRF7hi versus IRF7lo phenotypes with associated differences in clinical phenotypes.
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Affiliation(s)
- Siew-Kim Khoo
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia
| | - James Read
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia
| | - Kimberley Franks
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia
| | - Guicheng Zhang
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia.,School of Public Health, Curtin University, Perth, Western Australia 6102, Australia.,Centre for Genetic Origins of Health and Disease, The University of Western Australia, Perth, Western Australia 6009, Australia and Curtin University, Perth, Western Australia 6102, Australia
| | - Joelene Bizzintino
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia
| | - Laura Coleman
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia
| | - Christopher McCrae
- Respiratory Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca, Gothenburg, 431 53 Mölndal, Sweden
| | - Lisa Öberg
- Respiratory Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca, Gothenburg, 431 53 Mölndal, Sweden
| | - Niamh M Troy
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia
| | - Franciska Prastanti
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia
| | - Janet Everard
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia
| | - Stephen Oo
- Division of Paediatrics, School of Medicine, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Meredith L Borland
- Division of Paediatrics, School of Medicine, The University of Western Australia, Perth, Western Australia 6009, Australia.,Perth Children's Hospital, Perth, Western Australia 6009, Australia; and.,Division of Emergency Medicine, School of Medicine, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Rose A Maciewicz
- Respiratory Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca, Gothenburg, 431 53 Mölndal, Sweden
| | - Peter N Le Souëf
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia.,Division of Paediatrics, School of Medicine, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Ingrid A Laing
- Division of Cardiovascular and Respiratory Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia.,Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia
| | - Anthony Bosco
- Telethon Kids Institute, The University of Western Australia, Perth, Western Australia 6008, Australia;
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29
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Guide snoRNAs: Drivers or Passengers in Human Disease? BIOLOGY 2018; 8:biology8010001. [PMID: 30577491 PMCID: PMC6466398 DOI: 10.3390/biology8010001] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 12/16/2018] [Accepted: 12/18/2018] [Indexed: 01/17/2023]
Abstract
In every domain of life, RNA-protein interactions play a significant role in co- and post-transcriptional modifications and mRNA translation. RNA performs diverse roles inside the cell, and therefore any aberrancy in their function can cause various diseases. During maturation from its primary transcript, RNA undergoes several functionally important post-transcriptional modifications including pseudouridylation and ribose 2′-O-methylation. These modifications play a critical role in the stability of the RNA. In the last few decades, small nucleolar RNAs (snoRNAs) were revealed to be one of the main components to guide these modifications. Due to their active links to the nucleoside modification, deregulation in the snoRNA expressions can cause multiple disorders in humans. Additionally, host genes carrying snoRNA-encoding sequences in their introns also show differential expression in disease. Although few reports support a causal link between snoRNA expression and disease manifestation, this emerging field will have an impact on the way we think about biomarkers or identify novel targets for therapy. This review focuses on the intriguing aspect of snoRNAs that function as a guide in post-transcriptional RNA modification, and regulation of their host genes in human disease.
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30
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Carr TF, Stern DA, Halonen M, Wright AL, Martinez FD. Non-atopic rhinitis at age 6 is associated with subsequent development of asthma. Clin Exp Allergy 2018; 49:35-43. [PMID: 30220097 DOI: 10.1111/cea.13276] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 08/24/2018] [Accepted: 09/01/2018] [Indexed: 11/29/2022]
Abstract
BACKGROUND It has been postulated that the association between allergic rhinitis and asthma is attributable to the progressive clinical expression of respiratory inflammation during childhood. The role of non-allergic rhinitis in early life in relation to subsequent asthma has not been extensively explored. OBJECTIVE We sought to determine whether rhinitis in early life was associated with risk of asthma development into adulthood, and whether this relationship is independent of allergic sensitization. METHODS Participants were identified from the Tucson Children's Respiratory Study, a non-selected birth cohort. Allergy skin prick testing was performed at age 6 years using house dust mix, Bermuda, mesquite, olive, mulberry, careless weed, and Alternaria aeroallergens. Atopy was defined as ≥1 positive tests. Physician-diagnosed active asthma from age 6 to 32 and physician-diagnosed rhinitis at age 6 were determined by questionnaire. Participants with asthma or active wheezing at age 6 were excluded from analyses. Risk estimates were obtained with Cox regression. RESULTS There were 521 participants who met inclusion criteria. The hazard ratio for subsequently acquiring a diagnosis of asthma between the ages of 8 and 32 for those with non-atopic rhinitis was 2.1 (95% CI: 1.2, 3.4, P = 0.005), compared with the non-atopic no rhinitis group, after adjusting for sex, ethnicity, maternal asthma, maternal education and smoking, and history of 4+ colds per year at age 6. Among the atopic participants, both the active and no rhinitis groups were more likely to develop and have asthma through age 32. The relation between non-atopic rhinitis and asthma was independent of total serum IgE levels at age 6. CONCLUSION AND CLINICAL RELEVANCE Childhood rhinitis, even in the absence of atopy, confers significant risk for asthma development through adulthood. These findings underscore the importance of non-allergic mechanisms in the development of asthma.
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Affiliation(s)
- Tara F Carr
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Arizona
| | - Debra A Stern
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Arizona
| | - Marilyn Halonen
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Arizona
| | - Anne L Wright
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Arizona
| | - Fernando D Martinez
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Arizona
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31
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Farzan N, Vijverberg SJ, Kabesch M, Sterk PJ, Maitland-van der Zee AH. The use of pharmacogenomics, epigenomics, and transcriptomics to improve childhood asthma management: Where do we stand? Pediatr Pulmonol 2018; 53:836-845. [PMID: 29493882 DOI: 10.1002/ppul.23976] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 02/01/2018] [Indexed: 01/11/2023]
Abstract
Asthma is a complex multifactorial disease and it is the most common chronic disease in children. There is a high variability in response to asthma treatment, even in patients with good adherence to maintenance treatment, and a correct inhalation technique. Distinct underlying disease mechanisms in childhood asthma might be the reason of this heterogeneity. A deeper knowledge of the underlying molecular mechanisms of asthma has led to the recent development of advanced and mechanism-based treatments such as biologicals. However, biologicals are recommended only for patients with specific asthma phenotypes who remain uncontrolled despite high dosages of conventional asthma treatment. One of the main unmet needs in their application is lack of clinically available biomarkers to individualize pediatric asthma management and guide treatment. Pharmacogenomics, epigenomics, and transcriptomics are three omics fields that are rapidly advancing and can provide tools to identify novel asthma mechanisms and biomarkers to guide treatment. Pharmacogenomics focuses on variants in the DNA, epigenomics studies heritable changes that do not involve changes in the DNA sequence but lead to alteration of gene expression, and transcriptomics investigates gene expression by studying the complete set of mRNA transcripts in a cell or a population of cells. Advances in high-throughput technologies and statistical tools together with well-phenotyped patient inclusion and collaborations between different centers will expand our knowledge of underlying molecular mechanisms involved in disease onset and progress. Furthermore, it could help to select and stratify appropriate therapeutic strategies for subgroups of patients and hopefully bring precision medicine to daily practice.
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Affiliation(s)
- Niloufar Farzan
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Susanne J Vijverberg
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
| | - Peter J Sterk
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
| | - Anke H Maitland-van der Zee
- Department of Respiratory Medicine, Academic Medical Center (AMC), University of Amsterdam, Amsterdam, The Netherlands
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32
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Benfante A, Di Marco F, Terraneo S, Centanni S, Scichilone N. Dynamic hyperinflation during the 6-min walk test in severely asthmatic subjects. ERJ Open Res 2018; 4:00143-2017. [PMID: 29796391 PMCID: PMC5958274 DOI: 10.1183/23120541.00143-2017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/28/2018] [Indexed: 01/28/2023] Open
Abstract
We tested the hypothesis that dynamic hyperinflation develops in severe asthmatic subjects during exercise. Changes in inspiratory capacity (IC) were measured during the 6-min walk test (6MWT) in severe asthmatic subjects compared with chronic obstructive pulmonary disease (COPD) subjects with a similar degree of bronchial obstruction. We assessed whether changes in IC were associated with changes in dyspnoea perception. 27 severe asthmatic subjects (10 males and 17 females) and 43 COPD subjects (35 males and eight females) were recruited. The two groups performed similarly in the 6MWT (p=0.90). At the end of the test, the Borg score increased significantly in both groups (mean difference: for asthmatic subjects 1.7±1.6; p<0.0001; for COPD subjects 3.1±1.9; p<0.0001). IC measured at the beginning of 6MWT was not different between groups (2.25±0.47 L in asthmatic subjects versus 2.38±0.60 L in COPD subjects; p=0.32) and decreased in both groups (mean difference: for asthmatic subjects 0.160 L; p=0.02; for COPD subjects 0.164 L; p<0.0001). However, changes in IC were significantly associated with changes in the Borg score in the COPD group (r2=0.17; p=0.006), but not in the asthma group (r2=0.06; p=0.20). In severe asthmatic subjects, IC significantly drops during the 6MWT to the same extent as COPD subjects with a similar degree of lung impairment, indicating the development of dynamic hyperinflation. Contrary to COPD, in asthmatic subjects the occurrence of dynamic hyperinflation was not associated with changes in dyspnoea perception. Severe asthma is characterised by occurrence of dynamic hyperinflation during exercise; inspiratory capacity drops in severe asthmatic subjects during the 6MWT to the same extent as in COPD subjects with similar lung impairmenthttp://ow.ly/InfQ30jjivW
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Affiliation(s)
- Alida Benfante
- Dipartimento Biomedico di Medicina Interna e Specialistica, Sezione di Pneumologia, University of Palermo, Palermo, Italy.,These two authors contributed equally to this work
| | - Fabiano Di Marco
- Respiratory Unit, Ospedale San Paolo, ASST Santi Paolo e Carlo, Dept of Health Sciences, Università degli Studi di Milano, Milan, Italy.,These two authors contributed equally to this work
| | - Silvia Terraneo
- Respiratory Unit, Ospedale San Paolo, ASST Santi Paolo e Carlo, Dept of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Stefano Centanni
- Respiratory Unit, Ospedale San Paolo, ASST Santi Paolo e Carlo, Dept of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Nicola Scichilone
- Dipartimento Biomedico di Medicina Interna e Specialistica, Sezione di Pneumologia, University of Palermo, Palermo, Italy
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33
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Abstract
Asthma has been the most common chronic disease in children that places a major burden for affected people and their families.An integrated analysis of microarrays studies was performed to identify differentially expressed genes (DEGs) in childhood asthma compared with normal control. We also obtained the differentially methylated genes (DMGs) in childhood asthma according to GEO. The genes that were both differentially expressed and differentially methylated were identified. Functional annotation and protein-protein interaction network construction were performed to interpret biological functions of DEGs. We performed q-RT-PCR to verify the expression of selected DEGs.One DNA methylation and 3 gene expression datasets were obtained. Four hundred forty-one DEGs and 1209 DMGs in childhood asthma were identified. Among which, 16 genes were both differentially expressed and differentially methylated in childhood asthma. Natural killer cell mediated cytotoxicity pathway, Jak-STAT signaling pathway, and Wnt signaling pathway were 3 significantly enriched pathways in childhood asthma according to our KEGG enrichment analysis. The PPI network of top 20 up- and downregulated DEGs consisted of 822 nodes and 904 edges and 2 hub proteins (UBQLN4 and MID2) were identified. The expression of 8 DEGs (GZMB, FGFBP2, CLC, TBX21, ALOX15, IL12RB2, UBQLN4) was verified by qRT-PCR and only the expression of GZMB and FGFBP2 was inconsistent with our integrated analysis.Our finding was helpful to elucidate the underlying mechanism of childhood asthma and develop new potential diagnostic biomarker and provide clues for drug design.
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Affiliation(s)
| | | | - Yu-Hua Mu
- Department of General Surgery, Rizhao People's Hospital, Rizhao, China
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34
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Jones AC, Troy NM, White E, Hollams EM, Gout AM, Ling KM, Kicic A, Stick SM, Sly PD, Holt PG, Hall GL, Bosco A. Persistent activation of interlinked type 2 airway epithelial gene networks in sputum-derived cells from aeroallergen-sensitized symptomatic asthmatics. Sci Rep 2018; 8:1511. [PMID: 29367592 PMCID: PMC5784090 DOI: 10.1038/s41598-018-19837-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 01/04/2018] [Indexed: 02/08/2023] Open
Abstract
Atopic asthma is a persistent disease characterized by intermittent wheeze and progressive loss of lung function. The disease is thought to be driven primarily by chronic aeroallergen-induced type 2-associated inflammation. However, the vast majority of atopics do not develop asthma despite ongoing aeroallergen exposure, suggesting additional mechanisms operate in conjunction with type 2 immunity to drive asthma pathogenesis. We employed RNA-Seq profiling of sputum-derived cells to identify gene networks operative at baseline in house dust mite-sensitized (HDMS) subjects with/without wheezing history that are characteristic of the ongoing asthmatic state. The expression of type 2 effectors (IL-5, IL-13) was equivalent in both cohorts of subjects. However, in HDMS-wheezers they were associated with upregulation of two coexpression modules comprising multiple type 2- and epithelial-associated genes. The first module was interlinked by the hubs EGFR, ERBB2, CDH1 and IL-13. The second module was associated with CDHR3 and mucociliary clearance genes. Our findings provide new insight into the molecular mechanisms operative at baseline in the airway mucosa in atopic asthmatics undergoing natural aeroallergen exposure, and suggest that susceptibility to asthma amongst these subjects involves complex interactions between type 2- and epithelial-associated gene networks, which are not operative in equivalently sensitized/exposed atopic non-asthmatics.
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Affiliation(s)
- Anya C Jones
- Telethon Kids Institute, The University of Western Australia, Perth, Australia.,School of Paediatrics and Child Health, The University of Western Australia, Perth, Australia
| | - Niamh M Troy
- Telethon Kids Institute, The University of Western Australia, Perth, Australia.,School of Paediatrics and Child Health, The University of Western Australia, Perth, Australia
| | - Elisha White
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Elysia M Hollams
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Alexander M Gout
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Kak-Ming Ling
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Anthony Kicic
- Telethon Kids Institute, The University of Western Australia, Perth, Australia.,School of Paediatrics and Child Health, The University of Western Australia, Perth, Australia.,Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, Australia.,Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia, Perth, Australia
| | - Stephen M Stick
- Telethon Kids Institute, The University of Western Australia, Perth, Australia.,School of Paediatrics and Child Health, The University of Western Australia, Perth, Australia.,Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, Australia.,Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia, Perth, Australia
| | - Peter D Sly
- Child Health Research Centre, The University of Queensland, Brisbane, Australia
| | - Patrick G Holt
- Telethon Kids Institute, The University of Western Australia, Perth, Australia.,Child Health Research Centre, The University of Queensland, Brisbane, Australia
| | - Graham L Hall
- Telethon Kids Institute, The University of Western Australia, Perth, Australia.,School of Physiotherapy and Exercise Science, Curtin University, Perth, Australia.,Centre of Child Health Research, The University of Western Australia, Perth, Australia
| | - Anthony Bosco
- Telethon Kids Institute, The University of Western Australia, Perth, Australia.
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35
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Jones AC, Bosco A. Using Network Analysis to Understand Severe Asthma Phenotypes. Am J Respir Crit Care Med 2017; 195:1409-1411. [PMID: 28569573 DOI: 10.1164/rccm.201612-2572ed] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Anya C Jones
- 1 Telethon Kids Institute The University of Western Australia Perth, Australia
| | - Anthony Bosco
- 1 Telethon Kids Institute The University of Western Australia Perth, Australia
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36
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Xi Y, Troy NM, Anderson D, Pena OM, Lynch JP, Phipps S, Bosco A, Upham JW. Critical Role of Plasmacytoid Dendritic Cells in Regulating Gene Expression and Innate Immune Responses to Human Rhinovirus-16. Front Immunol 2017; 8:1351. [PMID: 29118754 PMCID: PMC5660993 DOI: 10.3389/fimmu.2017.01351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/03/2017] [Indexed: 11/16/2022] Open
Abstract
Though human rhinoviruses (HRVs) are usually innocuous viruses, they can trigger serious consequences in certain individuals, especially in the setting of impaired interferon (IFN) synthesis. Plasmacytoid dendritic cells (pDCs) are key IFN producing cells, though we know little about the role of pDC in HRV-induced immune responses. Herein, we used gene expression microarrays to examine HRV-activated peripheral blood mononuclear cells (PBMCs) from healthy people, in combination with pDC depletion, to assess whether observed gene expression patterns were pDC dependent. As expected, pDC depletion led to a major reduction in IFN-α release. This was associated with profound differences in gene expression between intact PBMC and pDC-depleted PBMC, and major changes in upstream regulators: 70–80% of the HRV activated genes appeared to be pDC dependent. Real-time PCR confirmed key changes in gene expression, in which the following selected genes were shown to be highly pDC dependent: the transcription factor IRF7, both IL-27 chains (IL-27p28 and EBI3), the alpha chain of the IL-15 receptor (IL-15RA) and the IFN-related gene IFI27. HRV-induced IL-6, IFN-γ, and IL-27 protein synthesis were also highly pDC dependent. Supplementing pDC-depleted cultures with recombinant IL-15, IFN-γ, IL-27, or IL-6 was able to restore the IFN-α response, thereby compensating for the absence of pDC. Though pDC comprise only a minority population of migratory leukocytes, our findings highlight the profound extent to which these cells contribute to the immune response to HRV.
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Affiliation(s)
- Yang Xi
- Lung and Allergy Research Center, Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Niamh M Troy
- Systems Immunology, Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Denise Anderson
- Systems Immunology, Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - Olga M Pena
- Lung and Allergy Research Center, Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Jason P Lynch
- Respiratory Immunology Group, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Simon Phipps
- Respiratory Immunology Group, QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Anthony Bosco
- Systems Immunology, Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia
| | - John W Upham
- Lung and Allergy Research Center, Diamantina Institute, The University of Queensland, Brisbane, QLD, Australia.,Department of Respiratory Medicine, Princess Alexandra Hospital, Woolloongabba, QLD, Australia
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37
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Wisniewski JA, Muehling LM, Eccles JD, Capaldo BJ, Agrawal R, Shirley DA, Patrie JT, Workman LJ, Schuyler AJ, Lawrence MG, Teague WG, Woodfolk JA. T H1 signatures are present in the lower airways of children with severe asthma, regardless of allergic status. J Allergy Clin Immunol 2017; 141:2048-2060.e13. [PMID: 28939412 DOI: 10.1016/j.jaci.2017.08.020] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 07/13/2017] [Accepted: 08/15/2017] [Indexed: 12/31/2022]
Abstract
BACKGROUND The pathogenesis of severe asthma in childhood remains poorly understood. OBJECTIVE We sought to construct the immunologic landscape in the airways of children with severe asthma. METHODS Comprehensive analysis of multiple cell types and mediators was performed by using flow cytometry and a multiplex assay with bronchoalveolar lavage (BAL) specimens (n = 68) from 52 highly characterized allergic and nonallergic children (0.5-17 years) with severe treatment-refractory asthma. Multiple relationships were tested by using linear mixed-effects modeling. RESULTS Memory CCR5+ TH1 cells were enriched in BAL fluid versus blood, and pathogenic respiratory viruses and bacteria were readily detected. IFN-γ+IL-17+ and IFN-γ-IL-17+ subsets constituted secondary TH types, and BAL fluid CD8+ T cells were almost exclusively IFN-γ+. The TH17-associated mediators IL-23 and macrophage inflammatory protein 3α/CCL20 were highly expressed. Despite low TH2 numbers, TH2 cytokines were detected, and TH2 skewing correlated with total IgE levels. Type 2 innate lymphoid cells and basophils were scarce in BAL fluid. Levels of IL-5, IL-33, and IL-28A/IFN-λ2 were increased in multisensitized children and correlated with IgE levels to dust mite, ryegrass, and fungi but not cat, ragweed, or food sources. Additionally, levels of IL-5, but no other cytokine, increased with age and correlated with eosinophil numbers in BAL fluid and blood. Both plasmacytoid and IgE+FcεRI+ myeloid dendritic cells were present in BAL fluid. CONCLUSIONS The lower airways of children with severe asthma display a dominant TH1 signature and atypical cytokine profiles that link to allergic status. Our findings deviate from established paradigms and warrant further assessment of the pathogenicity of TH1 cells in patients with severe asthma.
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Affiliation(s)
- Julia A Wisniewski
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Va; Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, Va
| | - Lyndsey M Muehling
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Va
| | - Jacob D Eccles
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Va
| | - Brian J Capaldo
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Va
| | - Rachana Agrawal
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Va
| | - Debbie-Ann Shirley
- Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, Va
| | - James T Patrie
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Va
| | - Lisa J Workman
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Va
| | - Alexander J Schuyler
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Va
| | - Monica G Lawrence
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Va
| | - W Gerald Teague
- Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, Va
| | - Judith A Woodfolk
- Department of Medicine, University of Virginia School of Medicine, Charlottesville, Va.
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38
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Analysis of temporal expression profiles after sciatic nerve injury by bioinformatic method. Sci Rep 2017; 7:9818. [PMID: 28852045 PMCID: PMC5575162 DOI: 10.1038/s41598-017-10127-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/04/2017] [Indexed: 02/05/2023] Open
Abstract
After Peripheral nerve injuries (PNI), many complicated pathophysiologic processes will happen. A global view of functional changes following PNI is essential for the looking for the adequate therapeutic approaches. In this study, we performed an in-depth analysis on the temporal expression profiles after sciatic nerve injury by bioinformatic methods, including (1) cluster analysis of the samples; (2) identification of gene co-expression modules(CEMs) correlated with the time points; (3) analysis of differentially expressed genes at each time point (DEGs-ET); (4) analysis of differentially expressed genes varying over time (DEGs-OT); (5) creating Pairwise Correlation Plot for the samples; (6) Time Series Regression Analysis; (7) Determining the pathway, GO (gene ontology) and drug by enrichment analysis. We found that at a 3 h "window period" some specific gene expression may exist after PNI, and responses to lipopolysaccharide (LPS) and TNF signaling pathway may play important roles, suggesting that the inflammatory microenvironment exists after PNI. We also found that troglitazone was closely associated with the change of gene expression after PNI. Therefore, the further evaluation of the precise mechanism of troglitazone on PNI is needed and it may contribute to the development of new drugs for patients with PNI.
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39
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Gelfand EW, Joetham A, Wang M, Takeda K, Schedel M. Spectrum of T-lymphocyte activities regulating allergic lung inflammation. Immunol Rev 2017; 278:63-86. [PMID: 28658551 PMCID: PMC5501488 DOI: 10.1111/imr.12561] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Despite advances in the treatment of asthma, optimization of symptom control remains an unmet need in many patients. These patients, labeled severe asthma, are responsible for a substantial fraction of the disease burden. In these patients, research is needed to define the cellular and molecular pathways contributing to disease which in large part are refractory to corticosteroid treatment. The causes of steroid-resistant asthma are multifactorial and result from complex interactions of genetics, environmental factors, and innate and adaptive immunity. Adaptive immunity, addressed here, integrates the activities of distinct T-cell subsets and by definition is dynamic and responsive to an ever-changing environment and the influences of epigenetic modifications. These T-cell subsets exhibit different susceptibilities to the actions of corticosteroids and, in some, corticosteroids enhance their functional activation. Moreover, these subsets are not fixed in lineage differentiation but can undergo transcriptional reprogramming in a bidirectional manner between protective and pathogenic effector states. Together, these factors contribute to asthma heterogeneity between patients but also in the same patient at different stages of their disease. Only by carefully defining mechanistic pathways, delineating their sensitivity to corticosteroids, and determining the balance between regulatory and effector pathways will precision medicine become a reality with selective and effective application of targeted therapies.
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Affiliation(s)
- Erwin W Gelfand
- Division of Cell Biology, Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Anthony Joetham
- Division of Cell Biology, Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Meiqin Wang
- Division of Cell Biology, Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Katsuyuki Takeda
- Division of Cell Biology, Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Michaela Schedel
- Division of Cell Biology, Department of Pediatrics, National Jewish Health, Denver, CO, USA
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40
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Heymann PW, Nguyen HT, Steinke JW, Turner RB, Woodfolk JA, Platts-Mills TAE, Martin L, He H, Biagini Myers J, Lindsey M, Sivaprasad U, Medvedovic M, Mahi N, Carper H, Murphy DD, Patrie J, Khurana Hershey GK. Rhinovirus infection results in stronger and more persistent genomic dysregulation: Evidence for altered innate immune response in asthmatics at baseline, early in infection, and during convalescence. PLoS One 2017; 12:e0178096. [PMID: 28552993 PMCID: PMC5446117 DOI: 10.1371/journal.pone.0178096] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 05/07/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Rhinovirus (HRV) is associated with the large majority of virus-induced asthma exacerbations in children and young adults, but the mechanisms remain poorly defined. METHODS Asthmatics and non-asthmatic controls were inoculated with HRV-A16, and nasal epithelial samples were obtained 7 days before, 36 hours after, and 7 days after viral inoculation. RNA was extracted and subjected to RNA-seq analysis. RESULTS At baseline, 57 genes were differentially expressed between asthmatics and controls, and the asthmatics had decreased expression of viral replication inhibitors and increased expression of genes involved in inflammation. At 36 hours (before the emergence of peak symptoms), 1329 genes were significantly altered from baseline in the asthmatics compared to 62 genes in the controls. At this time point, asthmatics lacked an increase in IL-10 signaling observed in the controls. At 7 days following HRV inoculation, 222 genes were significantly dysregulated in the asthmatics, whereas only 4 genes were dysregulated among controls. At this time point, the controls but not asthmatics demonstrated upregulation of SPINK5. CONCLUSIONS As judged by the magnitude and persistence of dysregulated genes, asthmatics have a substantially different host response to HRV-A16 infection compared with non-asthmatic controls. Gene expression differences illuminate biologically plausible mechanisms that contribute to a better understanding of the pathogenesis of HRV-induced asthma exacerbations.
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Affiliation(s)
- Peter W. Heymann
- Division of Allergy, Immunology and Respiratory Medicine, Department of Pediatrics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Internal Medicine, Asthma and Allergic Diseases Center, University of Virginia, Charlottesville, Virginia, United States of America
| | - Huyen-Tran Nguyen
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, United States of America
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - John W. Steinke
- Department of Internal Medicine, Asthma and Allergic Diseases Center, University of Virginia, Charlottesville, Virginia, United States of America
| | - Ronald B. Turner
- Division of Infectious Diseases, Department of Pediatrics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Judith A. Woodfolk
- Department of Internal Medicine, Asthma and Allergic Diseases Center, University of Virginia, Charlottesville, Virginia, United States of America
| | - Thomas A. E. Platts-Mills
- Department of Internal Medicine, Asthma and Allergic Diseases Center, University of Virginia, Charlottesville, Virginia, United States of America
| | - Lisa Martin
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Hua He
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Jocelyn Biagini Myers
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Mark Lindsey
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Umasundari Sivaprasad
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Mario Medvedovic
- Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Naim Mahi
- Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Holliday Carper
- Division of Allergy, Immunology and Respiratory Medicine, Department of Pediatrics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Deborah D. Murphy
- Division of Allergy, Immunology and Respiratory Medicine, Department of Pediatrics, University of Virginia, Charlottesville, Virginia, United States of America
| | - James Patrie
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, United States of America
| | - Gurjit K. Khurana Hershey
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, United States of America
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41
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Dynamic versus static biomarkers in cancer immune checkpoint blockade: unravelling complexity. Nat Rev Drug Discov 2017; 16:264-272. [PMID: 28057932 DOI: 10.1038/nrd.2016.233] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recently, there has been a coordinated effort from academic institutions and the pharmaceutical industry to identify biomarkers that can predict responses to immune checkpoint blockade in cancer. Several biomarkers have been identified; however, none has reliably predicted response in a sufficiently rigorous manner for routine use. Here, we argue that the therapeutic response to immune checkpoint blockade is a critical state transition of a complex system. Such systems are highly sensitive to initial conditions, and critical transitions are notoriously difficult to predict far in advance. Nevertheless, warning signals can be detected closer to the tipping point. Advances in mathematics and network biology are starting to make it possible to identify such warning signals. We propose that these dynamic biomarkers could prove to be useful in distinguishing responding from non-responding patients, as well as facilitate the identification of new therapeutic targets for combination therapy.
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42
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Park HW, Tantisira KG. Genetic Signatures of Asthma Exacerbation. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2017; 9:191-199. [PMID: 28293925 PMCID: PMC5352570 DOI: 10.4168/aair.2017.9.3.191] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 10/14/2016] [Accepted: 10/18/2016] [Indexed: 01/15/2023]
Abstract
Asthma exacerbation (AE) usually denotes worsening of asthma symptoms that requires intense management to prevent further deterioration. AE has been reported to correlate with clinical and demographic factors, such as race, gender, and treatment compliance as well as environmental factors, such as viral infection, smoking, and air pollution. In addition, recent observations suggest that there are likely to be genetic factors specific to AE. Understanding genetic factors specific to AE is essential to develop therapy tailored for exacerbation-prone asthma. Here, we summarize the results of studies involving genetic risk factors for AE. To simplify and enhance understanding, we reviewed the studies according to the following categories: hypothesis-driven approaches, hypothesis-free approaches, gene-environment interactions, and pharmacogenetics.
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Affiliation(s)
- Heung Woo Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.,The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kelan G Tantisira
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.
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Sibilano R, Gaudenzio N, DeGorter MK, Reber LL, Hernandez JD, Starkl PM, Zurek OW, Tsai M, Zahner S, Montgomery SB, Roers A, Kronenberg M, Yu M, Galli SJ. A TNFRSF14-FcɛRI-mast cell pathway contributes to development of multiple features of asthma pathology in mice. Nat Commun 2016; 7:13696. [PMID: 27982078 PMCID: PMC5171877 DOI: 10.1038/ncomms13696] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 10/26/2016] [Indexed: 01/07/2023] Open
Abstract
Asthma has multiple features, including airway hyperreactivity, inflammation and remodelling. The TNF superfamily member TNFSF14 (LIGHT), via interactions with the receptor TNFRSF14 (HVEM), can support TH2 cell generation and longevity and promote airway remodelling in mouse models of asthma, but the mechanisms by which TNFSF14 functions in this setting are incompletely understood. Here we find that mouse and human mast cells (MCs) express TNFRSF14 and that TNFSF14:TNFRSF14 interactions can enhance IgE-mediated MC signalling and mediator production. In mouse models of asthma, TNFRSF14 blockade with a neutralizing antibody administered after antigen sensitization, or genetic deletion of Tnfrsf14, diminishes plasma levels of antigen-specific IgG1 and IgE antibodies, airway hyperreactivity, airway inflammation and airway remodelling. Finally, by analysing two types of genetically MC-deficient mice after engrafting MCs that either do or do not express TNFRSF14, we show that TNFRSF14 expression on MCs significantly contributes to the development of multiple features of asthma pathology.
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Affiliation(s)
- Riccardo Sibilano
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Nicolas Gaudenzio
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Marianne K. DeGorter
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Laurent L. Reber
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Immunology, Unit of Antibodies in Therapy and Pathology, INSERM U1222, Institut Pasteur, Paris 75015, France
| | - Joseph D. Hernandez
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Philipp M. Starkl
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences and Department of Medicine I, Research Laboratory of Infection Biology, Medical University of Vienna, Vienna 1090, Austria
| | - Oliwia W. Zurek
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Mindy Tsai
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Sonja Zahner
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, USA
| | - Stephen B. Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Axel Roers
- Institute for Immunology, Technische Universität Dresden, Dresden 01307, Germany
| | - Mitchell Kronenberg
- Division of Developmental Immunology, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037, USA
| | - Mang Yu
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Stephen J. Galli
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Microbiology and Immunology and Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, California 94305, USA
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44
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Rhinovirus-induced asthma exacerbations and risk populations. Curr Opin Allergy Clin Immunol 2016; 16:179-85. [PMID: 26836624 DOI: 10.1097/aci.0000000000000245] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PURPOSE OF REVIEW This article discusses recent findings into the mechanisms that determine how viruses trigger asthma exacerbations. RECENT FINDINGS Substantial progress has been made in our understanding of the pathogenesis of virus-induced asthma exacerbations. This includes new insights into the role of bacteria, the regulation of interferon responses, and the discovery of innate immune pathways that link viral infections with allergic inflammation. Progress has also been made in elucidating the genetic risk factors for asthma exacerbations, most notably the contribution of the ORMDL3/GSDMB locus on 17q, the mechanisms underlying the farming effect, and the discovery that CDHR3 binds to rhinovirus species C. SUMMARY Asthma exacerbations are heterogeneous conditions that involve the complex interplay between environmental exposures and innate and adaptive immune function in genetically predisposed individuals. Recent insights into the interrelationships between these factors provide new opportunities for therapeutic intervention.
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Troy NM, Bosco A. Respiratory viral infections and host responses; insights from genomics. Respir Res 2016; 17:156. [PMID: 27871304 PMCID: PMC5117516 DOI: 10.1186/s12931-016-0474-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 11/10/2016] [Indexed: 01/23/2023] Open
Abstract
Respiratory viral infections are a leading cause of disease and mortality. The severity of these illnesses can vary markedly from mild or asymptomatic upper airway infections to severe wheezing, bronchiolitis or pneumonia. In this article, we review the viral sensing pathways and organizing principles that govern the innate immune response to infection. Then, we reconstruct the molecular networks that differentiate symptomatic from asymptomatic respiratory viral infections, and identify the underlying molecular drivers of these networks. Finally, we discuss unique aspects of the biology and pathogenesis of infections with respiratory syncytial virus, rhinovirus and influenza, drawing on insights from genomics.
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Affiliation(s)
- Niamh M Troy
- Telethon Kids Institute, The University of Western Australia, Subiaco, Australia
| | - Anthony Bosco
- Telethon Kids Institute, The University of Western Australia, Subiaco, Australia.
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Stein MM, Hrusch CL, Gozdz J, Igartua C, Pivniouk V, Murray SE, Ledford JG, Marques Dos Santos M, Anderson RL, Metwali N, Neilson JW, Maier RM, Gilbert JA, Holbreich M, Thorne PS, Martinez FD, von Mutius E, Vercelli D, Ober C, Sperling AI. Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children. N Engl J Med 2016; 375:411-421. [PMID: 27518660 PMCID: PMC5137793 DOI: 10.1056/nejmoa1508749] [Citation(s) in RCA: 635] [Impact Index Per Article: 79.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND The Amish and Hutterites are U.S. agricultural populations whose lifestyles are remarkably similar in many respects but whose farming practices, in particular, are distinct; the former follow traditional farming practices whereas the latter use industrialized farming practices. The populations also show striking disparities in the prevalence of asthma, and little is known about the immune responses underlying these disparities. METHODS We studied environmental exposures, genetic ancestry, and immune profiles among 60 Amish and Hutterite children, measuring levels of allergens and endotoxins and assessing the microbiome composition of indoor dust samples. Whole blood was collected to measure serum IgE levels, cytokine responses, and gene expression, and peripheral-blood leukocytes were phenotyped with flow cytometry. The effects of dust extracts obtained from Amish and Hutterite homes on immune and airway responses were assessed in a murine model of experimental allergic asthma. RESULTS Despite the similar genetic ancestries and lifestyles of Amish and Hutterite children, the prevalence of asthma and allergic sensitization was 4 and 6 times as low in the Amish, whereas median endotoxin levels in Amish house dust was 6.8 times as high. Differences in microbial composition were also observed in dust samples from Amish and Hutterite homes. Profound differences in the proportions, phenotypes, and functions of innate immune cells were also found between the two groups of children. In a mouse model of experimental allergic asthma, the intranasal instillation of dust extracts from Amish but not Hutterite homes significantly inhibited airway hyperreactivity and eosinophilia. These protective effects were abrogated in mice that were deficient in MyD88 and Trif, molecules that are critical in innate immune signaling. CONCLUSIONS The results of our studies in humans and mice indicate that the Amish environment provides protection against asthma by engaging and shaping the innate immune response. (Funded by the National Institutes of Health and others.).
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Affiliation(s)
- Michelle M Stein
- Department of Human Genetics (M.M. Stein, C.I., R.L.A., C.O.), the Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology (C.L.H., A.I.S.), the Department of Ecology and Evolution (J.A.G.), and the Department of Surgery (J.A.G.), University of Chicago, Chicago, and the Institute for Genomic and Systems Biology, Argonne National Laboratory, Argonne (J.A.G.) - all in Illinois; the NIEHS Training Program in Environmental Toxicology and Graduate Program in Cellular and Molecular Medicine (J.G.), and the Departments of Cellular and Molecular Medicine (V.P., D.V.), Medicine (J.G.L.), Chemical and Environmental Engineering (M. Marques dos Santos), and Soil, Water, and Environmental Science (J.W.N., R.M.M.), University of Arizona, and the Arizona Respiratory Center and Bio5 Institute (J.G., V.P., S.E.M., J.G.L., F.D.M., D.V.) - all in Tucson; the Department of Occupational and Environmental Health, University of Iowa, Iowa City (N.M., P.S.T.); Allergy and Asthma Consultants, Indianapolis (M.H.); and Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany (E.M.)
| | - Cara L Hrusch
- Department of Human Genetics (M.M. Stein, C.I., R.L.A., C.O.), the Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology (C.L.H., A.I.S.), the Department of Ecology and Evolution (J.A.G.), and the Department of Surgery (J.A.G.), University of Chicago, Chicago, and the Institute for Genomic and Systems Biology, Argonne National Laboratory, Argonne (J.A.G.) - all in Illinois; the NIEHS Training Program in Environmental Toxicology and Graduate Program in Cellular and Molecular Medicine (J.G.), and the Departments of Cellular and Molecular Medicine (V.P., D.V.), Medicine (J.G.L.), Chemical and Environmental Engineering (M. Marques dos Santos), and Soil, Water, and Environmental Science (J.W.N., R.M.M.), University of Arizona, and the Arizona Respiratory Center and Bio5 Institute (J.G., V.P., S.E.M., J.G.L., F.D.M., D.V.) - all in Tucson; the Department of Occupational and Environmental Health, University of Iowa, Iowa City (N.M., P.S.T.); Allergy and Asthma Consultants, Indianapolis (M.H.); and Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany (E.M.)
| | - Justyna Gozdz
- Department of Human Genetics (M.M. Stein, C.I., R.L.A., C.O.), the Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology (C.L.H., A.I.S.), the Department of Ecology and Evolution (J.A.G.), and the Department of Surgery (J.A.G.), University of Chicago, Chicago, and the Institute for Genomic and Systems Biology, Argonne National Laboratory, Argonne (J.A.G.) - all in Illinois; the NIEHS Training Program in Environmental Toxicology and Graduate Program in Cellular and Molecular Medicine (J.G.), and the Departments of Cellular and Molecular Medicine (V.P., D.V.), Medicine (J.G.L.), Chemical and Environmental Engineering (M. Marques dos Santos), and Soil, Water, and Environmental Science (J.W.N., R.M.M.), University of Arizona, and the Arizona Respiratory Center and Bio5 Institute (J.G., V.P., S.E.M., J.G.L., F.D.M., D.V.) - all in Tucson; the Department of Occupational and Environmental Health, University of Iowa, Iowa City (N.M., P.S.T.); Allergy and Asthma Consultants, Indianapolis (M.H.); and Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany (E.M.)
| | - Catherine Igartua
- Department of Human Genetics (M.M. Stein, C.I., R.L.A., C.O.), the Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology (C.L.H., A.I.S.), the Department of Ecology and Evolution (J.A.G.), and the Department of Surgery (J.A.G.), University of Chicago, Chicago, and the Institute for Genomic and Systems Biology, Argonne National Laboratory, Argonne (J.A.G.) - all in Illinois; the NIEHS Training Program in Environmental Toxicology and Graduate Program in Cellular and Molecular Medicine (J.G.), and the Departments of Cellular and Molecular Medicine (V.P., D.V.), Medicine (J.G.L.), Chemical and Environmental Engineering (M. Marques dos Santos), and Soil, Water, and Environmental Science (J.W.N., R.M.M.), University of Arizona, and the Arizona Respiratory Center and Bio5 Institute (J.G., V.P., S.E.M., J.G.L., F.D.M., D.V.) - all in Tucson; the Department of Occupational and Environmental Health, University of Iowa, Iowa City (N.M., P.S.T.); Allergy and Asthma Consultants, Indianapolis (M.H.); and Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany (E.M.)
| | - Vadim Pivniouk
- Department of Human Genetics (M.M. Stein, C.I., R.L.A., C.O.), the Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology (C.L.H., A.I.S.), the Department of Ecology and Evolution (J.A.G.), and the Department of Surgery (J.A.G.), University of Chicago, Chicago, and the Institute for Genomic and Systems Biology, Argonne National Laboratory, Argonne (J.A.G.) - all in Illinois; the NIEHS Training Program in Environmental Toxicology and Graduate Program in Cellular and Molecular Medicine (J.G.), and the Departments of Cellular and Molecular Medicine (V.P., D.V.), Medicine (J.G.L.), Chemical and Environmental Engineering (M. Marques dos Santos), and Soil, Water, and Environmental Science (J.W.N., R.M.M.), University of Arizona, and the Arizona Respiratory Center and Bio5 Institute (J.G., V.P., S.E.M., J.G.L., F.D.M., D.V.) - all in Tucson; the Department of Occupational and Environmental Health, University of Iowa, Iowa City (N.M., P.S.T.); Allergy and Asthma Consultants, Indianapolis (M.H.); and Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany (E.M.)
| | - Sean E Murray
- Department of Human Genetics (M.M. Stein, C.I., R.L.A., C.O.), the Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology (C.L.H., A.I.S.), the Department of Ecology and Evolution (J.A.G.), and the Department of Surgery (J.A.G.), University of Chicago, Chicago, and the Institute for Genomic and Systems Biology, Argonne National Laboratory, Argonne (J.A.G.) - all in Illinois; the NIEHS Training Program in Environmental Toxicology and Graduate Program in Cellular and Molecular Medicine (J.G.), and the Departments of Cellular and Molecular Medicine (V.P., D.V.), Medicine (J.G.L.), Chemical and Environmental Engineering (M. Marques dos Santos), and Soil, Water, and Environmental Science (J.W.N., R.M.M.), University of Arizona, and the Arizona Respiratory Center and Bio5 Institute (J.G., V.P., S.E.M., J.G.L., F.D.M., D.V.) - all in Tucson; the Department of Occupational and Environmental Health, University of Iowa, Iowa City (N.M., P.S.T.); Allergy and Asthma Consultants, Indianapolis (M.H.); and Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany (E.M.)
| | - Julie G Ledford
- Department of Human Genetics (M.M. Stein, C.I., R.L.A., C.O.), the Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology (C.L.H., A.I.S.), the Department of Ecology and Evolution (J.A.G.), and the Department of Surgery (J.A.G.), University of Chicago, Chicago, and the Institute for Genomic and Systems Biology, Argonne National Laboratory, Argonne (J.A.G.) - all in Illinois; the NIEHS Training Program in Environmental Toxicology and Graduate Program in Cellular and Molecular Medicine (J.G.), and the Departments of Cellular and Molecular Medicine (V.P., D.V.), Medicine (J.G.L.), Chemical and Environmental Engineering (M. Marques dos Santos), and Soil, Water, and Environmental Science (J.W.N., R.M.M.), University of Arizona, and the Arizona Respiratory Center and Bio5 Institute (J.G., V.P., S.E.M., J.G.L., F.D.M., D.V.) - all in Tucson; the Department of Occupational and Environmental Health, University of Iowa, Iowa City (N.M., P.S.T.); Allergy and Asthma Consultants, Indianapolis (M.H.); and Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany (E.M.)
| | - Mauricius Marques Dos Santos
- Department of Human Genetics (M.M. Stein, C.I., R.L.A., C.O.), the Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology (C.L.H., A.I.S.), the Department of Ecology and Evolution (J.A.G.), and the Department of Surgery (J.A.G.), University of Chicago, Chicago, and the Institute for Genomic and Systems Biology, Argonne National Laboratory, Argonne (J.A.G.) - all in Illinois; the NIEHS Training Program in Environmental Toxicology and Graduate Program in Cellular and Molecular Medicine (J.G.), and the Departments of Cellular and Molecular Medicine (V.P., D.V.), Medicine (J.G.L.), Chemical and Environmental Engineering (M. Marques dos Santos), and Soil, Water, and Environmental Science (J.W.N., R.M.M.), University of Arizona, and the Arizona Respiratory Center and Bio5 Institute (J.G., V.P., S.E.M., J.G.L., F.D.M., D.V.) - all in Tucson; the Department of Occupational and Environmental Health, University of Iowa, Iowa City (N.M., P.S.T.); Allergy and Asthma Consultants, Indianapolis (M.H.); and Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany (E.M.)
| | - Rebecca L Anderson
- Department of Human Genetics (M.M. Stein, C.I., R.L.A., C.O.), the Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology (C.L.H., A.I.S.), the Department of Ecology and Evolution (J.A.G.), and the Department of Surgery (J.A.G.), University of Chicago, Chicago, and the Institute for Genomic and Systems Biology, Argonne National Laboratory, Argonne (J.A.G.) - all in Illinois; the NIEHS Training Program in Environmental Toxicology and Graduate Program in Cellular and Molecular Medicine (J.G.), and the Departments of Cellular and Molecular Medicine (V.P., D.V.), Medicine (J.G.L.), Chemical and Environmental Engineering (M. Marques dos Santos), and Soil, Water, and Environmental Science (J.W.N., R.M.M.), University of Arizona, and the Arizona Respiratory Center and Bio5 Institute (J.G., V.P., S.E.M., J.G.L., F.D.M., D.V.) - all in Tucson; the Department of Occupational and Environmental Health, University of Iowa, Iowa City (N.M., P.S.T.); Allergy and Asthma Consultants, Indianapolis (M.H.); and Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany (E.M.)
| | - Nervana Metwali
- Department of Human Genetics (M.M. Stein, C.I., R.L.A., C.O.), the Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology (C.L.H., A.I.S.), the Department of Ecology and Evolution (J.A.G.), and the Department of Surgery (J.A.G.), University of Chicago, Chicago, and the Institute for Genomic and Systems Biology, Argonne National Laboratory, Argonne (J.A.G.) - all in Illinois; the NIEHS Training Program in Environmental Toxicology and Graduate Program in Cellular and Molecular Medicine (J.G.), and the Departments of Cellular and Molecular Medicine (V.P., D.V.), Medicine (J.G.L.), Chemical and Environmental Engineering (M. Marques dos Santos), and Soil, Water, and Environmental Science (J.W.N., R.M.M.), University of Arizona, and the Arizona Respiratory Center and Bio5 Institute (J.G., V.P., S.E.M., J.G.L., F.D.M., D.V.) - all in Tucson; the Department of Occupational and Environmental Health, University of Iowa, Iowa City (N.M., P.S.T.); Allergy and Asthma Consultants, Indianapolis (M.H.); and Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany (E.M.)
| | - Julia W Neilson
- Department of Human Genetics (M.M. Stein, C.I., R.L.A., C.O.), the Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology (C.L.H., A.I.S.), the Department of Ecology and Evolution (J.A.G.), and the Department of Surgery (J.A.G.), University of Chicago, Chicago, and the Institute for Genomic and Systems Biology, Argonne National Laboratory, Argonne (J.A.G.) - all in Illinois; the NIEHS Training Program in Environmental Toxicology and Graduate Program in Cellular and Molecular Medicine (J.G.), and the Departments of Cellular and Molecular Medicine (V.P., D.V.), Medicine (J.G.L.), Chemical and Environmental Engineering (M. Marques dos Santos), and Soil, Water, and Environmental Science (J.W.N., R.M.M.), University of Arizona, and the Arizona Respiratory Center and Bio5 Institute (J.G., V.P., S.E.M., J.G.L., F.D.M., D.V.) - all in Tucson; the Department of Occupational and Environmental Health, University of Iowa, Iowa City (N.M., P.S.T.); Allergy and Asthma Consultants, Indianapolis (M.H.); and Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany (E.M.)
| | - Raina M Maier
- Department of Human Genetics (M.M. Stein, C.I., R.L.A., C.O.), the Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology (C.L.H., A.I.S.), the Department of Ecology and Evolution (J.A.G.), and the Department of Surgery (J.A.G.), University of Chicago, Chicago, and the Institute for Genomic and Systems Biology, Argonne National Laboratory, Argonne (J.A.G.) - all in Illinois; the NIEHS Training Program in Environmental Toxicology and Graduate Program in Cellular and Molecular Medicine (J.G.), and the Departments of Cellular and Molecular Medicine (V.P., D.V.), Medicine (J.G.L.), Chemical and Environmental Engineering (M. Marques dos Santos), and Soil, Water, and Environmental Science (J.W.N., R.M.M.), University of Arizona, and the Arizona Respiratory Center and Bio5 Institute (J.G., V.P., S.E.M., J.G.L., F.D.M., D.V.) - all in Tucson; the Department of Occupational and Environmental Health, University of Iowa, Iowa City (N.M., P.S.T.); Allergy and Asthma Consultants, Indianapolis (M.H.); and Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany (E.M.)
| | - Jack A Gilbert
- Department of Human Genetics (M.M. Stein, C.I., R.L.A., C.O.), the Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology (C.L.H., A.I.S.), the Department of Ecology and Evolution (J.A.G.), and the Department of Surgery (J.A.G.), University of Chicago, Chicago, and the Institute for Genomic and Systems Biology, Argonne National Laboratory, Argonne (J.A.G.) - all in Illinois; the NIEHS Training Program in Environmental Toxicology and Graduate Program in Cellular and Molecular Medicine (J.G.), and the Departments of Cellular and Molecular Medicine (V.P., D.V.), Medicine (J.G.L.), Chemical and Environmental Engineering (M. Marques dos Santos), and Soil, Water, and Environmental Science (J.W.N., R.M.M.), University of Arizona, and the Arizona Respiratory Center and Bio5 Institute (J.G., V.P., S.E.M., J.G.L., F.D.M., D.V.) - all in Tucson; the Department of Occupational and Environmental Health, University of Iowa, Iowa City (N.M., P.S.T.); Allergy and Asthma Consultants, Indianapolis (M.H.); and Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany (E.M.)
| | - Mark Holbreich
- Department of Human Genetics (M.M. Stein, C.I., R.L.A., C.O.), the Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology (C.L.H., A.I.S.), the Department of Ecology and Evolution (J.A.G.), and the Department of Surgery (J.A.G.), University of Chicago, Chicago, and the Institute for Genomic and Systems Biology, Argonne National Laboratory, Argonne (J.A.G.) - all in Illinois; the NIEHS Training Program in Environmental Toxicology and Graduate Program in Cellular and Molecular Medicine (J.G.), and the Departments of Cellular and Molecular Medicine (V.P., D.V.), Medicine (J.G.L.), Chemical and Environmental Engineering (M. Marques dos Santos), and Soil, Water, and Environmental Science (J.W.N., R.M.M.), University of Arizona, and the Arizona Respiratory Center and Bio5 Institute (J.G., V.P., S.E.M., J.G.L., F.D.M., D.V.) - all in Tucson; the Department of Occupational and Environmental Health, University of Iowa, Iowa City (N.M., P.S.T.); Allergy and Asthma Consultants, Indianapolis (M.H.); and Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany (E.M.)
| | - Peter S Thorne
- Department of Human Genetics (M.M. Stein, C.I., R.L.A., C.O.), the Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology (C.L.H., A.I.S.), the Department of Ecology and Evolution (J.A.G.), and the Department of Surgery (J.A.G.), University of Chicago, Chicago, and the Institute for Genomic and Systems Biology, Argonne National Laboratory, Argonne (J.A.G.) - all in Illinois; the NIEHS Training Program in Environmental Toxicology and Graduate Program in Cellular and Molecular Medicine (J.G.), and the Departments of Cellular and Molecular Medicine (V.P., D.V.), Medicine (J.G.L.), Chemical and Environmental Engineering (M. Marques dos Santos), and Soil, Water, and Environmental Science (J.W.N., R.M.M.), University of Arizona, and the Arizona Respiratory Center and Bio5 Institute (J.G., V.P., S.E.M., J.G.L., F.D.M., D.V.) - all in Tucson; the Department of Occupational and Environmental Health, University of Iowa, Iowa City (N.M., P.S.T.); Allergy and Asthma Consultants, Indianapolis (M.H.); and Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany (E.M.)
| | - Fernando D Martinez
- Department of Human Genetics (M.M. Stein, C.I., R.L.A., C.O.), the Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology (C.L.H., A.I.S.), the Department of Ecology and Evolution (J.A.G.), and the Department of Surgery (J.A.G.), University of Chicago, Chicago, and the Institute for Genomic and Systems Biology, Argonne National Laboratory, Argonne (J.A.G.) - all in Illinois; the NIEHS Training Program in Environmental Toxicology and Graduate Program in Cellular and Molecular Medicine (J.G.), and the Departments of Cellular and Molecular Medicine (V.P., D.V.), Medicine (J.G.L.), Chemical and Environmental Engineering (M. Marques dos Santos), and Soil, Water, and Environmental Science (J.W.N., R.M.M.), University of Arizona, and the Arizona Respiratory Center and Bio5 Institute (J.G., V.P., S.E.M., J.G.L., F.D.M., D.V.) - all in Tucson; the Department of Occupational and Environmental Health, University of Iowa, Iowa City (N.M., P.S.T.); Allergy and Asthma Consultants, Indianapolis (M.H.); and Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany (E.M.)
| | - Erika von Mutius
- Department of Human Genetics (M.M. Stein, C.I., R.L.A., C.O.), the Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology (C.L.H., A.I.S.), the Department of Ecology and Evolution (J.A.G.), and the Department of Surgery (J.A.G.), University of Chicago, Chicago, and the Institute for Genomic and Systems Biology, Argonne National Laboratory, Argonne (J.A.G.) - all in Illinois; the NIEHS Training Program in Environmental Toxicology and Graduate Program in Cellular and Molecular Medicine (J.G.), and the Departments of Cellular and Molecular Medicine (V.P., D.V.), Medicine (J.G.L.), Chemical and Environmental Engineering (M. Marques dos Santos), and Soil, Water, and Environmental Science (J.W.N., R.M.M.), University of Arizona, and the Arizona Respiratory Center and Bio5 Institute (J.G., V.P., S.E.M., J.G.L., F.D.M., D.V.) - all in Tucson; the Department of Occupational and Environmental Health, University of Iowa, Iowa City (N.M., P.S.T.); Allergy and Asthma Consultants, Indianapolis (M.H.); and Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany (E.M.)
| | - Donata Vercelli
- Department of Human Genetics (M.M. Stein, C.I., R.L.A., C.O.), the Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology (C.L.H., A.I.S.), the Department of Ecology and Evolution (J.A.G.), and the Department of Surgery (J.A.G.), University of Chicago, Chicago, and the Institute for Genomic and Systems Biology, Argonne National Laboratory, Argonne (J.A.G.) - all in Illinois; the NIEHS Training Program in Environmental Toxicology and Graduate Program in Cellular and Molecular Medicine (J.G.), and the Departments of Cellular and Molecular Medicine (V.P., D.V.), Medicine (J.G.L.), Chemical and Environmental Engineering (M. Marques dos Santos), and Soil, Water, and Environmental Science (J.W.N., R.M.M.), University of Arizona, and the Arizona Respiratory Center and Bio5 Institute (J.G., V.P., S.E.M., J.G.L., F.D.M., D.V.) - all in Tucson; the Department of Occupational and Environmental Health, University of Iowa, Iowa City (N.M., P.S.T.); Allergy and Asthma Consultants, Indianapolis (M.H.); and Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany (E.M.)
| | - Carole Ober
- Department of Human Genetics (M.M. Stein, C.I., R.L.A., C.O.), the Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology (C.L.H., A.I.S.), the Department of Ecology and Evolution (J.A.G.), and the Department of Surgery (J.A.G.), University of Chicago, Chicago, and the Institute for Genomic and Systems Biology, Argonne National Laboratory, Argonne (J.A.G.) - all in Illinois; the NIEHS Training Program in Environmental Toxicology and Graduate Program in Cellular and Molecular Medicine (J.G.), and the Departments of Cellular and Molecular Medicine (V.P., D.V.), Medicine (J.G.L.), Chemical and Environmental Engineering (M. Marques dos Santos), and Soil, Water, and Environmental Science (J.W.N., R.M.M.), University of Arizona, and the Arizona Respiratory Center and Bio5 Institute (J.G., V.P., S.E.M., J.G.L., F.D.M., D.V.) - all in Tucson; the Department of Occupational and Environmental Health, University of Iowa, Iowa City (N.M., P.S.T.); Allergy and Asthma Consultants, Indianapolis (M.H.); and Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany (E.M.)
| | - Anne I Sperling
- Department of Human Genetics (M.M. Stein, C.I., R.L.A., C.O.), the Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology (C.L.H., A.I.S.), the Department of Ecology and Evolution (J.A.G.), and the Department of Surgery (J.A.G.), University of Chicago, Chicago, and the Institute for Genomic and Systems Biology, Argonne National Laboratory, Argonne (J.A.G.) - all in Illinois; the NIEHS Training Program in Environmental Toxicology and Graduate Program in Cellular and Molecular Medicine (J.G.), and the Departments of Cellular and Molecular Medicine (V.P., D.V.), Medicine (J.G.L.), Chemical and Environmental Engineering (M. Marques dos Santos), and Soil, Water, and Environmental Science (J.W.N., R.M.M.), University of Arizona, and the Arizona Respiratory Center and Bio5 Institute (J.G., V.P., S.E.M., J.G.L., F.D.M., D.V.) - all in Tucson; the Department of Occupational and Environmental Health, University of Iowa, Iowa City (N.M., P.S.T.); Allergy and Asthma Consultants, Indianapolis (M.H.); and Dr. von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany (E.M.)
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47
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Bønnelykke K, Ober C. Leveraging gene-environment interactions and endotypes for asthma gene discovery. J Allergy Clin Immunol 2016; 137:667-79. [PMID: 26947980 DOI: 10.1016/j.jaci.2016.01.006] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/30/2015] [Accepted: 01/08/2016] [Indexed: 12/20/2022]
Abstract
Asthma is a heterogeneous clinical syndrome that includes subtypes of disease with different underlying causes and disease mechanisms. Asthma is caused by a complex interaction between genes and environmental exposures; early-life exposures in particular play an important role. Asthma is also heritable, and a number of susceptibility variants have been discovered in genome-wide association studies, although the known risk alleles explain only a small proportion of the heritability. In this review, we present evidence supporting the hypothesis that focusing on more specific asthma phenotypes, such as childhood asthma with severe exacerbations, and on relevant exposures that are involved in gene-environment interactions (GEIs), such as rhinovirus infections, will improve detection of asthma genes and our understanding of the underlying mechanisms. We will discuss the challenges of considering GEIs and the advantages of studying responses to asthma-associated exposures in clinical birth cohorts, as well as in cell models of GEIs, to dissect the context-specific nature of genotypic risks, to prioritize variants in genome-wide association studies, and to identify pathways involved in pathogenesis in subgroups of patients. We propose that such approaches, in spite of their many challenges, present great opportunities for better understanding of asthma pathogenesis and heterogeneity and, ultimately, for improving prevention and treatment of disease.
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Affiliation(s)
- Klaus Bønnelykke
- COPSAC (Copenhagen Prospective Studies on Asthma in Childhood), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill.
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48
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Kicic A, Stevens PT, Sutanto EN, Kicic-Starcevich E, Ling KM, Looi K, Martinovich KM, Garratt LW, Iosifidis T, Shaw NC, Buckley AG, Rigby PJ, Lannigan FJ, Knight DA, Stick SM. Impaired airway epithelial cell responses from children with asthma to rhinoviral infection. Clin Exp Allergy 2016; 46:1441-1455. [PMID: 27238549 DOI: 10.1111/cea.12767] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 05/21/2016] [Accepted: 05/25/2016] [Indexed: 12/01/2022]
Abstract
BACKGROUND The airway epithelium forms an effective immune and physical barrier that is essential for protecting the lung from potentially harmful inhaled stimuli including viruses. Human rhinovirus (HRV) infection is a known trigger of asthma exacerbations, although the mechanism by which this occurs is not fully understood. OBJECTIVE To explore the relationship between apoptotic, innate immune and inflammatory responses to HRV infection in airway epithelial cells (AECs) obtained from children with asthma and non-asthmatic controls. In addition, to test the hypothesis that aberrant repair of epithelium from asthmatics is further dysregulated by HRV infection. METHODS Airway epithelial brushings were obtained from 39 asthmatic and 36 non-asthmatic children. Primary cultures were established and exposed to HRV1b and HRV14. Virus receptor number, virus replication and progeny release were determined. Epithelial cell apoptosis, IFN-β production, inflammatory cytokine release and epithelial wound repair and proliferation were also measured. RESULTS Virus proliferation and release was greater in airway epithelial cells from asthmatics but this was not related to the number of virus receptors. In epithelial cells from asthmatic children, virus infection dampened apoptosis, reduced IFN-β production and increased inflammatory cytokine production. HRV1b infection also inhibited wound repair capacity of epithelial cells isolated from non-asthmatic children and exaggerated the defective repair response seen in epithelial cells from asthmatics. Addition of IFN-β restored apoptosis, suppressed virus replication and improved repair of airway epithelial cells from asthmatics but did not reduce inflammatory cytokine production. CONCLUSIONS Collectively, HRV infection delays repair and inhibits apoptotic processes in epithelial cells from non-asthmatic and asthmatic children. The delayed repair is further exaggerated in cells from asthmatic children and is only partially reversed by exogenous IFN-β.
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Affiliation(s)
- A Kicic
- Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, WA, Australia. .,School of Paediatrics and Child Health, The University of Western Australia, Nedlands, WA, Australia. .,Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, WA, Australia. .,Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia and Harry Perkins Institute of Medical Research, Nedlands, WA, Australia.
| | - P T Stevens
- School of Paediatrics and Child Health, The University of Western Australia, Nedlands, WA, Australia.,Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, WA, Australia
| | - E N Sutanto
- Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, WA, Australia.,Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, WA, Australia
| | - E Kicic-Starcevich
- Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, WA, Australia.,Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, WA, Australia
| | - K-M Ling
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, WA, Australia
| | - K Looi
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, WA, Australia
| | - K M Martinovich
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, WA, Australia
| | - L W Garratt
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, WA, Australia
| | - T Iosifidis
- School of Paediatrics and Child Health, The University of Western Australia, Nedlands, WA, Australia.,Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia and Harry Perkins Institute of Medical Research, Nedlands, WA, Australia
| | - N C Shaw
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, WA, Australia
| | - A G Buckley
- Centre of Microscopy, Characterisation and Analysis, The University of Western Australia, Nedlands, WA, Australia
| | - P J Rigby
- Centre of Microscopy, Characterisation and Analysis, The University of Western Australia, Nedlands, WA, Australia
| | - F J Lannigan
- School of Medicine, Notre Dame University, Fremantle, WA, Australia
| | - D A Knight
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Callaghan, NSW, Australia.,Priority Research Centre for Asthma and Respiratory Disease, Hunter Medical Research Institute, Newcastle, NSW, Australia.,Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, BC, Canada
| | - S M Stick
- Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, WA, Australia.,School of Paediatrics and Child Health, The University of Western Australia, Nedlands, WA, Australia.,Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, WA, Australia.,Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia and Harry Perkins Institute of Medical Research, Nedlands, WA, Australia
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49
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Troy NM, Hollams EM, Holt PG, Bosco A. Differential gene network analysis for the identification of asthma-associated therapeutic targets in allergen-specific T-helper memory responses. BMC Med Genomics 2016; 9:9. [PMID: 26922672 PMCID: PMC4769846 DOI: 10.1186/s12920-016-0171-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/22/2016] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Asthma is strongly associated with allergic sensitization, but the mechanisms that determine why only a subset of atopics develop asthma are not well understood. The aim of this study was to test the hypothesis that variations in allergen-driven CD4 T cell responses are associated with susceptibility to expression of asthma symptoms. METHODS The study population consisted of house dust mite (HDM) sensitized atopics with current asthma (n = 22), HDM-sensitized atopics without current asthma (n = 26), and HDM-nonsensitized controls (n = 24). Peripheral blood mononuclear cells from these groups were cultured in the presence or absence of HDM extract for 24 h. CD4 T cells were then isolated by immunomagnetic separation, and gene expression patterns were profiled on microarrays. RESULTS Differential network analysis of HDM-induced CD4 T cell responses in sensitized atopics with or without asthma unveiled a cohort of asthma-associated genes that escaped detection by more conventional data analysis techniques. These asthma-associated genes were enriched for targets of STAT6 signaling, and they were nested within a larger coexpression module comprising 406 genes. Upstream regulator analysis suggested that this module was driven primarily by IL-2, IL-4, and TNF signaling; reconstruction of the wiring diagram of the module revealed a series of hub genes involved in inflammation (IL-1B, NFkB, STAT1, STAT3), apoptosis (BCL2, MYC), and regulatory T cells (IL-2Ra, FoxP3). Finally, we identified several negative regulators of asthmatic CD4 T cell responses to allergens (e.g. IL-10, type I interferons, microRNAs, drugs, metabolites), and these represent logical candidates for therapeutic intervention. CONCLUSION Differential network analysis of allergen-induced CD4 T cell responses can unmask covert disease-associated genes and pin point novel therapeutic targets.
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Affiliation(s)
- Niamh M Troy
- Telethon Kids Institute, The University of Western Australia, Crawley, Australia.
| | - Elysia M Hollams
- Telethon Kids Institute, The University of Western Australia, Crawley, Australia.
| | - Patrick G Holt
- Telethon Kids Institute, The University of Western Australia, Crawley, Australia. .,Queensland Children's Medical Research Institute, The University of Queensland, Brisbane, Australia.
| | - Anthony Bosco
- Telethon Kids Institute, The University of Western Australia, Crawley, Australia.
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50
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Foong RE, Bosco A, Jones AC, Gout A, Gorman S, Hart PH, Zosky GR. The effects of in utero vitamin D deficiency on airway smooth muscle mass and lung function. Am J Respir Cell Mol Biol 2016; 53:664-75. [PMID: 25867172 DOI: 10.1165/rcmb.2014-0356oc] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
We have previously demonstrated increased airway smooth muscle (ASM) mass and airway hyperresponsiveness in whole-life vitamin D-deficient female mice. In this study, we aimed to uncover the molecular mechanisms contributing to altered lung structure and function. RNA was extracted from lung tissue of whole-life vitamin D-deficient and -replete female mice, and gene expression patterns were profiled by RNA sequencing. The data showed that genes involved in embryonic organ development, pattern formation, branching morphogenesis, Wingless/Int signaling, and inflammation were differentially expressed in vitamin D-deficient mice. Network analysis suggested that differentially expressed genes were connected by the hubs matrix metallopeptidase 9; NF-κ light polypeptide gene enhancer in B cells inhibitor, α; epidermal growth factor receptor; and E1A binding protein p300. Given our findings that developmental pathways may be altered, we investigated if the timing of vitamin D exposure (in utero vs. postnatal) had an impact on lung health outcomes. Gene expression was measured in in utero or postnatal vitamin D-deficient mice, as well as whole-life vitamin D-deficient and -replete mice at 8 weeks of age. Baseline lung function, airway hyperresponsiveness, and airway inflammation were measured and lungs fixed for lung structure assessment using stereological methods and quantification of ASM mass. In utero vitamin D deficiency was sufficient to increase ASM mass and baseline airway resistance and alter lung structure. There were increased neutrophils but decreased lymphocytes in bronchoalveolar lavage. Expression of inflammatory molecules S100A9 and S100A8 was mainly increased in postnatal vitamin D-deficient mice. These observations suggest that in utero vitamin D deficiency can alter lung structure and function and increase inflammation, contributing to symptoms in chronic diseases, such as asthma.
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Affiliation(s)
- Rachel E Foong
- 1 Telethon Kids Institute, the University of Western Australia, Perth, Western Australia, Australia; and
| | - Anthony Bosco
- 1 Telethon Kids Institute, the University of Western Australia, Perth, Western Australia, Australia; and
| | - Anya C Jones
- 1 Telethon Kids Institute, the University of Western Australia, Perth, Western Australia, Australia; and
| | - Alex Gout
- 1 Telethon Kids Institute, the University of Western Australia, Perth, Western Australia, Australia; and
| | - Shelley Gorman
- 1 Telethon Kids Institute, the University of Western Australia, Perth, Western Australia, Australia; and
| | - Prue H Hart
- 1 Telethon Kids Institute, the University of Western Australia, Perth, Western Australia, Australia; and
| | - Graeme R Zosky
- 2 School of Medicine, Faculty of Health Science, University of Tasmania, Hobart, Tasmania, Australia
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