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Liao Y, Cavalcante RG, Waller JB, Deng F, Scruggs AM, Huang YJ, Atasoy U, Chen Y, Huang SK. Differences in the DNA methylome of T cells in adults with asthma of varying severity. Clin Epigenetics 2024; 16:139. [PMID: 39380119 PMCID: PMC11459694 DOI: 10.1186/s13148-024-01750-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Accepted: 09/20/2024] [Indexed: 10/10/2024] Open
Abstract
BACKGROUND DNA methylation plays a critical role in asthma development, but differences in DNA methylation among adults with varying asthma severity are less well-defined. OBJECTIVE To examine how DNA methylomic patterns differ among adults with asthma based on asthma severity and airway inflammation. METHODS Peripheral blood T cells from 35 adults with asthma in Beijing, China, were serially collected over time (130 samples total) and analyzed for global DNA methylation using the Illumina MethylationEPIC Array. Differential methylation was compared among subjects with varying airway inflammation and severity, as measured by fraction of exhaled nitric oxide, forced expiratory volume in one second (FEV1), and Asthma Control Test (ACT) scores. RESULTS Significant differences in DNA methylation were noted among subjects with different degrees of airway inflammation and asthma severity. These differences in DNA methylation were annotated to genes that were enriched in pathways related to asthma or T cell function and included gene ontology categories related to MHC class II assembly, T cell activation, interleukin (IL)-1, and IL-12. Genes related to P450 drug metabolism, glutathione metabolism, and developmental pathways were also differentially methylated in comparisons between subjects with high vs low FEV1 and ACT. Notable genes that were differentially methylated based on asthma severity included RUNX3, several members of the HLA family, AGT, PTPRC, PTPRJ, and several genes downstream of the JAK2 and TNF signaling pathway. CONCLUSION These findings demonstrate how adults with asthma of varying severity possess differences in peripheral blood T cell DNA methylation that contribute to differences in clinical indices of asthma.
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Affiliation(s)
- Yixuan Liao
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, No.49, Huayuan North Road, Haidian District, Beijing, 100191, China
- Department of Pulmonary and Critical Care Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Raymond G Cavalcante
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan B Waller
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, 6301 MSRB III, 1150 W Medical Center Dr., Ann Arbor, MI, 48109, USA
| | - Furong Deng
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, China
| | - Anne M Scruggs
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, 6301 MSRB III, 1150 W Medical Center Dr., Ann Arbor, MI, 48109, USA
| | - Yvonne J Huang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, 6301 MSRB III, 1150 W Medical Center Dr., Ann Arbor, MI, 48109, USA
| | - Ulus Atasoy
- Division of Allergy and Clinical Immunology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Yahong Chen
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, No.49, Huayuan North Road, Haidian District, Beijing, 100191, China.
| | - Steven K Huang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, 6301 MSRB III, 1150 W Medical Center Dr., Ann Arbor, MI, 48109, USA.
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Karp T, Faiz A, van Nijnatten J, Kerstjens HAM, Boudewijn I, Kraft M, Vonk JM, Nawijn MC, Heijink IH, Beghé B, Rabe KF, Papi A, Brightling C, Singh D, van der Molen T, Siddiqui S, Christenson S, Guryev V, van den Berge M. Nasal epithelial gene expression identifies relevant asthma endotypes in the ATLANTIS study. Thorax 2024; 79:905-914. [PMID: 39009441 DOI: 10.1136/thorax-2023-221230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 06/18/2024] [Indexed: 07/17/2024]
Abstract
INTRODUCTION Asthma is an inflammatory airways disease encompassing multiple phenotypes and endotypes. Several studies suggested gene expression in nasal epithelium to serve as a proxy for bronchial epithelium, being a non-invasive approach to investigate lung diseases. We hypothesised that molecular differences in upper airway epithelium reflect asthma-associated differences in the lower airways and are associated with clinical expression of asthma. METHODS We analysed nasal epithelial gene expression data from 369 patients with asthma and 58 non-asthmatic controls from the Assessment of Small Airways Involvement in Asthma study. Unsupervised hierarchical clustering was performed on asthma-associated genes. Asthma-associated gene signatures were replicated in independent cohorts with nasal and bronchial brushes data by comparing Gene Set Variation Analysis scores between asthma patients and non-asthmatic controls. RESULTS We identified 67 higher expressed and 59 lower expressed genes in nasal epithelium from asthma patients compared with controls (false discovery rate<0.05), including CLCA1, CST1 and POSTN, genes well known to reflect asthma in bronchial airway epithelium. Hierarchical clustering revealed several molecular asthma endotypes with distinct clinical characteristics, including an endotype with higher blood and sputum eosinophils, high fractional exhaled nitric oxide, and more severe small airway dysfunction, as reflected by lower forced expiratory flow at 50%. In an independent cohort, we demonstrated that genes higher expressed in the nasal epithelium reflect asthma-associated changes in the lower airways. CONCLUSION Our results show that the nasal epithelial gene expression profile reflects asthma-related processes in the lower airways. We suggest that nasal epithelium may be a useful non-invasive tool to identify asthma endotypes and may advance personalised management of the disease.
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Affiliation(s)
- Tatiana Karp
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Alen Faiz
- Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Jos van Nijnatten
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Huib A M Kerstjens
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Ilse Boudewijn
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Monica Kraft
- Samuel Bronfman Department of Medicine, Icahn School of Medicine, Mount Sinai Medical Center, New York, New York, USA
| | - Judith M Vonk
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Irene H Heijink
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Bianca Beghé
- Department of Respiratory Diseases, University of Modena and Reggio Emilia, Modena, Italy
| | - Klaus F Rabe
- Department of Medicine, Christian Albrechts University Kiel, Kiel and LungenClinic, Grosshansdorf, Germany
| | - Alberto Papi
- Section of Respiratory Medicine, Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Chris Brightling
- The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Dave Singh
- Centre for Respiratory Medicine and Allergy, University of Manchester, Manchester University NHS Foundation Trust, Manchester, UK
| | - Thys van der Molen
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of General Practice and Elderly Care Medicine, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Salman Siddiqui
- Imperial College London National Heart and Lung Institute, London, UK
| | - Stephanie Christenson
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California San Francisco, San Francisco, California, USA
| | - Victor Guryev
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center, Groningen, The Netherlands
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Wang Z, Chow L, Das S, Impastato R, Manchester AC, Dow S. Host-microbe interactions in the nasal cavity of dogs with chronic idiopathic rhinitis. Front Vet Sci 2024; 11:1385471. [PMID: 39188898 PMCID: PMC11345268 DOI: 10.3389/fvets.2024.1385471] [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: 02/12/2024] [Accepted: 07/22/2024] [Indexed: 08/28/2024] Open
Abstract
Chronic rhinitis (CR) is a frustrating clinical syndrome in dogs and our understanding of the disease pathogenesis in is limited. Increasingly, host-microbe interactions are considered key drives of clinical disease in sites of persistent mucosal inflammation such as the nasal and oral cavities. Therefore, we applied next generation sequencing tools to interrogate abnormalities present in the nose of dogs with CR and compared immune and microbiome profiles to those of healthy dogs. Host nasal cell transcriptomes were evaluated by RNA sequencing, while microbial communities were assessed by 16S rRNA sequencing. Correlation analysis was then used to identify significant interactions between nasal cell transcriptomes and the nasal microbiome and how these interactions were altered in animals with CR. Notably, we observed significant downregulation of multiple genes associated with ciliary function in dogs with CR, suggesting a previously undetected role for ciliary dysfunction in this syndrome. We also found significant upregulation of immune genes related to the TNF-α and interferon pathways. The nasal microbiome was also significantly altered in CR dogs, with overrepresentation of several potential pathobionts. Interactome analysis revealed significant correlations between bacteria in the genus Porphyromonas and the upregulated host inflammatory responses in dogs with CR, as well as defective ciliary function which was correlated with Streptococcus abundance. These findings provide new insights into host-microbe interactions in a canine model of CR and indicate the presence of potentially causal relationships between nasal pathobionts and the development of nasal inflammation and ciliary dysfunction.
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Affiliation(s)
| | | | | | | | | | - Steven Dow
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, United States
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Liao Y, Cavalcante R, Waller J, Deng F, Scruggs A, Huang Y, Atasoy U, Chen Y, Huang S. Differences in the DNA Methylome of T cells in Adults With Asthma of Varying Severity. RESEARCH SQUARE 2024:rs.3.rs-4476948. [PMID: 38946998 PMCID: PMC11213176 DOI: 10.21203/rs.3.rs-4476948/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Background DNA methylation plays a critical role in asthma development, but differences in DNA methylation among adults with varying asthma severity or asthma endotypes are less well-defined. Objective To examine how DNA methylomic patterns differ among adults with asthma based on asthma severity and airway inflammation. Methods Peripheral blood T cells from 35 adults with asthma in Beijing, China were serially collected over time (130 samples total) and analyzed for global DNA methylation using the Illumina MethylationEPIC Array. Differential methylation was compared among subjects with varying airway inflammation and severity, as measured by fraction of exhaled nitric oxide, forced expiratory volume in one second (FEV1), and Asthma Control Test (ACT) scores. Results Significant differences in DNA methylation were noted among subjects with different degrees of airway inflammation and asthma severity. These differences in DNA methylation were annotated to genes that were enriched in pathways related to asthma or T cell function and included gene ontology categories related to MHC class II assembly, T cell activation, interleukin (IL)-1, and IL-12. Genes related to P450 drug metabolism, glutathione metabolism, and developmental pathways were also differentially methylated in comparisons between subjects with high vs low FEV1 and ACT. Notable genes that were differentially methylated based on asthma severity included RUNX3, several members of the HLA family, AGT, PTPRC, PTPRJ, and several genes downstream of the JAK2 and TNF signaling pathway. Conclusion These findings demonstrate how adults with asthma of varying severity possess differences in peripheral blood T cell DNA methylation that contribute to the phenotype and severity of their overall disease.
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Georas SN, Khurana S. Update on asthma biology. J Allergy Clin Immunol 2024; 153:1215-1228. [PMID: 38341182 DOI: 10.1016/j.jaci.2024.01.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/17/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024]
Abstract
This is an exciting time to be conducting asthma research. The recent development of targeted asthma biologics has validated the power of basic research to discover new molecules amenable to therapeutic intervention. Advances in high-throughput sequencing are providing a wealth of "omics" data about genetic and epigenetic underpinnings of asthma, as well as about new cellular interacting networks and potential endotypes in asthma. Airway epithelial cells have emerged not only as key sensors of the outside environment but also as central drivers of dysregulated mucosal immune responses in asthma. Emerging data suggest that the airway epithelium in asthma remembers prior encounters with environmental exposures, resulting in potentially long-lasting changes in structure and metabolism that render asthmatic individuals susceptible to subsequent exposures. Here we summarize recent insights into asthma biology, focusing on studies using human cells or tissue that were published in the past 2 years. The studies are organized thematically into 6 content areas to draw connections and spur future research (on genetics and epigenetics, prenatal and early-life origins, microbiome, immune and inflammatory pathways, asthma endotypes and biomarkers, and lung structural alterations). We highlight recent studies of airway epithelial dysfunction and response to viral infections and conclude with a framework for considering how bidirectional interactions between alterations in airway structure and mucosal immunity can lead to sustained lung dysfunction in asthma.
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Affiliation(s)
- Steve N Georas
- Division of Pulmonary and Critical Care Medicine, University of Rochester Medical Center, Rochester, NY.
| | - Sandhya Khurana
- Division of Pulmonary and Critical Care Medicine, University of Rochester Medical Center, Rochester, NY
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Bunyavanich S, Becker PM, Altman MC, Lasky-Su J, Ober C, Zengler K, Berdyshev E, Bonneau R, Chatila T, Chatterjee N, Chung KF, Cutcliffe C, Davidson W, Dong G, Fang G, Fulkerson P, Himes BE, Liang L, Mathias RA, Ogino S, Petrosino J, Price ND, Schadt E, Schofield J, Seibold MA, Steen H, Wheatley L, Zhang H, Togias A, Hasegawa K. Analytical challenges in omics research on asthma and allergy: A National Institute of Allergy and Infectious Diseases workshop. J Allergy Clin Immunol 2024; 153:954-968. [PMID: 38295882 PMCID: PMC10999353 DOI: 10.1016/j.jaci.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/29/2024]
Abstract
Studies of asthma and allergy are generating increasing volumes of omics data for analysis and interpretation. The National Institute of Allergy and Infectious Diseases (NIAID) assembled a workshop comprising investigators studying asthma and allergic diseases using omics approaches, omics investigators from outside the field, and NIAID medical and scientific officers to discuss the following areas in asthma and allergy research: genomics, epigenomics, transcriptomics, microbiomics, metabolomics, proteomics, lipidomics, integrative omics, systems biology, and causal inference. Current states of the art, present challenges, novel and emerging strategies, and priorities for progress were presented and discussed for each area. This workshop report summarizes the major points and conclusions from this NIAID workshop. As a group, the investigators underscored the imperatives for rigorous analytic frameworks, integration of different omics data types, cross-disciplinary interaction, strategies for overcoming current limitations, and the overarching goal to improve scientific understanding and care of asthma and allergic diseases.
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Affiliation(s)
| | - Patrice M Becker
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | | | - Jessica Lasky-Su
- Brigham & Women's Hospital and Harvard Medical School, Boston, Mass
| | | | | | | | | | - Talal Chatila
- Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | | | | | | | - Wendy Davidson
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Gang Dong
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Gang Fang
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Patricia Fulkerson
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | | | - Liming Liang
- Harvard T. H. Chan School of Public Health, Boston, Mass
| | | | - Shuji Ogino
- Brigham & Women's Hospital and Harvard Medical School, Boston, Mass; Harvard T. H. Chan School of Public Health, Boston, Mass; Broad Institute of MIT and Harvard, Boston, Mass
| | | | | | - Eric Schadt
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Max A Seibold
- National Jewish Health, Denver, Colo; University of Colorado School of Medicine, Aurora, Colo
| | - Hanno Steen
- Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Lisa Wheatley
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Hongmei Zhang
- School of Public Health, University of Memphis, Memphis, Tenn
| | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Kohei Hasegawa
- Massachusetts General Hospital and Harvard Medical School, Boston, Mass
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Tutino M, Hankinson J, Murray C, Lowe L, Kerry G, Rattray M, Custovic A, Johnston SL, Shi C, Orozco G, Eyre S, Martin P, Simpson A, Curtin JA. Identification of differences in CD4 + T-cell gene expression between people with asthma and healthy controls. Sci Rep 2023; 13:22796. [PMID: 38129444 PMCID: PMC10739740 DOI: 10.1038/s41598-023-49135-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
Functional enrichment analysis of genome-wide association study (GWAS)-summary statistics has suggested that CD4+ T-cells play an important role in asthma pathogenesis. Despite this, CD4+ T-cells are under-represented in asthma transcriptome studies. To fill the gap, 3'-RNA-Seq was used to generate gene expression data on CD4+ T-cells (isolated within 2 h from collection) from peripheral blood from participants with well-controlled asthma (n = 32) and healthy controls (n = 11). Weighted Gene Co-expression Network Analysis (WGCNA) was used to identify sets of co-expressed genes (modules) associated with the asthma phenotype. We identified three modules associated with asthma, which are strongly enriched for GWAS-identified asthma genes, antigen processing/presentation and immune response to viral infections. Through integration of publicly available eQTL and GWAS summary statistics (colocalisation), and protein-protein interaction (PPI) data, we identified PTPRC, a potential druggable target, as a putative master regulator of the asthma gene-expression profiles. Using a co-expression network approach, with integration of external genetic and PPI data, we showed that CD4+ T-cells from peripheral blood from asthmatics have different expression profiles, albeit small in magnitude, compared to healthy controls, for sets of genes involved in immune response to viral infections (upregulated) and antigen processing/presentation (downregulated).
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Affiliation(s)
- Mauro Tutino
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK.
| | - Jenny Hankinson
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Clare Murray
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
- Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Lesley Lowe
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
- Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Gina Kerry
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
- Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Magnus Rattray
- Division of Informatics, Imaging and Data Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Adnan Custovic
- National Heart and Lung Institute, Asthma UK Centre in Allergic Mechanisms of Asthma, Imperial College London, London, UK
| | - Sebastian L Johnston
- National Heart and Lung Institute, Asthma UK Centre in Allergic Mechanisms of Asthma, Imperial College London, London, UK
| | - Chenfu Shi
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Gisela Orozco
- Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, UK
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Stephen Eyre
- Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, UK
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Paul Martin
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Angela Simpson
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
| | - John A Curtin
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
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Denning DW, Pfavayi LT. Poorly controlled asthma - Easy wins and future prospects for addressing fungal allergy. Allergol Int 2023; 72:493-506. [PMID: 37544851 DOI: 10.1016/j.alit.2023.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/25/2023] [Accepted: 06/28/2023] [Indexed: 08/08/2023] Open
Abstract
Poorly controlled asthma is especially common in low resource countries. Aside from lack of access to, or poor technique with, inhaled beta-2 agonists and corticosteroids, the most problematic forms of asthma are frequently associated with both fungal allergy and exposure, especially in adults leading to more asthma exacerbations and worse asthma. The umbrella term 'fungal asthma' describes many disorders linked to fungal exposure and/or allergy to fungi. One fungal asthma endotype, ABPA, is usually marked by a very high IgE and its differential diagnosis is reviewed. Both ABPA and fungal bronchitis in bronchiectasis are marked by thick excess airway mucus production. Dermatophyte skin infection can worsen asthma and eradication of the skin infection improves asthma. Exposure to fungi in the workplace, home and schools, often in damp or water-damaged buildings worsens asthma, and remediation improves symptom control and reduces exacerbations. Antifungal therapy is beneficial for fungal asthma as demonstrated in nine of 13 randomised controlled studies, reducing symptoms, corticosteroid need and exacerbations while improving lung function. Other useful therapies include azithromycin and some biologics approved for the treatment of severe asthma. If all individuals with poorly controlled and severe asthma could be 'relieved' of their fungal allergy and infection through antifungal therapy without systemic corticosteroids, the health benefits would be enormous and relatively inexpensive, improving the long term health of over 20 million adults and many children. Antifungal therapy carries some toxicity, drug interactions and triazole resistance risks, and data are incomplete. Here we summarise what is known and what remains uncertain about this complex topic.
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Affiliation(s)
- David W Denning
- Manchester Fungal Infection Group, The University of Manchester and Manchester Academic Health Science Centre, Manchester, UK.
| | - Lorraine T Pfavayi
- Institute of Immunology & Infection Research, Ashworth Laboratories, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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Zhang L, Chun Y, Irizar H, Arditi Z, Grishina G, Grishin A, Vicencio A, Bunyavanich S. Integrated study of systemic and local airway transcriptomes in asthma reveals causal mediation of systemic effects by airway key drivers. Genome Med 2023; 15:71. [PMID: 37730635 PMCID: PMC10512627 DOI: 10.1186/s13073-023-01222-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/18/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Systemic and local profiles have each been associated with asthma, but parsing causal relationships between system-wide and airway-specific processes can be challenging. We sought to investigate systemic and airway processes in asthma and their causal relationships. METHODS Three hundred forty-one participants with persistent asthma and non-asthmatic controls were recruited and underwent peripheral blood mononuclear cell (PBMC) collection and nasal brushing. Transcriptome-wide RNA sequencing of the PBMC and nasal samples and a series of analyses were then performed using a discovery and independent test set approach at each step to ensure rigor. Analytic steps included differential expression analyses, coexpression and probabilistic causal (Bayesian) network constructions, key driver analyses, and causal mediation models. RESULTS Among the 341 participants, the median age was 13 years (IQR = 10-16), 164 (48%) were female, and 200 (58.7%) had persistent asthma with mean Asthma Control Test (ACT) score 16.6 (SD = 4.2). PBMC genes associated with asthma were enriched in co-expression modules for NK cell-mediated cytotoxicity (fold enrichment = 4.5, FDR = 6.47 × 10-32) and interleukin production (fold enrichment = 2.0, FDR = 1.01 × 10-15). Probabilistic causal network and key driver analyses identified NK cell granule protein (NKG7, fold change = 22.7, FDR = 1.02 × 10-31) and perforin (PRF1, fold change = 14.9, FDR = 1.31 × 10-22) as key drivers predicted to causally regulate PBMC asthma modules. Nasal genes associated with asthma were enriched in the tricarboxylic acid (TCA) cycle module (fold enrichment = 7.5 FDR = 5.09 × 10-107), with network analyses identifying G3BP stress granule assembly factor 1 (G3BP1, fold change = 9.1 FDR = 2.77 × 10-5) and InaD-like protein (INADL, fold change = 5.3 FDR = 2.98 × 10-9) as nasal key drivers. Causal mediation analyses revealed that associations between PBMC key drivers and asthma are causally mediated by nasal key drivers (FDR = 0.0076 to 0.015). CONCLUSIONS Integrated study of the systemic and airway transcriptomes in a well-phenotyped asthma cohort identified causal key drivers of asthma among PBMC and nasal transcripts. Associations between PBMC key drivers and asthma are causally mediated by nasal key drivers.
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Affiliation(s)
- Lingdi Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Yoojin Chun
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Haritz Irizar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Zoe Arditi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Galina Grishina
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Alexander Grishin
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Alfin Vicencio
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA
| | - Supinda Bunyavanich
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA.
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, USA.
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10
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Urbančič J, Košak Soklič T, Demšar Luzar A, Hočevar Boltežar I, Korošec P, Rijavec M. Transcriptomic Differentiation of Phenotypes in Chronic Rhinosinusitis and Its Implications for Understanding the Underlying Mechanisms. Int J Mol Sci 2023; 24:ijms24065541. [PMID: 36982612 PMCID: PMC10051401 DOI: 10.3390/ijms24065541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/04/2023] [Accepted: 03/12/2023] [Indexed: 03/16/2023] Open
Abstract
Chronic rhinosinusitis (CRS) is a multifaceted disease with variable clinical courses and outcomes. We aimed to determine CRS-associated nasal-tissue transcriptome in clinically well-characterized and phenotyped individuals, to gain a novel insight into the biological pathways of the disease. RNA-sequencing of tissue samples of patients with CRS with polyps (CRSwNP), without polyps (CRSsNP), and controls were performed. Characterization of differently expressed genes (DEGs) and functional and pathway analysis was undertaken. We identified 782 common CRS-associated nasal-tissue DEGs, while 375 and 328 DEGs were CRSwNP- and CRSsNP-specific, respectively. Common key DEGs were found to be involved in dendritic cell maturation, the neuroinflammation pathway, and the inhibition of the matrix metalloproteinases. Distinct CRSwNP-specific DEGs were involved in NF-kβ canonical pathways, Toll-like receptor signaling, HIF1α regulation, and the Th2 pathway. CRSsNP involved the NFAT pathway and changes in the calcium pathway. Our findings offer new insights into the common and distinct molecular mechanisms underlying CRSwNP and CRSsNP, providing further understanding of the complex pathophysiology of the CRS, with future research directions for novel treatment strategies.
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Affiliation(s)
- Jure Urbančič
- Department of Otorhinolaryngology and Cervicofacial Surgery, University Medical Centre Ljubljana, Zaloska 2, SI-1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
- Correspondence:
| | - Tanja Košak Soklič
- Department of Otorhinolaryngology and Cervicofacial Surgery, University Medical Centre Ljubljana, Zaloska 2, SI-1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
| | - Ajda Demšar Luzar
- Laboratory for Clinical Immunology and Molecular Genetics, University Clinic of Respiratory and Allergic Diseases Golnik, Golnik 36, SI-4204 Golnik, Slovenia
| | - Irena Hočevar Boltežar
- Department of Otorhinolaryngology and Cervicofacial Surgery, University Medical Centre Ljubljana, Zaloska 2, SI-1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Vrazov trg 2, SI-1000 Ljubljana, Slovenia
| | - Peter Korošec
- Laboratory for Clinical Immunology and Molecular Genetics, University Clinic of Respiratory and Allergic Diseases Golnik, Golnik 36, SI-4204 Golnik, Slovenia
- Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Matija Rijavec
- Laboratory for Clinical Immunology and Molecular Genetics, University Clinic of Respiratory and Allergic Diseases Golnik, Golnik 36, SI-4204 Golnik, Slovenia
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
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11
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Kozlik-Siwiec P, Buregwa-Czuma S, Zawlik I, Dziedzina S, Myszka A, Zuk-Kuwik J, Siwiec-Kozlik A, Zarychta J, Okon K, Zareba L, Soja J, Jakiela B, Kepski M, Bazan JG, Bazan-Socha S. Co-Expression Analysis of Airway Epithelial Transcriptome in Asthma Patients with Eosinophilic vs. Non-Eosinophilic Airway Infiltration. Int J Mol Sci 2023; 24:3789. [PMID: 36835202 PMCID: PMC9959255 DOI: 10.3390/ijms24043789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/27/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
Asthma heterogeneity complicates the search for targeted treatment against airway inflammation and remodeling. We sought to investigate relations between eosinophilic inflammation, a phenotypic feature frequent in severe asthma, bronchial epithelial transcriptome, and functional and structural measures of airway remodeling. We compared epithelial gene expression, spirometry, airway cross-sectional geometry (computed tomography), reticular basement membrane thickness (histology), and blood and bronchoalveolar lavage (BAL) cytokines of n = 40 moderate to severe eosinophilic (EA) and non-eosinophilic asthma (NEA) patients distinguished by BAL eosinophilia. EA patients showed a similar extent of airway remodeling as NEA but had an increased expression of genes involved in the immune response and inflammation (e.g., KIR3DS1), reactive oxygen species generation (GYS2, ATPIF1), cell activation and proliferation (ANK3), cargo transporting (RAB4B, CPLX2), and tissue remodeling (FBLN1, SOX14, GSN), and a lower expression of genes involved in epithelial integrity (e.g., GJB1) and histone acetylation (SIN3A). Genes co-expressed in EA were involved in antiviral responses (e.g., ATP1B1), cell migration (EPS8L1, STOML3), cell adhesion (RAPH1), epithelial-mesenchymal transition (ASB3), and airway hyperreactivity and remodeling (FBN3, RECK), and several were linked to asthma in genome- (e.g., MRPL14, ASB3) or epigenome-wide association studies (CLC, GPI, SSCRB4, STRN4). Signaling pathways inferred from the co-expression pattern were associated with airway remodeling (e.g., TGF-β/Smad2/3, E2F/Rb, and Wnt/β-catenin).
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Affiliation(s)
- Pawel Kozlik-Siwiec
- Department of Internal Medicine, Jagiellonian University Medical College, 31-066 Krakow, Poland
- Haematology Clinical Department, University Hospital, 31-501 Krakow, Poland
| | - Sylwia Buregwa-Czuma
- College of Natural Sciences, Institute of Computer Science, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland
| | - Izabela Zawlik
- Centre for Innovative Research in Medical and Natural Sciences, Institute of Medical Sciences, Medical College, University of Rzeszow, Kopisto 2a, 35-959 Rzeszow, Poland
| | - Sylwia Dziedzina
- Department of Internal Medicine, Jagiellonian University Medical College, 31-066 Krakow, Poland
| | - Aleksander Myszka
- Institute of Medical Sciences, Medical College, University of Rzeszow, Kopisto 2a, 35-959 Rzeszow, Poland
| | - Joanna Zuk-Kuwik
- Haematology Clinical Department, University Hospital, 31-501 Krakow, Poland
- Haematology Department, Jagiellonian University Medical College, 31-501 Krakow, Poland
| | | | - Jacek Zarychta
- Department of Internal Medicine, Jagiellonian University Medical College, 31-066 Krakow, Poland
- Pulmonary Hospital, 34-736 Zakopane, Poland
| | - Krzysztof Okon
- Department of Pathology, Jagiellonian University Medical College, 33-332 Krakow, Poland
| | - Lech Zareba
- College of Natural Sciences, Institute of Computer Science, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland
| | - Jerzy Soja
- Department of Internal Medicine, Jagiellonian University Medical College, 31-066 Krakow, Poland
| | - Bogdan Jakiela
- Department of Internal Medicine, Jagiellonian University Medical College, 31-066 Krakow, Poland
| | - Michał Kepski
- College of Natural Sciences, Institute of Computer Science, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland
| | - Jan G. Bazan
- College of Natural Sciences, Institute of Computer Science, University of Rzeszow, Pigonia 1, 35-310 Rzeszow, Poland
| | - Stanislawa Bazan-Socha
- Department of Internal Medicine, Jagiellonian University Medical College, 31-066 Krakow, Poland
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12
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Baloh CH, Mathias RA. Recent progress in the genetic and epigenetic underpinnings of atopy. J Allergy Clin Immunol 2023; 151:60-69. [PMID: 36608983 PMCID: PMC9987265 DOI: 10.1016/j.jaci.2022.10.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 01/05/2023]
Abstract
In the past 2 years, there continue to be advances in our understanding of the genetic and epigenetic underpinnings of atopy pertaining to disease risk and disease severity. The joint role of genetics and the environment has been emphasized in multiple studies. Combining genetics with family history, biomarkers, and comorbidities is further refining our ability to predict the development of individual atopic diseases as well as the advancement of the atopic march. Polygenic risk scores will be an important next step for the field moving toward clinical translation of the genetic findings thus far. A systems biology approach, as illustrated by studies of the microbiome and epigenome, will be necessary to fully understand disease development and to develop increasingly targeted therapeutics.
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Affiliation(s)
- Carolyn H Baloh
- The Immune Tolerance Network, Benaroya Research Institute at Virginia Mason, Seattle, Wash; Department of Medicine, Harvard Medical School, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Mass
| | - Rasika A Mathias
- Department of Medicine, School of Medicine, Johns Hopkins University, Division of Allergy and Clinical Immunology, Baltimore, Md.
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13
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Irizar H, Chun Y, Arditi Z, Do A, Grishina G, Grishin A, Vicencio A, Bunyavanich S. Examination of host genetic effects on nasal microbiome composition. J Allergy Clin Immunol 2022; 150:1232-1236. [PMID: 35718139 PMCID: PMC9643606 DOI: 10.1016/j.jaci.2022.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/24/2022] [Accepted: 06/01/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Genetic predisposition increases risk for asthma, and distinct nasal microbial compositions are associated with asthma. Host genetics might shape nasal microbiome composition. OBJECTIVE We examined associations between host genetics and nasal microbiome composition. METHODS Nasal samples were collected from 584 participants from the Mount Sinai Health System, New York. Seventy-seven follow-up samples were collected from a subset of 40 participants. 16S rRNA sequencing and RNA sequencing were performed on nasal samples. Beta diversity was calculated, variant calling on RNA sequencing data was performed, and genetic relatedness between individuals was determined. Using linear regression models, we tested for associations between genetic relatedness and nasal microbiome composition. RESULTS The median age of the cohort was 14.6 (interquartile range 11.2-19.5) years, with participants representing diverse ancestries and 52.7% of the cohort being female. For participants who provided follow-up samples, the median time between samples was 5.1 (interquartile range 1.4-7.2) months. Nasal microbiome composition similarity as reflected by beta diversity was significantly higher within subjects over time versus between subjects (coefficient = 0.091, P = 2.84-7). There was no significant association between genetic relatedness and beta diversity (coefficient = -0.05, P = .29). Additional analyses exploring the relationship between beta diversity and genetic variance yielded similar results. CONCLUSION Host genetics has little influence on nasal microbiome composition.
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Affiliation(s)
- Haritz Irizar
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yoojin Chun
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Zoe Arditi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Anh Do
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Galina Grishina
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Alexander Grishin
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Alfin Vicencio
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Supinda Bunyavanich
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY.
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14
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Mainguy-Seers S, Beaudry F, Fernandez-Prada C, Martin JG, Lavoie JP. Neutrophil Extracellular Vesicles and Airway Smooth Muscle Proliferation in the Natural Model of Severe Asthma in Horses. Cells 2022; 11:3347. [PMID: 36359743 PMCID: PMC9653818 DOI: 10.3390/cells11213347] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 08/13/2023] Open
Abstract
Extracellular vesicles (EVs) contribute to intercellular communication through the transfer of their rich cargo to recipient cells. The EVs produced by LPS-stimulated neutrophils from healthy humans and horses increase airway smooth muscle (ASM) proliferation, but the roles of neutrophil EVs in asthma are largely unexplored. The aim of this study was to determine whether neutrophil-derived EVs isolated during the remission or exacerbation of asthma influence ASM proliferation differentially. Peripheral blood neutrophils were collected during remission and exacerbation in eight horses affected by severe asthma. The cells were cultured (±LPS), and their EVs were isolated by ultracentrifugation and characterized by laser scattering microscopy and proteomic analysis. The proliferation of ASM co-incubated with EVs was monitored in real time by electrical impedance. Two proteins were significantly upregulated during disease exacerbation in neutrophil EVs (MAST4 and Lrch4), while LPS stimulation greatly altered the proteomic profile. Those changes involved the upregulation of neutrophil degranulation products, including proteases known to induce myocyte proliferation. In agreement with the proteomic results, EVs from LPS-stimulated neutrophils increased ASM proliferation, without an effect of the disease status. The inhalation of environmental LPS could contribute to asthma pathogenesis by activating neutrophils and leading to ASM hyperplasia.
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Affiliation(s)
- Sophie Mainguy-Seers
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, St-Hyacinthe, QC J2S 2M2, Canada
| | - Francis Beaudry
- Department of Veterinary Biomedical Sciences, Faculty of Veterinary Medicine, Université de Montréal, St-Hyacinthe, QC J2S 2M2, Canada
| | - Christopher Fernandez-Prada
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, St-Hyacinthe, QC J2S 2M2, Canada
| | - James G. Martin
- Meakins Christie Laboratories, Research Institute of the McGill University Health Centre, Montréal, QC H4A 3J1, Canada
| | - Jean-Pierre Lavoie
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, St-Hyacinthe, QC J2S 2M2, Canada
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15
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Ye Q, Barrett N, Balestrieri B. Bioactive lipids: Accessible indicators toward improved diagnosis and treatment of asthma. J Allergy Clin Immunol 2022; 150:790-792. [PMID: 36029891 DOI: 10.1016/j.jaci.2022.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/18/2022] [Accepted: 08/22/2022] [Indexed: 01/21/2023]
Affiliation(s)
- Qihua Ye
- Department of Medicine, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Nora Barrett
- Department of Medicine, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass
| | - Barbara Balestrieri
- Department of Medicine, Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass.
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16
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Wang M, Tang S, Yang X, Xie X, Luo Y, He S, Li X, Feng X. Identification of key genes and pathways in chronic rhinosinusitis with nasal polyps and asthma comorbidity using bioinformatics approaches. Front Immunol 2022; 13:941547. [PMID: 36059464 PMCID: PMC9428751 DOI: 10.3389/fimmu.2022.941547] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/25/2022] [Indexed: 11/25/2022] Open
Abstract
Patients with chronic rhinosinusitis with nasal polyps (CRSwNP) and asthma comorbidity (ACRSwNP) present severe symptoms and are more likely to relapse. However, the pathogenesis of ACRSwNP is not fully understood. The aim of this study was to explore the underlying pathogenesis of ACRSwNP using bioinformatics approaches. ACRSwNP-related differentially expressed genes (DEGs) were identified by the analysis of the GSE23552 dataset. The clusterProfiler R package was used to carry out functional and pathway enrichment analysis. A protein–protein interaction (PPI) network was built using the STRING database to explore key genes in the pathogenesis of ACRSwNP. The bioinformatics analysis results were verified through qRT-PCR. The Connectivity Map (CMap) database was used to predict potential drugs for the treatment of ACRSwNP. A total of 36 DEGs were identified, which were mainly enriched in terms of regulation of immune response and detection sensory perception of taste. Thirteen hub genes including AZGP1, AQP9, GAPT, PIP, and PRR4 were identified as potential hub genes in ACRSwNP from the PPI network. Analysis of the GSE41861 dataset showed that upregulation of CST1 in nasal mucosa was associated with asthma. qRT-PCR detection confirmed the bioinformatics analysis results. Tacrolimus and spaglumic acid were identified as potential drugs for the treatment of ACRSwNP from the CMap database. The findings of this study provide insights into the pathogenesis of ACRSwNP and may provide a basis for the discovery of effective therapeutic modalities for ACRSwNP.
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Affiliation(s)
| | | | | | | | | | | | | | - Xin Feng
- *Correspondence: Xin Feng, ; Xuezhong Li,
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17
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Logotheti M, Agioutantis P, Katsaounou P, Loutrari H. Microbiome Research and Multi-Omics Integration for Personalized Medicine in Asthma. J Pers Med 2021; 11:jpm11121299. [PMID: 34945771 PMCID: PMC8707330 DOI: 10.3390/jpm11121299] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/13/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022] Open
Abstract
Asthma is a multifactorial inflammatory disorder of the respiratory system characterized by high diversity in clinical manifestations, underlying pathological mechanisms and response to treatment. It is generally established that human microbiota plays an essential role in shaping a healthy immune response, while its perturbation can cause chronic inflammation related to a wide range of diseases, including asthma. Systems biology approaches encompassing microbiome analysis can offer valuable platforms towards a global understanding of asthma complexity and improving patients' classification, status monitoring and therapeutic choices. In the present review, we summarize recent studies exploring the contribution of microbiota dysbiosis to asthma pathogenesis and heterogeneity in the context of asthma phenotypes-endotypes and administered medication. We subsequently focus on emerging efforts to gain deeper insights into microbiota-host interactions driving asthma complexity by integrating microbiome and host multi-omics data. One of the most prominent achievements of these research efforts is the association of refractory neutrophilic asthma with certain microbial signatures, including predominant pathogenic bacterial taxa (such as Proteobacteria phyla, Gammaproteobacteria class, especially species from Haemophilus and Moraxella genera). Overall, despite existing challenges, large-scale multi-omics endeavors may provide promising biomarkers and therapeutic targets for future development of novel microbe-based personalized strategies for diagnosis, prevention and/or treatment of uncontrollable asthma.
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Affiliation(s)
- Marianthi Logotheti
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece
| | - Panagiotis Agioutantis
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
| | - Paraskevi Katsaounou
- Pulmonary Dept First ICU, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, Ipsilantou 45-7, 10675 Athens, Greece;
| | - Heleni Loutrari
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
- Correspondence:
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18
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Li YC, Hsu HHL, Chun Y, Chiu PH, Arditi Z, Claudio L, Pandey G, Bunyavanich S. Machine learning-driven identification of early-life air toxic combinations associated with childhood asthma outcomes. J Clin Invest 2021; 131:152088. [PMID: 34609967 DOI: 10.1172/jci152088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 09/23/2021] [Indexed: 01/19/2023] Open
Abstract
Air pollution is a well-known contributor to asthma. Air toxics are hazardous air pollutants that cause or may cause serious health effects. Although individual air toxics have been associated with asthma, only a limited number of studies have specifically examined combinations of air toxics associated with the disease. We geocoded air toxic levels from the US National Air Toxics Assessment (NATA) to residential locations for participants of our AiRway in Asthma (ARIA) study. We then applied Data-driven ExposurE Profile extraction (DEEP), a machine learning-based method, to discover combinations of early-life air toxics associated with current use of daily asthma controller medication, lifetime emergency department visit for asthma, and lifetime overnight hospitalization for asthma. We discovered 20 multi-air toxic combinations and 18 single air toxics associated with at least 1 outcome. The multi-air toxic combinations included those containing acrylic acid, ethylidene dichloride, and hydroquinone, and they were significantly associated with asthma outcomes. Several air toxic members of the combinations would not have been identified by single air toxic analyses, supporting the use of machine learning-based methods designed to detect combinatorial effects. Our findings provide knowledge about air toxic combinations associated with childhood asthma.
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Affiliation(s)
| | - Hsiao-Hsien Leon Hsu
- Department of Environmental Medicine and Public Health.,Institute for Exposomic Research, and
| | | | | | - Zoe Arditi
- Department of Genetics and Genomic Sciences.,Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Luz Claudio
- Department of Environmental Medicine and Public Health.,Institute for Exposomic Research, and
| | - Gaurav Pandey
- Department of Genetics and Genomic Sciences.,Institute for Exposomic Research, and
| | - Supinda Bunyavanich
- Department of Genetics and Genomic Sciences.,Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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19
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Ano S, Kikuchi N, Matsuyama M, Nakajima M, Kondo Y, Masuda M, Osawa H, Ishii Y, Hizawa N. Transcriptome genetic differences between responders and non-responders before bronchial thermoplasty. J Asthma 2021; 59:1641-1651. [PMID: 34143700 DOI: 10.1080/02770903.2021.1945088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Bronchial thermoplasty (BT) is an endoscopic therapy used for the treatment of refractory asthma. Some predictive factors, for example the number of activations and severity of disease at baseline, have been used to determine the effectiveness of BT in treating patients with asthma. The aim of the present study was to comprehensively analyze RNA samples from the airway bronchial tissues of patients with severe asthma treated by BT, and to characterize each patient as a BT responder or non-responder. METHODS Eight patients with severe asthma scheduled to undergo BT and bronchus biopsies were recruited before the procedures were conducted. Extracted RNA samples from bronchial tissues were sequenced and differential gene expression analysis was carried out.Results/discussion: Subjects with Asthma Quality of Life Questionnaire score changes ≥0.5 for a period of 12 months were considered BT responders. Non-responders had score changes <0.5 for 12 months. Histopathology findings were similar to those reported previously, and no significant differences in the expression of α-smooth muscle actin and protein gene product 9.5 were observed between responders and non-responders. Transcriptome analysis at baseline identified 67 genes that were differentially expressed between responders and non-responders, including SLPI, MMP3, and MUC19, which were upregulated in responders. Although the differentially expressed gene products may have conflicting effects, genes in the airway epithelium and extracellular matrix of patients with severe asthma may determine the BT response. Our results identified possible transcriptomic changes that could be used to identify BT responders.
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Affiliation(s)
- Satoshi Ano
- The Department of Respiratory Medicine, National Hospital Organization Kasumigaura Medical Center, Tsuchiura, Japan
| | - Norihiro Kikuchi
- The Department of Respiratory Medicine, National Hospital Organization Kasumigaura Medical Center, Tsuchiura, Japan
| | - Masashi Matsuyama
- The Department of Respiratory Medicine, University of Tsukuba, Tsukuba, Japan
| | - Masayuki Nakajima
- The Department of Respiratory Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yuzuru Kondo
- The Department of Diagnostic Pathology, National Hospital Organization Kasumigaura Medical Center, Tsuchiura, Japan
| | - Michiko Masuda
- The Department of Respiratory Medicine, National Hospital Organization Kasumigaura Medical Center, Tsuchiura, Japan
| | - Hajime Osawa
- The Department of Respiratory Medicine, National Hospital Organization Kasumigaura Medical Center, Tsuchiura, Japan.,The Department of Respiratory Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yukio Ishii
- The Department of Respiratory Medicine, National Hospital Organization Kasumigaura Medical Center, Tsuchiura, Japan.,The Department of Respiratory Medicine, University of Tsukuba, Tsukuba, Japan
| | - Nobuyuki Hizawa
- The Department of Respiratory Medicine, University of Tsukuba, Tsukuba, Japan
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20
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Xia M, Wu Q, Chen P, Qian C. Regulatory T Cell-Related Gene Biomarkers in the Deterioration of Atherosclerosis. Front Cardiovasc Med 2021; 8:661709. [PMID: 34095251 PMCID: PMC8172618 DOI: 10.3389/fcvm.2021.661709] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/07/2021] [Indexed: 01/16/2023] Open
Abstract
Background: Regulatory T cells (Tregs) have shown to be protective against the development of atherosclerosis, a major pathological cause for cardiovascular events. Here, we aim to explore the roles of Tregs-related genes in atherosclerosis deterioration. Methods and Results: We downloaded the gene expression profile of 29 atherosclerotic samples from the Gene Expression Omnibus database with an accession number of GSE28829. The abundance of Tregs estimated by the CIBERSORT algorithm was negatively correlated with the atherosclerotic stage. Using the limma test and correlation analysis, a total of 159 differentially expressed Tregs-related genes (DETregRGs) between early and advanced atherosclerotic plaques were documented. Functional annotation analysis using the DAVID tool indicated that the DETregRGs were mainly enriched in inflammatory responses, immune-related mechanisms, and pathways such as complement and coagulation cascades, platelet activation, leukocyte trans-endothelial migration, vascular smooth muscle contraction, and so on. A protein-protein interaction network of the DETregRGs was then constructed, and five hub genes (PTPRC, C3AR1, CD53, TLR2, and CCR1) were derived from the network with node degrees ≥20. The expression patterns of these hub DETregRGs were further validated in several independent datasets. Finally, a single sample scoring method was used to build a gene signature for the five DETregRGs, which could distinguish patients with myocardial infarction from those with stable coronary disease. Conclusion: The results of this study will improve our understanding about the Tregs-associated molecular mechanisms in the progression of atherosclerosis and facilitate the discovery of novel biomarkers for acute cardiovascular events.
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Affiliation(s)
- Meng Xia
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Qingmeng Wu
- Healthcare-Associated Infections Control Center, The Affiliated Chinese Medicine Hospital of Southwest Medical University, Luzhou, China
| | - Pengfei Chen
- Department of Gastroenterology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, China
| | - Cheng Qian
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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21
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Tyler SR, Chun Y, Ribeiro VM, Grishina G, Grishin A, Hoffman GE, Do AN, Bunyavanich S. Merged Affinity Network Association Clustering: Joint multi-omic/clinical clustering to identify disease endotypes. Cell Rep 2021; 35:108975. [PMID: 33852839 PMCID: PMC8195153 DOI: 10.1016/j.celrep.2021.108975] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/25/2021] [Accepted: 03/18/2021] [Indexed: 12/21/2022] Open
Abstract
Although clinical and laboratory data have long been used to guide medical practice, this information is rarely integrated with multi-omic data to identify endotypes. We present Merged Affinity Network Association Clustering (MANAclust), a coding-free, automated pipeline enabling integration of categorical and numeric data spanning clinical and multi-omic profiles for unsupervised clustering to identify disease subsets. Using simulations and real-world data from The Cancer Genome Atlas, we demonstrate that MANAclust’s feature selection algorithms are accurate and outperform competitors. We also apply MANAclust to a clinically and multi-omically phenotyped asthma cohort. MANAclust identifies clinically and molecularly distinct clusters, including heterogeneous groups of “healthy controls” and viral and allergy-driven subsets of asthmatic subjects. We also find that subjects with similar clinical presentations have disparate molecular profiles, highlighting the need for additional testing to uncover asthma endotypes. This work facilitates data-driven personalized medicine through integration of clinical parameters with multi-omics. MANAclust is freely available at https://bitbucket.org/scottyler892/manaclust/src/master/. Clinical data commonly used in medical practice are underutilized in multi-omic analyses to identify disease endotypes. Tyler et al. present a python package called Merged Affinity Network Association Clustering (MANAclust) that automatically processes and integrates categorical and numeric data types, facilitating the inclusion of clinical data in multi-omic endotyping efforts.
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Affiliation(s)
- Scott R Tyler
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yoojin Chun
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Victoria M Ribeiro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Galina Grishina
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander Grishin
- Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gabriel E Hoffman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anh N Do
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Supinda Bunyavanich
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Division of Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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22
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Rayens E, Noble B, Vicencio A, Goldman DL, Bunyavanich S, Norris KA. Relationship of Pneumocystis antibody responses to paediatric asthma severity. BMJ Open Respir Res 2021; 8:8/1/e000842. [PMID: 33762359 PMCID: PMC7993353 DOI: 10.1136/bmjresp-2020-000842] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Although asthma is the most commonly diagnosed respiratory disease, its pathogenesis is complex, involving both genetic and environmental factors. A role for the respiratory microbiome in modifying asthma severity has been recently recognised. Airway colonisation by Pneumocystis jirovecii has previously been associated with multiple chronic lung diseases, including chronic obstructive pulmonary disease (COPD) and severe asthma (SA). Decreased incidence of Pneumocystis pneumonia in HIV-infected individuals and reduced severity of COPD is associated with naturally occurring antibody responses to the Pneumocystis antigen, Kexin (KEX1). METHODS 104 paediatric patients were screened for KEX1 IgG reciprocal end point titre (RET), including 51 with SA, 20 with mild/moderate asthma, 20 non-asthma and 13 with cystic fibrosis (CF) in a cross-sectional study. RESULTS Patients with SA had significantly reduced Pneumocystis KEX1 titres compared with patients with mild/moderate asthma (p=0.018) and CF (p=0.003). A binary KEX1 RET indicator was determined at a threshold of KEX1 RET=1000. Patients with SA had 4.40 (95% CI 1.28 to 13.25, p=0.014) and 17.92 (95% CI 4.15 to 66.62, p<0.001) times the odds of falling below that threshold compared with mild/moderate asthma and patients with CF, respectively. Moreover, KEX1 IgG RET did not correlate with tetanus toxoid IgG (r=0.21, p=0.82) or total IgE (r=0.03, p=0.76), indicating findings are specific to antibody responses to KEX1. CONCLUSIONS Paediatric patients with SA may be at higher risk for chronic Pneumocystis infections and asthma symptom exacerbation due to reduced levels of protective antibodies. Plasma KEX1 IgG titre may be a useful parameter in determining the clinical course of treatment for paediatric patients with asthma.
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Affiliation(s)
- Emily Rayens
- Center for Vaccines and Immunology, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
| | - Brenda Noble
- Center for Vaccines and Immunology, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
| | - Alfin Vicencio
- Pediatrics, Division of Pediatric Pulmonology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David L Goldman
- Departments of Pediatrics, Microbiology & Immunology, Children's Hospital at Montefiore, Bronx, New York, USA
| | - Supinda Bunyavanich
- Pediatrics, Division of Pediatric Pulmonology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Karen A Norris
- Center for Vaccines and Immunology, University of Georgia College of Veterinary Medicine, Athens, Georgia, USA
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