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Cremades-Jimeno L, de Pedro MÁ, López-Ramos M, Sastre J, Mínguez P, Fernández IM, Baos S, Cárdaba B. Prioritizing Molecular Biomarkers in Asthma and Respiratory Allergy Using Systems Biology. Front Immunol 2021; 12:640791. [PMID: 33936056 PMCID: PMC8081895 DOI: 10.3389/fimmu.2021.640791] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/15/2021] [Indexed: 01/29/2023] Open
Abstract
Highly prevalent respiratory diseases such as asthma and allergy remain a pressing health challenge. Currently, there is an unmet need for precise diagnostic tools capable of predicting the great heterogeneity of these illnesses. In a previous study of 94 asthma/respiratory allergy biomarker candidates, we defined a group of potential biomarkers to distinguish clinical phenotypes (i.e. nonallergic asthma, allergic asthma, respiratory allergy without asthma) and disease severity. Here, we analyze our experimental results using complex algorithmic approaches that establish holistic disease models (systems biology), combining these insights with information available in specialized databases developed worldwide. With this approach, we aim to prioritize the most relevant biomarkers according to their specificity and mechanistic implication with molecular motifs of the diseases. The Therapeutic Performance Mapping System (Anaxomics’ TPMS technology) was used to generate one mathematical model per disease: allergic asthma (AA), non-allergic asthma (NA), and respiratory allergy (RA), defining specific molecular motifs for each. The relationship of our molecular biomarker candidates and each disease was analyzed by artificial neural networks (ANNs) scores. These analyses prioritized molecular biomarkers specific to the diseases and to particular molecular motifs. As a first step, molecular characterization of the pathophysiological processes of AA defined 16 molecular motifs: 2 specific for AA, 2 shared with RA, and 12 shared with NA. Mechanistic analysis showed 17 proteins that were strongly related to AA. Eleven proteins were associated with RA and 16 proteins with NA. Specificity analysis showed that 12 proteins were specific to AA, 7 were specific to RA, and 2 to NA. Finally, a triggering analysis revealed a relevant role for AKT1, STAT1, and MAPK13 in all three conditions and for TLR4 in asthmatic diseases (AA and NA). In conclusion, this study has enabled us to prioritize biomarkers depending on the functionality associated with each disease and with specific molecular motifs, which could improve the definition and usefulness of new molecular biomarkers.
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Affiliation(s)
- Lucía Cremades-Jimeno
- Immunology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - María Ángeles de Pedro
- Immunology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - María López-Ramos
- Immunology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Joaquín Sastre
- Allergy Department, Fundación Jiménez Díaz, Madrid, Spain.,Center for Biomedical Network of Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - Pablo Mínguez
- Department of Genetics, IIS-Fundación Jiménez Díaz, UAM, Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | | | - Selene Baos
- Immunology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Blanca Cárdaba
- Immunology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Center for Biomedical Network of Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
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Bergantini L, d'Alessandro M, Cameli P, Bianchi F, Sestini P, Bargagli E, Refini RM. Personalized Approach of Severe Eosinophilic Asthma Patients Treated with Mepolizumab and Benralizumab. Int Arch Allergy Immunol 2020; 181:746-753. [PMID: 32731216 DOI: 10.1159/000508936] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 05/25/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND New anti-IL-5 antibodies, mepolizumab and benralizumab, have recently been approved for severe asthma, sharing the same inclusion criteria. OBJECTIVE To contribute on biomarkers research leading to the personalized choice, we investigated L-selectin, Krebs von den Lungen (KL-6), and lymphocyte subsets as bioindicators of airway hyper-responsiveness and remodeling. MATERIALS AND METHODS A cohort of 28 patients affected by severe eosinophilic asthma were treated with anti-IL-5 drugs. According to clinical parameters, patients were subdivided into early and partial responders. Lymphocytes subsets were analyzed through flow cytometry, while KL-6 and sL-selectin were analyzed on serum samples. Clinical, functional, and immunological data at baseline (T0), after 1 month (T1), and 6 months of therapy were collected in a database. RESULTS All treated patients showed an increase in the percentage of forced expiratory volume in the first second (FEV1) and FEV1/forced vital capacity ratio and a decrease of peripheral eosinophils for both drugs after 1 month of treatment. Mepolizumab-treated patients also showed decreased CD8+ and NKT-like cell percentages and a significant increase in sL-selectin concentrations between T0 and T1. Stratifying the cohort of our patients in early and partial responders at T0, they showed a reduction of peripheral eosinophils, sL-selectin and KL-6, while no differences were found at T0 between early and partial responders patients treated with benralizumab. CONCLUSIONS This real-life study provides new insights for the personalized approach to severe asthma therapy. Although preliminary, the results indicate that besides eosinophils, KL-6 and sL-selectin are useful as biomarkers of early response that can also involve in the pathogenesis of severe asthma.
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Affiliation(s)
- Laura Bergantini
- Department of Medical Sciences, Surgery and Neuroscience, Respiratory Disease and Lung Transplant Unit, Siena University, Siena, Italy,
| | - Miriana d'Alessandro
- Department of Medical Sciences, Surgery and Neuroscience, Respiratory Disease and Lung Transplant Unit, Siena University, Siena, Italy
| | - Paolo Cameli
- Department of Medical Sciences, Surgery and Neuroscience, Respiratory Disease and Lung Transplant Unit, Siena University, Siena, Italy
| | - Francesco Bianchi
- Department of Medical Sciences, Surgery and Neuroscience, Respiratory Disease and Lung Transplant Unit, Siena University, Siena, Italy
| | - Piersante Sestini
- Department of Medical Sciences, Surgery and Neuroscience, Respiratory Disease and Lung Transplant Unit, Siena University, Siena, Italy
| | - Elena Bargagli
- Department of Medical Sciences, Surgery and Neuroscience, Respiratory Disease and Lung Transplant Unit, Siena University, Siena, Italy
| | - Rosa Metella Refini
- Department of Medical Sciences, Surgery and Neuroscience, Respiratory Disease and Lung Transplant Unit, Siena University, Siena, Italy
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Cai P, Jiang T, Li B, Qin X, Lu Z, Le Y, Shen C, Yang Y, Zheng L, Zhao J. Comparison of rheumatoid arthritis (RA) and osteoarthritis (OA) based on microarray profiles of human joint fibroblast-like synoviocytes. Cell Biochem Funct 2018; 37:31-41. [PMID: 30468518 DOI: 10.1002/cbf.3370] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/15/2018] [Accepted: 10/30/2018] [Indexed: 12/22/2022]
Abstract
The purpose of the present study was to investigate the underlying molecular mechanism of osteoarthritis (OA) and rheumatoid arthritis (RA) based on microarray profiles. Three human joint fibroblast-like synoviocytes (FLSs) microarray profiles including 26 OA samples, 33 RA samples, and 20 healthy control (HC) samples were downloaded from the GEO database. Differentially expressed genes (DEGs) between OA and HC (DEGsOA) and RA and HC (DEGsRA) were identified. Co-expressed and specific genes were analysed between DEGsOA and DEGsRA. Gene ontology, KEGG pathway enrichment, PPI network, and GSEA were performed to predict the function of DEGs. Two hundred seventy-six and 410 differential genes in DEGsOA and DEGsRA were observed. One hundred fifty coexpressed genes and 126 OA-specific genes (SELE, SERPINE1, and NFKBIA were the key genes) between DEGsOA and DEGsRA were enriched in the tumour necrosis factor (TNF) signalling pathway. However, 260 RA-specific genes of which the key genes were CCR5, CCR7, CXCR4, CCL5, and CCR4 were enriched in chemokine signalling pathway. Therefore, FLSs might exert an inflammatory effect by regulating TNF signalling pathway, targeting SELE, SERPINE1, and NFKBIA during the process of OA. Although TNF signalling pathway was also involved in the synovitis of RA, chemokine signalling pathway played the key role in RA FLSs mediating cell migration, invasion, and release of chemotaxis. In addition, CCR5, CCR7, CXCR4, CCL5, and CCR4 might be hub genes in RA. The different biomarkers and pathways identified in OA and RA may provide references for further study. SIGNIFICANCE OF THE STUDY: This study revealed the similar and different mechanisms of FLSs and different biomarkers that might with important regulatory effects on RA and OA. In OA, FLSs played an inflammatory role through TNF signalling pathway, targeting SELE, SERPINE1, and NFKBIA. Although TNF signalling pathway was also involved in the synovitis of RA, chemokine signalling pathway was a crucial pathway in mediating FLSs migration, invasion, and release of chemotaxis. CCR5, CCR7, CXCR4, CCL5, and CCR4 might be keys genes in RA. We expect that our results will bring more comprehensively understanding between RA and OA for researchers.
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Affiliation(s)
- Peian Cai
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, Guangxi Collaborative Innovation Center for Biomedicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Department of Orthopaedics Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Tongmeng Jiang
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, Guangxi Collaborative Innovation Center for Biomedicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Department of Orthopaedics Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Department of Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Bo Li
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, Guangxi Collaborative Innovation Center for Biomedicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Department of Orthopaedics Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiong Qin
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, Guangxi Collaborative Innovation Center for Biomedicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Department of Orthopaedics Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhenhui Lu
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, Guangxi Collaborative Innovation Center for Biomedicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of Regenerative Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yiguan Le
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, Guangxi Collaborative Innovation Center for Biomedicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Department of Orthopaedics Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chong Shen
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, Guangxi Collaborative Innovation Center for Biomedicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Department of Orthopaedics Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yifeng Yang
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, Guangxi Collaborative Innovation Center for Biomedicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Department of Orthopaedics Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Li Zheng
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, Guangxi Collaborative Innovation Center for Biomedicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of Regenerative Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jinmin Zhao
- Guangxi Engineering Center in Biomedical Materials for Tissue and Organ Regeneration, Guangxi Collaborative Innovation Center for Biomedicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Department of Orthopaedics Trauma and Hand Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Department of Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of Regenerative Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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Eini P, Shirvani M, Hajilooi M, Esna-Ashari F. Comparison of L-selectin blood level and gene polymorphism in tuberculosis patients with healthy individuals. J Clin Lab Anal 2018; 32:e22409. [PMID: 29430726 DOI: 10.1002/jcla.22409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 01/22/2018] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND The inflammatory response to Mycobacterium tuberculosis bacilli influences tuberculosis (TB) progression. In this study, we aimed to identify the Phe206Leu polymorphism and serum L-selectin level in TB patients, compared to healthy individuals. METHODS Ninety patients with a diagnosis of TB and 90 healthy controls were selected in this study. The serum L-selectin level was determined, using ELISA. L-selectin polymorphism was also evaluated using PCR. For data analysis, SPSS was used at a significance level of 0.05. RESULTS According to the findings, the mean±SD age of the participants was 57.5 ± 18.4 and 56.5 ± 17.5 years in the TB and healthy groups, respectively. The TB group showed a significantly higher serum L-selectin level (1721.1 ± 330.9) versus the healthy controls (1624 ± 279). The L-selectin Phe allele frequencies were higher than the Leu allele frequencies in the main population, whereas the patients and controls were not significantly different. Eight (0.04%) subjects had Leu/Leu genotypes, 84 (46.6%) carried Phe/Leu genotypes, and 88 (48.8%) had Phe/Phe genotypes. Our results showed that the groups were not significantly different regarding L-selectin genotypes. CONCLUSION TB patients had a significantly higher serum L-selectin level, compared to the controls. Based on the findings, the incidence of TB and L-selectin polymorphism in the Phe206Leu gene had no significant association.
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Affiliation(s)
- Peyman Eini
- Department of Infectious Diseases, Hamadan University of Medical Sciences, Hamadan, Iran.,Brucellosis Research Center, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Maria Shirvani
- Department of Infectious Diseases, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mehrdad Hajilooi
- Department of Immunology, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Farzaneh Esna-Ashari
- Department of Community and Preventive Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
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Singh J, Shah R, Singh D. Inundation of asthma target research: Untangling asthma riddles. Pulm Pharmacol Ther 2016; 41:60-85. [PMID: 27667568 DOI: 10.1016/j.pupt.2016.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 08/11/2016] [Accepted: 09/20/2016] [Indexed: 12/31/2022]
Abstract
Asthma is an inveterate inflammatory disorder, delineated by the airway inflammation, bronchial hyperresponsiveness (BHR) and airway wall remodeling. Although, asthma is a vague term, and is recognized as heterogenous entity encompassing different phenotypes. Targeting single mediator or receptor did not prove much clinical significant, as asthma is complex disease involving myriad inflammatory mediators. Asthma may probably involve a large number of different types of molecular and cellular components interacting through complex pathophysiological pathways. This review covers the past, present, and future therapeutic approaches and pathophysiological mechanisms of asthma. Furthermore, review describe importance of targeting several mediators/modulators and receptor antagonists involved in the physiopathology of asthma. Novel targets for asthma research include Galectins, Immunological targets, K + Channels, Kinases and Transcription Factors, Toll-like receptors, Selectins and Transient receptor potential channels. But recent developments in asthma research are very promising, these include Bitter taste receptors (TAS2R) abated airway obstruction in mouse model of asthma and Calcium-sensing receptor obliterate inflammation and in bronchial hyperresponsiveness allergic asthma. All these progresses in asthma targets, and asthma phenotypes exploration are auspicious in untangling of asthma riddles.
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Affiliation(s)
- Jatinder Singh
- Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, 147002, Punjab, India
| | - Ramanpreet Shah
- Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, 147002, Punjab, India
| | - Dhandeep Singh
- Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, 147002, Punjab, India.
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