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Yuan Y, Zhu H, Huang S, Zhang Y, Shen Y. Establishment of a diagnostic model based on immune-related genes in children with asthma. Heliyon 2024; 10:e25735. [PMID: 38375253 PMCID: PMC10875436 DOI: 10.1016/j.heliyon.2024.e25735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/21/2024] Open
Abstract
Objective Allergic asthma is driven by an antigen-specific immune response. This study aimed to identify immune-related differentially expressed genes in childhood asthma and establish a classification diagnostic model based on these genes. Methods GSE65204 and GSE19187 were downloaded and served as training set and validation set. The immune cell composition was evaluated with ssGSEA algorithm based on the immune-related gene set. Modules that significantly related to the asthma were selected by WGCNA algorithm. The immune-related differentially expressed genes (DE-IRGs) were screened, the protein-protein interaction network and diagnostic model of DE-IRGs was constructed. The pathway and immune correlation analysis of hub DE-IRGs was analyzed. Results Eight immune cell types exhibited varying levels of abundance between the asthma and control groups. A total of 112 differentially expressed immune-related genes (DE-IRGs) was identified. Through the application of four ranking methods (MCC, MNC, DEGREE, and EPC), 17 hub DE-IRGs with overlapping significance were further selected. Subsequently, 8 optimized were identified using univariate logistic regression analysis and the LASSO regression algorithm, based on which a robust diagnostic model was constructed. Notably, TNF and CD40LG emerged as direct participants in asthma-related signaling pathways, displaying a positive correlation with the immune cell types of immature B cells, activated B cells, activated CD8 T cells, activated CD4 T cells, and myeloid-derived suppressor cells. Conclusion The diagnostic model constructed using the DE-IRGs (CCL5, CCR5, CD40LG, CD8A, IL2RB, PDCD1, TNF, and ZAP70) exhibited high and specific diagnostic value for childhood asthma. The diagnostic model may contribute to the diagnosis of childhood asthma.
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Affiliation(s)
- Yuyun Yuan
- Department of Pediatrics, Shanghai Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, 201999, China
| | - Honghua Zhu
- Department of Medical Imaging, Shanghai Seventh People's Hospital, Shanghai, 200137, China
| | - Sihong Huang
- Department of Pediatrics, Shanghai Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, 201999, China
| | - Yantao Zhang
- Department of Pediatrics, Shanghai Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, 201999, China
| | - Yiyun Shen
- Department of Pediatrics, Shanghai Baoshan Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai, 201999, China
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Sardon-Prado O, Diaz-Garcia C, Corcuera-Elosegui P, Korta-Murua J, Valverde-Molina J, Sanchez-Solis M. Severe Asthma and Biological Therapies: Now and the Future. J Clin Med 2023; 12:5846. [PMID: 37762787 PMCID: PMC10532431 DOI: 10.3390/jcm12185846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Recognition of phenotypic variability in pediatric asthma allows for a more personalized therapeutic approach. Knowledge of the underlying pathophysiological and molecular mechanisms (endotypes) of corresponding biomarkers and new treatments enables this strategy to progress. Biologic therapies for children with severe asthma are becoming more relevant in this sense. The T2 phenotype is the most prevalent in childhood and adolescence, and non-T2 phenotypes are usually rare. This document aims to review the mechanism of action, efficacy, and potential predictive and monitoring biomarkers of biological drugs, focusing on the pediatric population. The drugs currently available are omalizumab, mepolizumab, benralizumab, dupilumab, and 1ezepelumab, with some differences in administrative approval prescription criteria between the U.S. Food and Drug Administration (FDA) and the European Medicines Agency (EMA). Previously, we described the characteristics of severe asthma in children and its diagnostic and therapeutic management.
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Affiliation(s)
- Olaia Sardon-Prado
- Division of Paediatric Respiratory Medicine, Donostia University Hospital, 20014 San Sebastián, Spain; (O.S.-P.); (P.C.-E.); (J.K.-M.)
- Department of Pediatrics, University of the Basque Country (UPV/EHU), 20014 Leioa, Spain
| | - Carolina Diaz-Garcia
- Paediatric Pulmonology and Allergy Unit, Santa Lucia General University Hospital, 30202 Cartagena, Spain;
| | - Paula Corcuera-Elosegui
- Division of Paediatric Respiratory Medicine, Donostia University Hospital, 20014 San Sebastián, Spain; (O.S.-P.); (P.C.-E.); (J.K.-M.)
| | - Javier Korta-Murua
- Division of Paediatric Respiratory Medicine, Donostia University Hospital, 20014 San Sebastián, Spain; (O.S.-P.); (P.C.-E.); (J.K.-M.)
| | - Jose Valverde-Molina
- Department of Paediatrics, Santa Lucía General University Hospital, 30202 Cartagena, Spain
- IMIB Biomedical Research Institute, 20120 Murcia, Spain;
| | - Manuel Sanchez-Solis
- IMIB Biomedical Research Institute, 20120 Murcia, Spain;
- Department of Pediatrics, University of Murcia, 20120 Murcia, Spain
- Paediatric Allergy and Pulmonology Units, Virgen de la Arrixaca University Children’s Hospital, 20120 Murcia, Spain
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Tsai CH, Lai ACY, Lin YC, Chi PY, Chen YC, Yang YH, Chen CH, Shen SY, Hwang TL, Su MW, Hsu IL, Huang YC, Maitland-van der Zee AH, McGeachie MJ, Tantisira KG, Chang YJ, Lee YL. Neutrophil extracellular trap production and CCL4L2 expression influence corticosteroid response in asthma. Sci Transl Med 2023; 15:eadf3843. [PMID: 37285400 DOI: 10.1126/scitranslmed.adf3843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/04/2023] [Indexed: 06/09/2023]
Abstract
The association between neutrophil extracellular traps (NETs) and response to inhaled corticosteroids (ICS) in asthma is unclear. To better understand this relationship, we analyzed the blood transcriptomes from children with controlled and uncontrolled asthma in the Taiwanese Consortium of Childhood Asthma Study using weighted gene coexpression network analysis and pathway enrichment methods. We identified 298 uncontrolled asthma-specific differentially expressed genes and one gene module associated with neutrophil-mediated immunity, highlighting a potential role for neutrophils in uncontrolled asthma. We also found that NET abundance was associated with nonresponse to ICS in patients. In a neutrophilic airway inflammation murine model, steroid treatment could not suppress neutrophilic inflammation and airway hyperreactivity. However, NET disruption with deoxyribonuclease I (DNase I) efficiently inhibited airway hyperreactivity and inflammation. Using neutrophil-specific transcriptomic profiles, we found that CCL4L2 was associated with ICS nonresponse in asthma, which was validated in human and murine lung tissue. CCL4L2 expression was also negatively correlated with pulmonary function change after ICS treatment. In summary, steroids fail to suppress neutrophilic airway inflammation, highlighting the potential need to use alternative therapies such as leukotriene receptor antagonists or DNase I that target the neutrophil-associated phenotype. Furthermore, these results highlight CCL4L2 as a potential therapeutic target for individuals with asthma refractory to ICS.
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Affiliation(s)
- Ching-Hui Tsai
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | | | - Yu-Cheng Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Po-Yu Chi
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Yun-Chi Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Yao-Hsu Yang
- Department of Pediatrics, National Taiwan University Hospital, Taipei 100, Taiwan
| | - Chien-Han Chen
- Department of Pediatrics, Fu Jen Catholic University Hospital, Fu Jen Catholic University, New Taipei City 243, Taiwan
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei City 242, Taiwan
| | - Sheng-Yeh Shen
- Department of Chest Medicine, MacKay Memorial Hospital, Taipei 104, Taiwan
| | - Tsong-Long Hwang
- Graduate Institute of Natural Products, School of Traditional Chinese Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Department of Anesthesiology, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Ming-Wei Su
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - I-Ling Hsu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Chi Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Anke H Maitland-van der Zee
- Department of Pulmonary Medicine, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Department of Pediatric Respiratory Medicine, Emma's Children Hospital, Amsterdam UMC, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
- Amsterdam Institute for Infection and Immunity, 1105 AZ Amsterdam, Netherlands
- Amsterdam Public Health, 1105 AZ Amsterdam, Netherlands
| | - Michael J McGeachie
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kelan G Tantisira
- Division of Respiratory Medicine, Department of Pediatrics, University of California San Diego, San Diego, CA 92123, USA
| | - Ya-Jen Chang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- Institute of Translational Medicine and New Drug Development, China Medical University, Taichung 404, Taiwan
| | - Yungling L Lee
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
- College of Public Health, China Medical University, Taichung 404, Taiwan
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei 115, Taiwan
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Wang Y, Wang J, Chen L, Zhang H, Yu L, Chi Y, Chen M, Cai Y. Efficacy of vitamin D supplementation on COPD and asthma control: A systematic review and meta-analysis. J Glob Health 2022; 12:04100. [PMID: 36520525 PMCID: PMC9754066 DOI: 10.7189/jogh.12.04100] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Background The role of vitamin D (VD) in the management of chronic obstructive pulmonary disease (COPD) and asthma remains largely undetermined. In the present meta-analysis, we aimed to comprehensively investigate the efficacy of VD in the treatment of COPD and asthma according to the latest update. Methods The PubMed, Embase, and Cochrane Library databases were searched from their inception to June 2, 2022. Randomized controlled trials (RCTs) comparing the efficacy of VD with placebo against COPD or asthma were included. Results A total of 11 RCTs consisting of 1183 COPD patients and 19 RCTs consisting of 2025 asthmatic patients were finally included. As for pulmonary function, FEV1/FVC was not changed significantly, while FEV1% was improved in the VD group. In the asthma subgroup, FEV1% was not changed significantly, while FEV1/FVC was improved in the VD group. For the questionnaire and rating scale, the mMRC (modified Medical Research Council) dyspnoea scale score for COPD and ACT (Asthma Control Test) score for asthma were not significantly changed, while the SGRQ (St. George's Respiratory Questionnaire) score for COPD was improved in the VD group. For inflammation indicators, IL-6 and IL-10 were statistically equivalent between the VD and placebo groups, while IgE, IL-5, and IL-10 (baseline VD deficiency subgroup) were improved in the VD group. The exacerbation, length of hospital stays, and mortality were statistically equivalent between the two groups. Conclusions VD supplementation improved the indicators of asthma and COPD, especially in pulmonary function, SGRQ scores, IL-5, and IgE. Registration The protocol could be found at PROSPERO with the registration number of CRD42020218058.
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Affiliation(s)
- Yuhang Wang
- Center of Medicine Clinical Research, Department of Pharmacy, Medical Supplies Center of PLA General Hospital, Beijing, China
| | - Jin Wang
- Center of Medicine Clinical Research, Department of Pharmacy, Medical Supplies Center of PLA General Hospital, Beijing, China
| | - Li Chen
- Department of Information, PLA General Hospital, Beijing, China
| | - Huan Zhang
- Center of Medicine Clinical Research, Department of Pharmacy, Medical Supplies Center of PLA General Hospital, Beijing, China
| | - Ling Yu
- Laboratory of Department of Pulmonary and Critical Care Medicine, PLA General Hospital, Beijing, China
| | - Yulong Chi
- Center of Medicine Clinical Research, Department of Pharmacy, Medical Supplies Center of PLA General Hospital, Beijing, China
| | - Mengli Chen
- Department of Pharmacy, Medical Supplies Center of PLA General Hospital, Beijing, China
| | - Yun Cai
- Center of Medicine Clinical Research, Department of Pharmacy, Medical Supplies Center of PLA General Hospital, Beijing, China
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Zhu Z, Camargo CA, Raita Y, Freishtat RJ, Fujiogi M, Hahn A, Mansbach JM, Spergel JM, Pérez-Losada M, Hasegawa K. Nasopharyngeal airway dual-transcriptome of infants with severe bronchiolitis and risk of childhood asthma: A multicenter prospective study. J Allergy Clin Immunol 2022; 150:806-816. [PMID: 35483507 PMCID: PMC9547815 DOI: 10.1016/j.jaci.2022.04.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 03/26/2022] [Accepted: 04/08/2022] [Indexed: 11/20/2022]
Abstract
BACKGROUND Severe bronchiolitis (ie, bronchiolitis requiring hospitalization) during infancy is a major risk factor for childhood asthma. However, the exact mechanism linking these common conditions remains unclear. OBJECTIVES This study sought to examine the integrated role of airway microbiome (both taxonomy and function) and host response in asthma development in this high-risk population. METHODS This multicenter prospective cohort study of 244 infants with severe bronchiolitis (median age, 3 months) examined the infants' nasopharyngeal metatranscriptomes (microbiomes) and transcriptomes (hosts), as well as metabolomes at hospitalization. The longitudinal relationships investigated include (1) major bacterial species (Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis), (2) microbial function, and (3) host response with risks of developing asthma by age 6 years. RESULTS First, the abundance of S pneumoniae was associated with greater risks of asthma (P = .01), particularly in infants with nonrhinovirus infection (Pinteraction = .04). Second, of 328 microbial functional pathways that are differentially enriched by asthma development, the top pathways (eg, fatty acid and glycolysis pathways; false discovery rate [FDR] < 1 × 10-12) were driven by these 3 major species (eg, positive association of S pneumoniae with glycolysis; FDR < 0.001). These microbial functional pathways were validated with the parallel metabolome data. Third, 104 transcriptome pathways were differentially enriched (FDR < .05)-for example, downregulated interferon-α and -γ and upregulated T-cell activation pathways. S pneumoniae was associated with most differentially expressed transcripts (eg, DAGLB; FDR < 0.05). CONCLUSIONS By applying metatranscriptomic, transcriptomic, and metabolomic approaches to a multicenter cohort of infants with bronchiolitis, this study found an interplay between major bacterial species, their function, and host response in the airway, and their longitudinal relationship with asthma development.
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Affiliation(s)
- Zhaozhong Zhu
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, Mass.
| | - Carlos A Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, Mass
| | - Yoshihiko Raita
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, Mass
| | - Robert J Freishtat
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC; Division of Emergency Medicine, Children's National Hospital, Washington, DC; Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Michimasa Fujiogi
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, Mass
| | - Andrea Hahn
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC; Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC; Division of Infectious Diseases, Children's National Hospital, Washington, DC
| | - Jonathan M Mansbach
- Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, Mass
| | - Jonathan M Spergel
- Division of Allergy and Immunology, Children's Hospital of Philadelphia, Perelman School of Medicine at University of Pennsylvania, Philadelphia, Pa
| | - Marcos Pérez-Losada
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, George Washington University School of Medicine and Health Sciences, Washington, DC; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Boston, Mass
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Cao X, Ding L, Mersha TB. Development and validation of an RNA-seq-based transcriptomic risk score for asthma. Sci Rep 2022; 12. [PMID: 35606385 PMCID: PMC9126925 DOI: 10.1038/s41598-022-12199-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/04/2022] [Indexed: 11/30/2022] Open
Abstract
Recent progress in RNA sequencing (RNA-seq) allows us to explore whole-genome gene expression profiles and to develop predictive model for disease risk. The objective of this study was to develop and validate an RNA-seq-based transcriptomic risk score (RSRS) for disease risk prediction that can simultaneously accommodate demographic information. We analyzed RNA-seq gene expression data from 441 asthmatic and 254 non-asthmatic samples. Logistic least absolute shrinkage and selection operator (Lasso) regression analysis in the training set identified 73 differentially expressed genes (DEG) to form a weighted RSRS that discriminated asthmatics from healthy subjects with area under the curve (AUC) of 0.80 in the testing set after adjustment for age and gender. The 73-gene RSRS was validated in three independent RNA-seq datasets and achieved AUCs of 0.70, 0.77 and 0.60, respectively. To explore their biological and molecular functions in asthma phenotype, we examined the 73 genes by enrichment pathway analysis and found that these genes were significantly (p < 0.0001) enriched for DNA replication, recombination, and repair, cell-to-cell signaling and interaction, and eumelanin biosynthesis and developmental disorder. Further in-silico analyses of the 73 genes using Connectivity map shows that drugs (mepacrine, dactolisib) and genetic perturbagens (PAK1, GSR, RBM15 and TNFRSF12A) were identified and could potentially be repurposed for treating asthma. These findings show the promise for RNA-seq risk scores to stratify and predict disease risk.
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Perez-Garcia J, Herrera-Luis E, Lorenzo-Diaz F, González M, Sardón O, Villar J, Pino-Yanes M. Precision Medicine in Childhood Asthma: Omic Studies of Treatment Response. Int J Mol Sci 2020; 21:E2908. [PMID: 32326339 DOI: 10.3390/ijms21082908] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/11/2020] [Accepted: 04/17/2020] [Indexed: 12/12/2022] Open
Abstract
Asthma is a heterogeneous and multifactorial respiratory disease with an important impact on childhood. Difficult-to-treat asthma is not uncommon among children, and it causes a high burden to the patient, caregivers, and society. This review aims to summarize the recent findings on pediatric asthma treatment response revealed by different omic approaches conducted in 2018–2019. A total of 13 studies were performed during this period to assess the role of genomics, epigenomics, transcriptomics, metabolomics, and the microbiome in the response to short-acting beta agonists, inhaled corticosteroids, and leukotriene receptor antagonists. These studies have identified novel associations of genetic markers, epigenetic modifications, metabolites, bacteria, and molecular mechanisms involved in asthma treatment response. This knowledge will allow us establishing molecular biomarkers that could be integrated with clinical information to improve the management of children with asthma.
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