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Zhang YD, Chen YR, Zhang W, Tang BQ. Assessing prospective molecular biomarkers and functional pathways in severe asthma based on a machine learning method and bioinformatics analyses. J Asthma 2024:1-16. [PMID: 39392250 DOI: 10.1080/02770903.2024.2409991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 09/14/2024] [Accepted: 09/24/2024] [Indexed: 10/12/2024]
Abstract
BACKGROUND Severe asthma, which differs significantly from typical asthma, involves specific molecular biomarkers that enhance our understanding and diagnostic capabilities. The objective of this study is to assess the biological processes underlying severe asthma and to detect key molecular biomarkers. METHODS We used Weighted Gene Co-Expression Network Analysis (WGCNA) to detect hub genes in the GSE143303 dataset and indicated their functions and regulatory mechanisms using Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Gene Ontology (GO) annotations. In the GSE147878 dataset, we used Gene Set Enrichment Analysis (GSEA) to determine the regulatory directions of gene sets. We detected differentially expressed genes in the GSE143303 and GSE64913 datasets, constructed a Least Absolute Shrinkage and Selection Operator (LASSO) regression model, and validated the model using the GSE147878 dataset and real-time quantitative PCR (RT-qPCR) to confirm the molecular biomarkers. RESULTS Using WGCNA, we discovered modules that were strongly correlated with clinical features, specifically the purple module (r = 0.53) and the midnight blue module (r = -0.65). The hub genes within these modules were enriched in pathways related to mitochondrial function and oxidative phosphorylation. GSEA in the GSE147878 dataset revealed significant enrichment of upregulated gene sets associated with oxidative phosphorylation and downregulated gene sets related to asthma. We discovered 12 commonly regulated genes in the GSE143303 and GSE64913 datasets and developed a LASSO regression model. The model corresponding to lambda.min selected nine genes, including TFCP2L1, KRT6A, FCER1A, and CCL5, which demonstrated predictive value. These genes were significantly upregulated or under expressed in severe asthma, as validated by RT-qPCR. CONCLUSION Mitochondrial abnormalities affecting oxidative phosphorylation play a critical role in severe asthma. Key molecular biomarkers like TFCP2L1, KRT6A, FCER1A, and CCL5, are essential for detecting severe asthma. This research significantly enhances the understanding and diagnosis of severe asthma.
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Affiliation(s)
- Ya-Da Zhang
- Department of Pneumology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yi-Ren Chen
- Department of Pneumology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wei Zhang
- Department of Pulmonary Disease, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Bin-Qing Tang
- Department of Pneumology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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2
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Slimmen LJM, Giacalone VD, Schofield C, Horati H, Manaï BHAN, Estevão SC, Garratt LW, Peng L, Tirouvanziam R, Janssens HM, Unger WWJ. Airway macrophages display decreased expression of receptors mediating and regulating scavenging in early cystic fibrosis lung disease. Front Immunol 2023; 14:1202009. [PMID: 37457715 PMCID: PMC10338875 DOI: 10.3389/fimmu.2023.1202009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/05/2023] [Indexed: 07/18/2023] Open
Abstract
Background Cystic fibrosis (CF) airway disease is characterized by chronic inflammation, featuring neutrophil influx to the lumen. Airway macrophages (AMs) can promote both inflammation and resolution, and are thus critical to maintaining and restoring homeostasis. CF AM functions, specifically scavenging activity and resolution of inflammation, have been shown to be impaired, yet underlying processes remain unknown. We hypothesized that impaired CF AM function results from an altered expression of receptors that mediate or regulate scavenging, and set out to investigate changes in expression of these markers during the early stages of CF lung disease. Methods Bronchoalveolar lavage fluid (BALF) was collected from 50 children with CF aged 1, 3 or 5 years. BALF cells were analyzed using flow cytometry. Expression levels of surface markers on AMs were expressed as median fluorescence intensities (MFI) or percentage of AMs positive for these markers. The effect of age and neutrophilic inflammation, among other variables, on marker expression was assessed with a multivariate linear regression model. Results AM expression of scavenger receptor CD163 decreased with age (p = 0.016) and was negatively correlated with BALF %neutrophils (r = -0.34, p = 0.016). AM expression of immune checkpoint molecule SIRPα also decreased with age (p = 0.0006), but did not correlate with BALF %neutrophils. Percentage of AMs expressing lipid scavenger CD36 was low overall (mean 20.1% ± 16.5) and did not correlate with other factors. Conversely, expression of immune checkpoint PD-1 was observed on the majority of AMs (mean PD-1pos 72.9% ± 11.8), but it, too, was not affected by age or BALF %neutrophils. Compared to matched blood monocytes, AMs had a higher expression of CD16, CD91, and PD-1, and a lower expression of CD163, SIRPα and CD36. Conclusion In BALF of preschool children with CF, higher age and/or increased neutrophilic inflammation coincided with decreased expression of scavenger receptors on AMs. Expression of scavenging receptors and regulators showed a distinctly different pattern in AMs compared to blood monocytes. These findings suggest AM capacity to counter inflammation and promote homeostasis reduces during initiation of CF airway disease and highlight new avenues of investigation into impaired CF AM function.
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Affiliation(s)
- Lisa J. M. Slimmen
- Division of Respiratory Medicine and Allergology, Department of Pediatrics, Erasmus University Medical Centre, Rotterdam, Netherlands
- Laboratory of Pediatrics, Infection and Immunity Group, Department of Pediatrics, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Vincent D. Giacalone
- Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Craig Schofield
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Hamed Horati
- Division of Respiratory Medicine and Allergology, Department of Pediatrics, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Badies H. A. N. Manaï
- Division of Respiratory Medicine and Allergology, Department of Pediatrics, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Silvia C. Estevão
- Laboratory of Pediatrics, Infection and Immunity Group, Department of Pediatrics, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Luke W. Garratt
- Telethon Kids Institute, University of Western Australia, Perth, WA, Australia
| | - Limin Peng
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Rabindra Tirouvanziam
- Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA, United States
| | - Hettie M. Janssens
- Division of Respiratory Medicine and Allergology, Department of Pediatrics, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Wendy W. J. Unger
- Laboratory of Pediatrics, Infection and Immunity Group, Department of Pediatrics, Erasmus University Medical Centre, Rotterdam, Netherlands
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Mostafa GA, Ibrahim HM, Al Sayed Shehab A, Gendy YGE, Aly DMM, Shousha GAH. Up-regulated serum levels of soluble CD25 and soluble CD163 in pediatric patients with SARS-CoV-2. Eur J Pediatr 2022; 181:2299-2309. [PMID: 35233677 PMCID: PMC8888270 DOI: 10.1007/s00431-022-04398-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/22/2022] [Accepted: 01/25/2022] [Indexed: 02/02/2023]
Abstract
Similar to hemophagocytic lymphohistiocytosis (HLH), some patients with SARS-CoV-2 have cytokine storm. Serum soluble interleukin-2 receptor (sCD25) and soluble CD163 (sCD163) are potential diagnostic biomarkers for HLH that help in guiding its treatment. This study was the first to investigate serum sCD25 and sCD163 levels in SARS-CoV-2. Serum sCD25 and sCD163 were measured by ELISA in 29 patients with SARS-CoV-2, aged between 2 months and 16 years (13 had COVID-19 and 16 had multisystem inflammatory syndrome in children (MIS-C)), in comparison to 30 age- and sex-matched healthy control children and 10 patients with HLH. Levels of these markers were re-measured in 21 patients with SARS-CoV-2 who were followed up 3 months after recovery. Patients with SARS-CoV-2 had significantly higher serum sCD25 and sCD163 than healthy control children (P < 0.001). SARS-CoV-2 patients had significantly higher sCD25 than patients with HLH (P < 0.05). Serum sCD25 was a good differentiating marker between patients with SARS-CoV-2 and HLH. Although there was a significant decrease of serum sCD25 and sCD163 of the 21 SARS-CoV-2 patients who were followed up, these levels were still significantly higher than the healthy controls levels (P < 0.001). Conclusion: Serum sCD25 and sCD163 levels were up-regulated in SARS-CoV-2 patients. Serum sCD25 was a good differentiating marker between SARS-CoV-2 and HLH. This initial report requires further studies, on large scales, to investigate the relationship between SARS-CoV-2 and both sCD25 and sCD163, including the disease severity and outcome. The therapeutic role of sCD25 and sCD163 antagonists should also be studied in SARS-CoV-2 patients. What is Known: • Similar to hemophagocytic lymphohistiocytosis (HLH), some patients with COVID-19 have cytokine storm due to excessive pro-inflammatory host response. • Serum soluble interleukin-2 receptor (sCD25) and soluble CD163 (sCD163) are potential diagnostic biomarkers for HLH. Monitoring of serum sCD25 and sCD163 levels can also help in guiding the treatment. What is New: • Serum sCD25 and sCD163 levels are up-regulated in patients with COVID-19, including patients presenting with multisystem inflammatory syndrome in children (MIS-C). • Serum sCD25 is a good differentiating marker between SARS-CoV-2 and HLH.
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Affiliation(s)
- Gehan Ahmed Mostafa
- Department of Pediatrics, Faculty of Medicine, Ain Shams University, Nasr City, 17 Asem Abd El-Hamid Street off Makram Ebaid, Cairo, Egypt.
| | - Hanan Mohamed Ibrahim
- Department of Pediatrics, Faculty of Medicine, Ain Shams University, Nasr City, 17 Asem Abd El-Hamid Street off Makram Ebaid, Cairo, Egypt
| | - Abeer Al Sayed Shehab
- Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Yasmin Gamal El Gendy
- Department of Pediatrics, Faculty of Medicine, Ain Shams University, Nasr City, 17 Asem Abd El-Hamid Street off Makram Ebaid, Cairo, Egypt
| | - Dina Medhat Mohamed Aly
- Department of Pediatrics, Faculty of Medicine, Ain Shams University, Nasr City, 17 Asem Abd El-Hamid Street off Makram Ebaid, Cairo, Egypt
| | - Ghada Abdel Haleem Shousha
- Department of Pediatrics, Faculty of Medicine, Ain Shams University, Nasr City, 17 Asem Abd El-Hamid Street off Makram Ebaid, Cairo, Egypt
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Zhao MZ, Li Y, Han HY, Mo LH, Yang G, Liu ZQ, Ma C, Yang PC, Liu S. Specific Ag-guiding nano-vaccines attenuate neutrophil-dominant allergic asthma. Mol Immunol 2020; 129:103-111. [PMID: 33229073 DOI: 10.1016/j.molimm.2020.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/23/2020] [Accepted: 11/06/2020] [Indexed: 01/21/2023]
Abstract
Polymorphonuclear neutrophils (PMN) are one fraction of the major inflammatory cells in allergic asthma (asthma, in short); the role of PMN in the asthma pathogenesis is not fully understood yet. This study aims to investigate the effects of specific Ag-guiding exosomes on suppressing the neutrophil-dominant airway inflammation. In this study, BALB/c mice were immunized with ovalbumin plus complete Freund adjuvant to induce an asthma model featured with neutrophil-dominant lung inflammation. The Ag specific PMN (sPMN)-targeting exosomes (tExo), that were exosomes carrying a complex of specific Ag/anti-CD64 Ab and Fas ligand, were constructed to be used to alleviate neutrophilic asthma in mice. We found that sPMNs were the major cellular component in bronchoalveolar lavage fluid (BALF) in asthma mice, while less than 3% PMNs in naive control mice. The sPMNs expressed higher levels of CD64, which formed complexes with Ag-specific IgG (sIgG). The sIgG/CD64 complex-carrying PMNs could be activated upon exposing to specific Ags. Exposure to tExos induced Ag-specific PMNs apoptosis. Administration of tExos efficiently suppressed experimental asthma. We conclude that a fraction of sPMN was identified in the airway of asthma mice. The sPMNs could be activated upon exposure to specific Ags. tExos could induce sPMNs apoptosis, that show the translational potential in the treatment of asthma.
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Affiliation(s)
- Mei-Zhen Zhao
- Guangdong Provincial Key Laboratory of New Drug Screening, State Key Laboratory of Organ Failure Research, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China; Department of Clinical Laboratory, Longgang E.N.T Hospital & Shenzhen Key Laboratory of E.N.T, Institute of E.N.T., Shenzhen, China
| | - Yan Li
- Research Center of Allergy & Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Hai-Yang Han
- Research Center of Allergy & Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Li-Hua Mo
- Research Center of Allergy & Immunology, Shenzhen University School of Medicine, Shenzhen, China
| | - Gui Yang
- Department of Otolaryngology, Longgang Central Hospital, Shenzhen, China
| | - Zhi-Qiang Liu
- Department of Clinical Laboratory, Longgang E.N.T Hospital & Shenzhen Key Laboratory of E.N.T, Institute of E.N.T., Shenzhen, China
| | - Chang Ma
- Department of Respirology, Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Ping-Chang Yang
- Research Center of Allergy & Immunology, Shenzhen University School of Medicine, Shenzhen, China; Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Shenzhen, China.
| | - Shuwen Liu
- Guangdong Provincial Key Laboratory of New Drug Screening, State Key Laboratory of Organ Failure Research, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China.
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Laulajainen-Hongisto A, Toppila-Salmi SK, Luukkainen A, Kern R. Airway Epithelial Dynamics in Allergy and Related Chronic Inflammatory Airway Diseases. Front Cell Dev Biol 2020; 8:204. [PMID: 32292784 PMCID: PMC7118214 DOI: 10.3389/fcell.2020.00204] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/10/2020] [Indexed: 12/12/2022] Open
Abstract
Allergic rhinitis, chronic rhinosinusitis, and asthma are highly prevalent, multifactorial chronic airway diseases. Several environmental and genetic factors affect airway epithelial dynamics leading to activation of inflammatory mechanisms in the airways. This review links environmental factors to host epithelial immunity in airway diseases. Understanding altered homeostasis of the airway epithelium might provide important targets for diagnostics and therapy of chronic airway diseases.
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Affiliation(s)
- Anu Laulajainen-Hongisto
- Department of Otorhinolaryngology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland.,Laboratory of Cellular and Molecular Immunology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czechia
| | - Sanna Katriina Toppila-Salmi
- Haartman Institute, Medicum, University of Helsinki, Helsinki, Finland.,Skin and Allergy Hospital, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Annika Luukkainen
- Haartman Institute, Medicum, University of Helsinki, Helsinki, Finland
| | - Robert Kern
- Department of Otolaryngology, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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Tam JS. Macrophages: Time to Take Notice. Ann Allergy Asthma Immunol 2020; 123:229. [PMID: 31477214 DOI: 10.1016/j.anai.2019.06.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 06/25/2019] [Indexed: 10/26/2022]
Affiliation(s)
- Jonathan S Tam
- Division of Clinical Immunology and Allergy, Department of Pediatrics, Children's Hospital Los Angeles, University of Southern California, Los Angeles, California.
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Abstract
PURPOSE OF REVIEW Asthma is a chronic inflammatory disease in which changes in macrophage polarization have been shown to contribute to the pathogenesis. The present review discusses the contribution of changes in macrophage function to asthma related to polarization changes and elaborates on possible therapeutic strategies targeting macrophage function and polarization. RECENT FINDINGS Macrophage function alterations were shown to contribute to asthma pathology in several ways. One is by impaired phagocytosis and efferocytosis. Another is by changing inflammation, by altered (anti)inflammatory cytokine production and induction of the inflammasome. Finally, macrophages can contribute to remodeling in asthma, although little evidence is present in humans yet.Novel therapeutic strategies targeting macrophages include dampening inflammation by changing polarization or by inhibiting the NLRP3 inflammasome, and by targeting efferocytosis. However, many of these studies were performed in animal models leaving their translation to the clinic for future research. SUMMARY The present review emphasizes the contribution of altered macrophage function to asthma, gives insight in possible new therapeutic strategies targeting macrophages, and indicates which knowledge gaps remain open.
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Affiliation(s)
- T. Anienke van der Veen
- Department of Molecular Pharmacology, Groningen Research Institute for Pharmacy
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen
| | - Linsey E.S. de Groot
- Department of Respiratory Medicine
- Department of Experimental Immunology (Amsterdam Infection & Immunity Institute), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Barbro N. Melgert
- Department of Molecular Pharmacology, Groningen Research Institute for Pharmacy
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen
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8
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Resolution of allergic asthma. Semin Immunopathol 2019; 41:665-674. [PMID: 31705318 DOI: 10.1007/s00281-019-00770-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 10/15/2019] [Indexed: 02/07/2023]
Abstract
Allergic asthma is an inflammatory disease of the airways characterized by recurrent episodes of wheezing and bronchoconstriction. Chronic inflammation may finally lead to structural damage followed by airway remodeling. Various studies in recent years contributed to unravel important aspects of the immunopathogenesis of asthma and adapted new pharmaceutical developments. Here, I consider some novel insights into the immunopathogenesis of asthma and the protective and pathogenic roles of some innate and adaptive immune cells as well as the function of soluble mediators such as cytokines. Particular attention will be given to new concepts on resolution of chronic airway inflammation for prevention of airway structural damage.
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