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Sun P, Liu X, Wang Y, Shen R, Chen X, Li Z, Cui D, Wang J, Wang Q. Molecular characterization of allergic constitution based on network pharmacology and multi-omics analysis methods. Medicine (Baltimore) 2024; 103:e36892. [PMID: 38363941 PMCID: PMC10869101 DOI: 10.1097/md.0000000000036892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/18/2023] [Indexed: 02/18/2024] Open
Abstract
The objective of this study was to identify critical pathways associated with allergic constitution. Shared genes among allergic rhinitis (AR), asthma (AA), and atopic dermatitis (AD) were extracted from the GWAS catalog. RNA-seq data of AR, AA, and AD from gene expression omnibus (GEO) database were preprocessed and subjected to differential gene expression analysis. The differentially expressed genes (DEGs) were merged using the Robust Rank Aggregation (RRA) algorithm. Weighted gene co-expression network analysis (WGCNA) was performed to identify modules associated with allergies. Components of Guominkang (GMK) were obtained from 6 databases and activate components were identified by SwissADME website. Utilizing the SwissTarget Prediction, PharmMapper, SymMap, and HERB, the targets of GMK were predicted and subsequently validated using gene chip data from our team previous study. Differentially expressed proteins (DEPs) related to the allergic constitution were also extracted based on a previous study. Pathway enrichment analysis was performed using KOBAS-i on the GWAS, RRA, WGCNA modules, DEPs, and GMK targets. P values from multi-omics datasets were combined by meta-analysis, and Bonferroni correction was applied. The significant pathways were further validated using Gene Set Enrichment Analysis (GSEA) with intervention data of GMK. The GWAS results yielded 172 genes. Four datasets AR1, AA1, AD1, and AD2 were acquired from GSE75011, GSE125916, and GSE184237. The RRA algorithm identified 19 upregulated and 20 downregulated genes. WGCNA identified 5 significant modules, with the blue and turquoise modules displaying a moderate correlation with allergies. By performing network pharmacology analysis, we identified 127 active ingredients of GMK and predicted 618 targets. Validation using gene chip data confirmed 107 GMK targets. Single-omics pathway analysis was conducted using KOBAS-i, and 39 significant pathways were identified across multiple omics datasets. GSEA analysis using GMK intervention data identified 11 of 39 significant pathways as the final key pathways associated with the allergic constitution. Through multi-omics integrated pathway analysis, we identified 11 critical pathways of allergic constitution, including TH1 and TH2 cell differentiation, TLR cascade, and TH17 cell differentiation. Identifying these pathways suggests that the observed alterations at the pathway level may play significant roles in the molecular characteristics of the allergic constitution.
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Affiliation(s)
- Pengcheng Sun
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Xing Liu
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Yi Wang
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Rongmin Shen
- Beijing Heniantang Traditional Chinese Medicine Hospital, Beijing, China
| | - Xuemei Chen
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Zhuqing Li
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Diankun Cui
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Ji Wang
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Qi Wang
- National Institute of Traditional Chinese Medicine Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, China
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Rae W, Sowerby JM, Verhoeven D, Youssef M, Kotagiri P, Savinykh N, Coomber EL, Boneparth A, Chan A, Gong C, Jansen MH, du Long R, Santilli G, Simeoni I, Stephens J, Wu K, Zinicola M, Allen HL, Baxendale H, Kumararatne D, Gkrania-Klotsas E, Scheffler Mendoza SC, Yamazaki-Nakashimada MA, Ruiz LB, Rojas-Maruri CM, Lugo Reyes SO, Lyons PA, Williams AP, Hodson DJ, Bishop GA, Thrasher AJ, Thomas DC, Murphy MP, Vyse TJ, Milner JD, Kuijpers TW, Smith KGC. Immunodeficiency, autoimmunity, and increased risk of B cell malignancy in humans with TRAF3 mutations. Sci Immunol 2022; 7:eabn3800. [PMID: 35960817 DOI: 10.1126/sciimmunol.abn3800] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Tumor necrosis factor receptor-associated factor 3 (TRAF3) is a central regulator of immunity. TRAF3 is often somatically mutated in B cell malignancies, but its role in human immunity is not defined. Here, in five unrelated families, we describe an immune dysregulation syndrome of recurrent bacterial infections, autoimmunity, systemic inflammation, B cell lymphoproliferation, and hypergammaglobulinemia. Affected individuals each had monoallelic mutations in TRAF3 that reduced TRAF3 expression. Immunophenotyping showed that patients' B cells were dysregulated, exhibiting increased nuclear factor-κB 2 activation, elevated mitochondrial respiration, and heightened inflammatory responses. Patients had mild CD4+ T cell lymphopenia, with a reduced proportion of naïve T cells but increased regulatory T cells and circulating T follicular helper cells. Guided by this clinical phenotype, targeted analyses demonstrated that common genetic variants, which also reduce TRAF3 expression, are associated with an increased risk of B cell malignancies, systemic lupus erythematosus, higher immunoglobulin levels, and bacterial infections in the wider population. Reduced TRAF3 conveys disease risks by driving B cell hyperactivity via intrinsic activation of multiple intracellular proinflammatory pathways and increased mitochondrial respiration, with a likely contribution from dysregulated T cell help. Thus, we define monogenic TRAF3 haploinsufficiency syndrome and demonstrate how common TRAF3 variants affect a range of human diseases.
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Affiliation(s)
- William Rae
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - John M Sowerby
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Dorit Verhoeven
- Emma Children's Hospital, Amsterdam University Medical Center (AUMC), University of Amsterdam, Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Amsterdam, Netherlands
- Amsterdam University Medical Center (AUMC), University of Amsterdam, Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands
| | - Mariam Youssef
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Prasanti Kotagiri
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Natalia Savinykh
- NIHR Cambridge BRC Cell Phenotyping Hub, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Eve L Coomber
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alexis Boneparth
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Angela Chan
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Chun Gong
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Machiel H Jansen
- Emma Children's Hospital, Amsterdam University Medical Center (AUMC), University of Amsterdam, Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Amsterdam, Netherlands
- Amsterdam University Medical Center (AUMC), University of Amsterdam, Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands
| | - Romy du Long
- Amsterdam University Center (AUMC), University of Amsterdam, Department of Pathology, Amsterdam, Netherlands
| | | | - Ilenia Simeoni
- Department of Hematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- NIHR Bioresource-Rare Diseases, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
| | - Jonathan Stephens
- Department of Hematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- NIHR Bioresource-Rare Diseases, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
| | - Kejia Wu
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Marta Zinicola
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Hana Lango Allen
- NIHR Bioresource-Rare Diseases, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, UK
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Helen Baxendale
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge, UK
| | - Dinakantha Kumararatne
- Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK
| | - Effrossyni Gkrania-Klotsas
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
- Department of Infectious Diseases, Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Selma C Scheffler Mendoza
- Clinical Immunology Service, National Institute of Pediatrics, Secretariat of Health, Mexico City, Mexico
| | | | - Laura Berrón Ruiz
- Immune Deficiencies Laboratory, National Institute of Pediatrics, Secretariat of Health, Mexico City, Mexico
| | | | - Saul O Lugo Reyes
- Immune Deficiencies Laboratory, National Institute of Pediatrics, Secretariat of Health, Mexico City, Mexico
| | - Paul A Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Anthony P Williams
- Wessex Investigational Sciences Hub, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Daniel J Hodson
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Gail A Bishop
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
- Department of Internal Medicine, University of Iowa, IA, USA
- Veterans Affairs Medical Center, Iowa City, IA, USA
| | - Adrian J Thrasher
- UCL Great Ormond Street Institute of Child Health, London, UK
- Great Ormond Street Hospital for Children, NHS Foundation Trust, London, UK
| | - David C Thomas
- Department of Immunology and Inflammation, Center for Inflammatory Diseases, Imperial College London, London, UK
| | - Michael P Murphy
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge, UK
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Timothy J Vyse
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Joshua D Milner
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Taco W Kuijpers
- Emma Children's Hospital, Amsterdam University Medical Center (AUMC), University of Amsterdam, Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Amsterdam, Netherlands
- Amsterdam University Medical Center (AUMC), University of Amsterdam, Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam, Netherlands
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge School of Clinical Medicine, University of Cambridge, Cambridge, UK
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3
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Chen X, Wang R, Meng W, Zhang X. Exploration of the Molecular Mechanism of FUZI (Aconiti Lateralis Radix Praeparata) in Allergic Rhinitis Treatment Based on Network Pharmacology. Med Sci Monit 2020; 26:e920872. [PMID: 32114589 PMCID: PMC7065509 DOI: 10.12659/msm.920872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
FUZI (Aconiti Lateralis Radix Praeparata) is a traditional Chinese medicine herb used extensively for nourishing yang (regarded as the positive, male universal force), which is critical in treatment of allergic rhinitis. In this paper, FUZI was explored based on network pharmacology. The active components of FUZI were screened out, its protein targets were assessed, and the protein interaction network map was built with the differential protein of allergic rhinitis, as an attempt to determine the critical targets of FUZI for treating allergic rhinitis. Subsequently, DAVID was employed to explore the biological function and pathway enrichment to determine the biological pathway of FUZI for treating allergic rhinitis. As suggested by the results, FUZI is likely to affect the inhibition of inflammation and the regulation of immunity, probably reducing the incidence of allergic rhinitis, or alleviating nasal discomfort attributed to allergic inflammation. The targets and pathways of FUZI for treating allergic rhinitis assessed by network pharmacology provided a direction for our subsequent studies and may be a novel therapeutic target.
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Affiliation(s)
- Xiangjing Chen
- The First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China (mainland)
| | - Renzhong Wang
- Department of Otorhinolaryngology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China (mainland)
| | - Wei Meng
- Department of Otorhinolaryngology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China (mainland)
| | - Xin Zhang
- The First Clinical Medical College, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, China (mainland)
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Rodríguez-Galán A, Fernández-Messina L, Sánchez-Madrid F. Control of Immunoregulatory Molecules by miRNAs in T Cell Activation. Front Immunol 2018; 9:2148. [PMID: 30319616 PMCID: PMC6167432 DOI: 10.3389/fimmu.2018.02148] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 08/30/2018] [Indexed: 01/01/2023] Open
Abstract
MiRNA targeting of key immunoregulatory molecules fine-tunes the immune response. This mechanism boosts or dampens immune functions to preserve homeostasis while supporting the full development of effector functions. MiRNA expression changes during T cell activation, highlighting that their function is constrained by a specific spatiotemporal frame related to the signals that induce T cell-based effector functions. Here, we update the state of the art regarding the miRNAs that are differentially expressed during T cell stimulation. We also revisit the existing data on miRNA function in T cell activation, with a special focus on the modulation of the most relevant immunoregulatory molecules.
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Affiliation(s)
- Ana Rodríguez-Galán
- Servicio de Inmunología, Instituto de Investigación Sanitaria Princesa (IP), Hospital Universitario de la Princesa, Universidad Autónoma de Madrid, Madrid, Spain.,Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Lola Fernández-Messina
- Servicio de Inmunología, Instituto de Investigación Sanitaria Princesa (IP), Hospital Universitario de la Princesa, Universidad Autónoma de Madrid, Madrid, Spain.,Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
| | - Francisco Sánchez-Madrid
- Servicio de Inmunología, Instituto de Investigación Sanitaria Princesa (IP), Hospital Universitario de la Princesa, Universidad Autónoma de Madrid, Madrid, Spain.,Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, Madrid, Spain
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7
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Lu HY, Bauman BM, Arjunaraja S, Dorjbal B, Milner JD, Snow AL, Turvey SE. The CBM-opathies-A Rapidly Expanding Spectrum of Human Inborn Errors of Immunity Caused by Mutations in the CARD11-BCL10-MALT1 Complex. Front Immunol 2018; 9:2078. [PMID: 30283440 PMCID: PMC6156466 DOI: 10.3389/fimmu.2018.02078] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 08/22/2018] [Indexed: 01/06/2023] Open
Abstract
The caspase recruitment domain family member 11 (CARD11 or CARMA1)-B cell CLL/lymphoma 10 (BCL10)-MALT1 paracaspase (MALT1) [CBM] signalosome complex serves as a molecular bridge between cell surface antigen receptor signaling and the activation of the NF-κB, JNK, and mTORC1 signaling axes. This positions the CBM complex as a critical regulator of lymphocyte activation, proliferation, survival, and metabolism. Inborn errors in each of the CBM components have now been linked to a diverse group of human primary immunodeficiency diseases termed "CBM-opathies." Clinical manifestations range from severe combined immunodeficiency to selective B cell lymphocytosis, atopic disease, and specific humoral defects. This surprisingly broad spectrum of phenotypes underscores the importance of "tuning" CBM signaling to preserve immune homeostasis. Here, we review the distinct clinical and immunological phenotypes associated with human CBM complex mutations and introduce new avenues for targeted therapeutic intervention.
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Affiliation(s)
- Henry Y Lu
- Department of Pediatrics, British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC, Canada.,Experimental Medicine Program, Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada
| | - Bradly M Bauman
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Swadhinya Arjunaraja
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Batsukh Dorjbal
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Joshua D Milner
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Andrew L Snow
- Department of Pharmacology and Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, MD, United States
| | - Stuart E Turvey
- Department of Pediatrics, British Columbia Children's Hospital, The University of British Columbia, Vancouver, BC, Canada.,Experimental Medicine Program, Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada
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