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El-Hashim AZ, Khajah MA, Orabi KY, Balakrishnan S, Sary HG, Barakat AM. Treatment with onion bulb extract both prevents and reverses allergic inflammation in a murine model of asthma. PHARMACEUTICAL BIOLOGY 2024; 62:326-340. [PMID: 38584568 PMCID: PMC11003327 DOI: 10.1080/13880209.2024.2335187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 03/20/2024] [Indexed: 04/09/2024]
Abstract
CONTEXT Asthma presents a global health challenge. The main pharmacotherapy is synthetic chemicals and biological-based drugs that are costly, and have significant side effects. In contrast, use of natural products, such as onion (Allium cepa L., Amaryllidaceae) in the treatment of airway diseases has increased world-wide because of their perceived efficacy and little safety concerns. However, their pharmacological actions remain largely uncharacterized. OBJECTIVE We investigated whether onion bulb extract (OBE) can (1) reverse established asthma phenotype (therapeutic treatment) and/or (2) prevent the development of the asthma phenotype, if given before the immunization process (preventative treatment). MATERIALS AND METHODS Six groups of male Balb/c mice were established for the therapeutic (21 days) and five groups for the preventative (19 days) treatment protocols; including PBS and house dust mite (HDM)-challenged mice treated with vehicle or OBE (30, 60, and 100 mg/kg/i.p.). Airways inflammation was determined using cytology, histology, immunofluorescence, Western blot, and serum IgE. RESULTS Therapeutic (60 mg/kg/i.p.) and preventative (100 mg/kg/i.p.) OBE treatment resulted in down-regulation of HDM-induced airway cellular influx, histopathological changes and the increase in expression of pro-inflammatory signaling pathway EGFR, ERK1/2, AKT, pro-inflammatory cytokines and serum IgE. DISCUSSION AND CONCLUSION Our data show that OBE is an effective anti-inflammatory agent with both therapeutic and preventative anti-asthma effects. These findings imply that onion/OBE may be used as an adjunct therapeutic agent in established asthma and/or to prevent development of allergic asthma. However, further studies to identify the active constituents, and demonstrate proof-of-concept in humans are needed.
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Affiliation(s)
- Ahmed Z. El-Hashim
- Department of Pharmacology & Therapeutics, Faculty of Pharmacy, Kuwait University, Kuwait City, Kuwait
| | - Maitham A. Khajah
- Department of Pharmacology & Therapeutics, Faculty of Pharmacy, Kuwait University, Kuwait City, Kuwait
| | - Khaled Y. Orabi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kuwait University, Kuwait City, Kuwait
| | - Sowmya Balakrishnan
- Department of Pharmacology & Therapeutics, Faculty of Pharmacy, Kuwait University, Kuwait City, Kuwait
| | - Hanan G. Sary
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kuwait University, Kuwait City, Kuwait
| | - Ahmad M. Barakat
- Department of Pharmacology & Therapeutics, Faculty of Pharmacy, Kuwait University, Kuwait City, Kuwait
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Han X, Wu TQ, Bian Y, Chen L, Feng X. Asthma and risk of adverse pregnancy outcomes: A Mendelian randomization study. Heliyon 2024; 10:e33857. [PMID: 39044964 PMCID: PMC11263667 DOI: 10.1016/j.heliyon.2024.e33857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/25/2024] Open
Abstract
Background Multiple empirical investigations have indicated a connection between asthma and adverse pregnancy outcomes (APOs). Nevertheless, the effects of asthma on APOs remain uncertain. Methods We performed bi-directional Univariable Mendelian randomization (UVMR) analyses using combined information obtained from genome-wide association studies (GWAS) data that is publicly accessible. The principal approach used to analyze the causal association between asthma or age when diagnosed and APOs was the inverse variance weighted (IVW) method. The two types of data regarding exposure originate from the IEU Open GWAS project, which includes 56,167 and 47,222 European asthma patients, respectively. The data of four APOs were acquired via the GWAS dataset of the FinnGen collaboration. In addition, we implemented multivariable Mendelian randomization (MVMR), controlling for confounding factors such as smoking status, frequent drinking, body mass index (BMI), and live birth quantity. Furthermore, we executed several meticulous sensitivity studies to ascertain the reliability of our MR results. Results Following the implementation of the Bonferroni adjustment, the UVMR assessment revealed that in the IVW model, asthma was significantly linked to an elevated risk of spontaneous abortion (SA) (odds ratio [OR]: 1.115; 95 % confidence interval [CI]: 1.031-1.206; P = 0.006) and gestational diabetes mellitus (GDM) (OR: 1.125; 95 % CI: 1.037-1.220; P = 0.005). However, there was no causal correlation between asthma and preterm birth (PTB) (OR: 0.979; 95 % CI: 0.897-1.068; P = 0.629) or preeclampsia (PE) (OR: 1.059; 95 % CI: 0.951-1.179; P = 0.297). After adjusting for confounding factors, including smoking status, frequent drinking, BMI, and live birth quantity, the MVMR analysis shows a statistically significant causal relationship between asthma and SA or GDM. Furthermore, our investigation's findings did not reveal a substantial correlation between the age of asthma onset based on genetics and the likelihood of SA or GDM. The inverse MR outcomes indicate a lack of causal connection linking APOs to the incidence of asthma. The validity of these findings were verified by sensitivity analyses. Conclusions The evidence provided by this study proves that genetically determined asthma is linked to a higher likelihood of SA and GDM. Further research is required to examine potential pathways. However, no conclusive evidence has been found to support the increased risk of SA and GDM in early asthma diagnosis or the interaction between asthma and PTB or PE, indicating that confounding factors may affect the results of previous observational studies.
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Affiliation(s)
- Xinyu Han
- Department of First Clinical Medical College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Tian qiang Wu
- Department of First Clinical Medical College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yuanyuan Bian
- Department of First Clinical Medical College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Lu Chen
- Department of Gynecology, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
| | - Xiaoling Feng
- Department of Gynecology, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
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Zhao J, Liang S, Zhou B, Li M, Li L. A Comprehensive Analysis of Immunoglobulin E Levels, Allergen-Specific Sensitivities, and Clinical Manifestations in Allergic Dermatological Conditions: A Multicenter Retrospective Study in China. Clin Cosmet Investig Dermatol 2024; 17:499-512. [PMID: 38444403 PMCID: PMC10913895 DOI: 10.2147/ccid.s451117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/08/2024] [Indexed: 03/07/2024]
Abstract
Objective To assess the correlations between Immunoglobulin E (IgE) levels, pruritus, and lesion severity in patients with eczema, atopic dermatitis, or urticaria. Methods A retrospective study was conducted and data of 814 patients who visited the dermatology or allergy clinics of multiple hospitals, from December 2019 to December 2021, were collected. Patients were divided into children group (<18 years, 325 cases), adult group (18-60 years, 435 cases), and older population group (>60 years, 54 cases) based on the age. Baseline information, pruritus severity, severity of skin lesions, total IgE level, and specific IgE level were recorded to analyze the complex relationship between them. Results The prevalence of allergic conjunctivitis and allergic rhinitis in the children group was significantly higher than that in the adult and older population group (P < 0.01 or P < 0.05). The positive rate of specific IgE in children group was significantly higher than that in the adult and older population group (P < 0.01). The IgE levels in children with moderate pruritus were significantly lower than those of severe pruritus (63.39vs 114.42 IU/mL, P < 0.05). The IgE levels in children with mild and moderate skin lesions were significantly lower than those in children with severe skin lesions (58.95 vs 72.88 vs 169.15 IU/mL, P < 0.001 or P < 0.01, respectively). Conclusion Relationships among age, severity of skin pruritus and lesions, and allergen-specific IgE response are complex and subtle, displaying dynamic patterns.
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Affiliation(s)
- Jian Zhao
- Department of Dermatology, Beijing Friendship Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Surong Liang
- Beijing Luhe Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Boyang Zhou
- Department of Dermatology, Beijing Friendship Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Min Li
- Clinical Epidemiology and Evidence Based Medicine Unit, Beijing Friendship Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Linfeng Li
- Department of Dermatology, Beijing Friendship Hospital, Capital Medical University, Beijing, People’s Republic of China
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Coskunpinar E, Akcesme B, Tas SK, Aynaci A. Investigation of miRNAs that are effective in the pathogenesis of asthma. J Asthma 2023; 60:2145-2152. [PMID: 37314187 DOI: 10.1080/02770903.2023.2225605] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/11/2023] [Indexed: 06/15/2023]
Abstract
OBJECTIVES Asthma is a complex disease characterized by inflammation of the airways, involving epigenetic changes, in which genetic and environmental factors act together. MicroRNAs as candidate biomarkers stand out as target molecules in the diagnosis and treatment of immunological and inflammatory diseases. Our aim of this study is to identify miRNAs that are thought to be effective in the pathogenesis of allergic asthma and to reveal candidate biomarkers associated with the disease. METHODS Fifty patients, aged between 18-80 years, who were diagnosed with allergic asthma and 18 healthy volunteers were included in the study. After the collection 2 mL of total blood from volunteers, RNA isolation and cDNA synthesis were performed. For miRNA profile screening, expression analysis was performed by real-time PCR method using miScript miRNA PCR Array. GeneGlobe Data Analysis Center was used to evaluate dysregulated miRNAs. RESULTS In the allergic asthma group, 9 (18%) of the patients were male and 41 (82%) of them were female. In the control group, 7 (38.89%) were male and 11 (61.1%) were female (P:0.073). As a result of the research, the expression levels of miR-142-5p, miR-376c-3p and miR-22-3p were down-regulated, while miR-27b-3p, miR-26b-5p, miR-15b-5p and miR-29c-3p detected as up-regulated. DISCUSSION The results of our study suggest that miR142-5p, miR376c-3p and miR22-3p promote Ubiquitin-mediated proteolysis by inhibiting TGF-β expression through a mechanism involving the p53 signaling pathway. The deregulated miRNAs may be used as a diagnostic and prognostic biomarker in asthma.
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Affiliation(s)
- Ender Coskunpinar
- Department of Medical Biology, School of Medicine, University of Health Sciences, Istanbul, Turkey
| | - Betul Akcesme
- Department of Medical Biology, School of Medicine, University of Health Sciences, Istanbul, Turkey
| | - Sevgi Kalkanli Tas
- Department of Immunology, School of Medicine, University of Health Sciences, Istanbul, Turkey
| | - Aysun Aynaci
- Clinic of Chest Diseases, Istanbul Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
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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] [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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Cardenas A, Fadadu RP, Koppelman GH. Epigenome-wide association studies of allergic disease and the environment. J Allergy Clin Immunol 2023; 152:582-590. [PMID: 37295475 PMCID: PMC10564109 DOI: 10.1016/j.jaci.2023.05.020] [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: 03/31/2023] [Revised: 05/04/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
The epigenome is at the intersection of the environment, genotype, and cellular response. DNA methylation of cytosine nucleotides, the most studied epigenetic modification, has been systematically evaluated in human studies by using untargeted epigenome-wide association studies (EWASs) and shown to be both sensitive to environmental exposures and associated with allergic diseases. In this narrative review, we summarize findings from key EWASs previously conducted on this topic; interpret results from recent studies; and discuss the strengths, challenges, and opportunities regarding epigenetics research on the environment-allergy relationship. The majority of these EWASs have systematically investigated select environmental exposures during the prenatal and early childhood periods and allergy-associated epigenetic changes in leukocyte-isolated DNA and more recently in nasal cells. Overall, many studies have found consistent DNA methylation associations across cohorts for certain exposures, such as smoking (eg, aryl hydrocarbon receptor repressor gene [AHRR] gene), and allergic diseases (eg, EPX gene). We recommend the integration of both environmental exposures and allergy or asthma within long-term prospective designs to strengthen causality as well as biomarker development. Future studies should collect paired target tissues to examine compartment-specific epigenetic responses, incorporate genetic influences in DNA methylation (methylation quantitative trait locus), replicate findings across diverse populations, and carefully interpret epigenetic signatures from bulk, target tissue or isolated cells.
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Affiliation(s)
- Andres Cardenas
- Department of Epidemiology and Population Health, Stanford School of Medicine, Stanford University, Stanford, Calif
| | - Raj P Fadadu
- School of Medicine, University of California, San Francisco, Calif
| | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, Groningen, The Netherlands; Groningen Research Institute of Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
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Argentato PP, Guerra JVDS, Luzia LA, Ramos ES, Maschietto M, Rondó PHDC. Excessive Gestational Weight Gain Alters DNA Methylation and Influences Foetal and Neonatal Body Composition. EPIGENOMES 2023; 7:18. [PMID: 37606455 PMCID: PMC10443290 DOI: 10.3390/epigenomes7030018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Changes in body weight are associated with the regulation of DNA methylation (DNAm). In this study, we investigated the associations between maternal gestational weight gain-related DNAm and foetal and neonatal body composition. METHODS Brazilian pregnant women from the Araraquara Cohort Study were followed up during pregnancy, delivery, and after hospital discharge. Women with normal pre-pregnancy BMI were allocated into two groups: adequate gestational weight gain (AGWG, n = 45) and excessive gestational weight gain (EGWG, n = 30). Foetal and neonatal body composition was evaluated via ultrasound and plethysmography, respectively. DNAm was assessed in maternal blood using Illumina Infinium MethylationEPIC BeadChip arrays. Linear regression models were used to explore the associations between DNAm and foetal and neonatal body composition. RESULTS Maternal weight, GWG, neonatal weight, and fat mass were higher in the EGWG group. Analysis of DNAm identified 46 differentially methylated positions and 11 differentially methylated regions (DMRs) between the EGWG and AGWG groups. Nine human phenotypes were enriched for these 11 DMRs located in 13 genes (EMILIN1, HOXA5, CPT1B, CLDN9, ZFP57, BRCA1, POU5F1, ANKRD33, HLA-B, RANBP17, ZMYND11, DIP2C, TMEM232), highlighting the terms insulin resistance, and hyperglycaemia. Maternal DNAm was associated with foetal total thigh and arm tissues and subcutaneous thigh and arm fat, as well as with neonatal fat mass percentage and fat mass. CONCLUSION The methylation pattern in the EGWG group indicated a risk for developing chronic diseases and involvement of maternal DNAm in foetal lean and fat mass and in neonatal fat mass.
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Affiliation(s)
- Perla Pizzi Argentato
- Nutrition Department, School of Public Health, University of São Paulo, Avenida Dr. Arnaldo 715, São Paulo 01246-904, SP, Brazil; (P.P.A.); (L.A.L.)
| | - João Victor da Silva Guerra
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Centre for Research in Energy and Materials (CNPEM) and Graduate Program in Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, University of Campinas, Rua Giuseppe Máximo Scolfaro 10.000, Cidade Universitária, Campinas 13083-970, SP, Brazil;
| | - Liania Alves Luzia
- Nutrition Department, School of Public Health, University of São Paulo, Avenida Dr. Arnaldo 715, São Paulo 01246-904, SP, Brazil; (P.P.A.); (L.A.L.)
| | - Ester Silveira Ramos
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes 3900, Ribeirão Preto 14049-900, SP, Brazil;
| | - Mariana Maschietto
- Boldrini Children’s Hospital, University of Campinas, Rua Márcia Mendes 619, Cidade Universitária, Campinas 13083-884, SP, Brazil;
| | - Patrícia Helen de Carvalho Rondó
- Nutrition Department, School of Public Health, University of São Paulo, Avenida Dr. Arnaldo 715, São Paulo 01246-904, SP, Brazil; (P.P.A.); (L.A.L.)
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Ashmawy R, Zaki A, Baess A, El Sayed I. Efficacy and safety of inhaled heparin in asthmatic and chronic obstructive pulmonary disease patients: a systematic review and a meta-analysis. Sci Rep 2023; 13:13326. [PMID: 37587208 PMCID: PMC10432425 DOI: 10.1038/s41598-023-40489-8] [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: 03/22/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
Asthma and chronic obstructive pulmonary disease (COPD) are prevalent chronic respiratory disorders that cause significant morbidity and mortality. Some studies evaluated the use of inhaled unfractionated heparin (UFH) in the treatment of asthma and COPD. We aimed to synthesize the available evidence for the efficacy and safety of inhaled heparin in improving lung functions among asthmatic and COPD patients. A comprehensive search was performed using Pubmed, Embase, EBSCO, Scopus, Web of Science, Cochrane CENTRAL, WHO Clinical trials, clinicaltrials.gov, Iranian Clinical trials, Google Scholar, Research Gate, ProQuest Thesis, OVID, and medRxiv databases. Two independent reviewers included all pertinent articles according to PRISMA guidelines, and extract data independently. The two reviewers checked the quality of studies using the ROB2 tool. To determine the pooled effect estimate of the efficacy and safety of inhaled heparin, a meta-analysis was carried out using the R programming language. Publication bias was evaluated using Egger's regression test. The heterogeneity was explained using a meta-regression, and the quality of evidence was assessed by the GRADE approach. Twenty-six studies with a total of 581 patients were included in the qualitative analysis and 16 in the meta-analysis. The primary outcome was treatment success (improvement of lung function) that was measured by standardized mean differences (SMD) of the forced expiratory volume per second (FEV1) either per ml or percentage. Heparin has a large effect on both FEV1% and FEV1 ml when compared to the control group (SMD 2.7, 95% CI 1.00; 4.39; GRADE high, SMD 2.12, 95% CI - 1.49; 5.72: GRADE moderate, respectively). Secondary outcomes are other lung functions improving parameters such as PC20 (SMD 0.91, 95% CI - 0.15; 1.96). Meta-regression and subgroup analysis show that heparin type, dose, year of publication, study design, and quality of studies had a substantial effect. Regarding safety, inhaled heparin showed a good coagulation profile and mild tolerable side effects. Inhaled heparin showed improvement in lung functions either alone or when added to standard care. More large parallel RCTs are needed including COPD patients, children, and other types, and stages of asthmatic patients.
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Affiliation(s)
- Rasha Ashmawy
- Department of Clinical Research, Maamora Chest Hospital, MoHP, Alexandria, Egypt
| | - Adel Zaki
- Department of Biomedical Informatics and Medical Statistics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Ayman Baess
- Department of Chest Diseases, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Iman El Sayed
- Department of Biomedical Informatics and Medical Statistics, Medical Research Institute, Alexandria University, Alexandria, Egypt.
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Huang B, Liu M, Le G. LINC1810064F22Rik sequesters miR-206-5p away from HDAC4 to exacerbate allergic airway inflammation and airway remodeling in an ovalbumin mouse model of asthma. Int Immunopharmacol 2023; 119:110097. [PMID: 37068338 DOI: 10.1016/j.intimp.2023.110097] [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: 01/04/2023] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 04/19/2023]
Abstract
Allergic inflammation and airway remodeling frequently occur in asthma. This study clarifies a novel LINC1810064F22Rik-mediated ceRNA mechanism involved in asthma-induced allergic inflammation and airway remodeling based on bioinformatics analysis and in vivo and in vitro experiments. The differentially expressed lncRNAs and downstream effectors were predicted in silico. The targeting relationship among LINC1810064F22Rik, miR-206-5p, and HDAC4 was predicted by bioinformatics analysis, which was further validated by dual luciferase reporter gene assay. The asthma-like airway inflammation was induced in mice using ovalbumin (OVA) sensitization/challenge with immune adjuvant Al(OH)3, while alveolar epithelial cells (AECs) were exposed to IL-33 to mimic in vitro inflammatory environment. LINC1810064F22Rik and HDAC4 were highly expressed, while miR-206-5p was poorly expressed in the tracheal tissues of OVA mice and the IL-33-treated AECs. The OVA mice and IL-33-treated AECs were subjected to gain- or loss-of-function experiments to detect the interaction of LINC1810064F22Rik/miR-206-5p/HDAC4 axis and their effects on allergic inflammation and airway remodeling. LINC1810064F22Rik competitively bound to miR-206-5p, and miR-206-5p targeted and inhibited HDAC4. The in vivo animal experiments indicated that LINC1810064F22Rik promoted asthma-induced allergic inflammation and airway remodeling by sequestering miR-206-5p away from HDAC4. The evidence provided by our study highlighted the involvement of the LINC1810064F22Rik/miR-206-5p/HDAC4 axis in facilitating allergic airway inflammation and airway remodeling in OVA mice.
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Affiliation(s)
- Bin Huang
- Department of Pediatrics, Pingxiang People's Hospital, Pingxiang 337055, PR China.
| | - Ming Liu
- Department of Pediatrics, Pingxiang People's Hospital, Pingxiang 337055, PR China
| | - Gaozhong Le
- Department of Pediatrics, Pingxiang People's Hospital, Pingxiang 337055, PR China
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Entsie P, Kang Y, Amoafo EB, Schöneberg T, Liverani E. The Signaling Pathway of the ADP Receptor P2Y 12 in the Immune System: Recent Discoveries and New Challenges. Int J Mol Sci 2023; 24:6709. [PMID: 37047682 PMCID: PMC10095349 DOI: 10.3390/ijms24076709] [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: 01/16/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/07/2023] Open
Abstract
P2Y12 is a G-protein-coupled receptor that is activated upon ADP binding. Considering its well-established role in platelet activation, blocking P2Y12 has been used as a therapeutic strategy for antiplatelet aggregation in cardiovascular disease patients. However, receptor studies have shown that P2Y12 is functionally expressed not only in platelets and the microglia but also in other cells of the immune system, such as in monocytes, dendritic cells, and T lymphocytes. As a result, studies were carried out investigating whether therapies targeting P2Y12 could also ameliorate inflammatory conditions, such as sepsis, rheumatoid arthritis, neuroinflammation, cancer, COVID-19, atherosclerosis, and diabetes-associated inflammation in animal models and human subjects. This review reports what is known about the expression of P2Y12 in the cells of the immune system and the effect of P2Y12 activation and/or inhibition in inflammatory conditions. Lastly, we will discuss the major problems and challenges in studying this receptor and provide insights on how they can be overcome.
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Affiliation(s)
- Philomena Entsie
- Department of Pharmaceutical Sciences, School of Pharmacy, College of Health Professions, North Dakota State University, Fargo, ND 58105, USA
| | - Ying Kang
- Department of Pharmaceutical Sciences, School of Pharmacy, College of Health Professions, North Dakota State University, Fargo, ND 58105, USA
| | - Emmanuel Boadi Amoafo
- Department of Pharmaceutical Sciences, School of Pharmacy, College of Health Professions, North Dakota State University, Fargo, ND 58105, USA
| | - Torsten Schöneberg
- Division of Molecular Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, 04103 Leipzig, Germany
| | - Elisabetta Liverani
- Department of Pharmaceutical Sciences, School of Pharmacy, College of Health Professions, North Dakota State University, Fargo, ND 58105, USA
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Bhat S, Rotti H, Prasad K, Kabekkodu SP, Saadi AV, Shenoy SP, Joshi KS, Nesari TM, Shengule SA, Dedge AP, Gadgil MS, Dhumal VR, Salvi S, Satyamoorthy K. Genome-wide DNA methylation profiling after Ayurveda intervention to bronchial asthmatics identifies differential methylation in several transcription factors with immune process related function. J Ayurveda Integr Med 2023; 14:100692. [PMID: 37018893 PMCID: PMC10122039 DOI: 10.1016/j.jaim.2023.100692] [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: 12/15/2021] [Revised: 10/13/2022] [Accepted: 02/01/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND The Indian traditional medicinal system, Ayurveda, describes several lifestyle practices, processes and medicines as an intervention to treat asthma. Rasayana therapy is one of them and although these treatment modules show improvement in bronchial asthma, their mechanism of action, particularly the effect on DNA methylation, is largely understudied. OBJECTIVES Our study aimed at identifying the contribution of DNA methylation changes in modulating bronchial asthma phenotype upon Ayurveda intervention. MATERIALS AND METHODS In this study, genome-wide methylation profiling in peripheral blood DNA of healthy controls and bronchial asthmatics before (BT) and after (AT) Ayurveda treatment was performed using array-based profiling of reference-independent methylation status (aPRIMES) coupled to microarray technique. RESULTS We identified 4820 treatment-associated DNA methylation signatures (TADS) and 11,643 asthma-associated DNA methylation signatures (AADS), differentially methylated [FDR (≤0.1) adjusted p-values] in AT and HC groups respectively, compared to BT group. Neurotrophin TRK receptor signaling pathway was significantly enriched for differentially methylated genes in bronchial asthmatics, compared to AT and HC subjects. Additionally, we identified over 100 differentially methylated immune-related genes located in the promoter/5'-UTR regions of TADS and AADS. Various immediate-early response and immune regulatory genes with functions such as transcription factor activity (FOXD1, FOXD2, GATA6, HOXA3, HOXA5, MZF1, NFATC1, NKX2-2, NKX2-3, RUNX1, KLF11), G-protein coupled receptor activity (CXCR4, PTGER4), G-protein coupled receptor binding (UCN), DNA binding (JARID2, EBF2, SOX9), SNARE binding (CAPN10), transmembrane signaling receptor activity (GP1BB), integrin binding (ITGA6), calcium ion binding (PCDHGA12), actin binding (TRPM7, PANX1, TPM1), receptor tyrosine kinase binding (PIK3R2), receptor activity (GDNF), histone methyltransferase activity (MLL5), and catalytic activity (TSTA3) were found to show consistent methylation status between AT and HC group in microarray data. CONCLUSIONS Our study reports the DNA methylation-regulated genes in bronchial asthmatics showing improvement in symptoms after Ayurveda intervention. DNA methylation regulation in the identified genes and pathways represents the Ayurveda intervention responsive genes and may be further explored as diagnostic, prognostic, and therapeutic biomarkers for bronchial asthma in peripheral blood.
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Affiliation(s)
- Smitha Bhat
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Harish Rotti
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Keshava Prasad
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Shama Prasada Kabekkodu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Abdul Vahab Saadi
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Sushma P Shenoy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Kalpana S Joshi
- Department of Biotechnology, Sinhgad College of Engineering, S. P. University of Pune, Pune Maharashtra, India
| | - Tanuja M Nesari
- Department of Dravyaguna, Tilak Ayurved Mahavidyalaya, Pune, Maharashtra, India
| | - Sushant A Shengule
- Department of Biotechnology, Sinhgad College of Engineering, S. P. University of Pune, Pune Maharashtra, India
| | - Amrish P Dedge
- Department of Dravyaguna, Tilak Ayurved Mahavidyalaya, Pune, Maharashtra, India
| | - Maithili S Gadgil
- Department of Biotechnology, Sinhgad College of Engineering, S. P. University of Pune, Pune Maharashtra, India
| | - Vikram R Dhumal
- Department of Dravyaguna, Tilak Ayurved Mahavidyalaya, Pune, Maharashtra, India
| | - Sundeep Salvi
- Department of Pulmonary Medicine, Chest Research Foundation, Pune, Maharashtra, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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12
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Yang Z, Wen P, Chen J, Kang J, Xiang Y, Ding S, Gao L, Tong X, Guo A. DNA methylation regulatory patterns and underlying pathways behind the co-pathogenesis of allergic rhinitis and chronic spontaneous urticaria. Front Immunol 2023; 13:1053558. [PMID: 36713372 PMCID: PMC9875140 DOI: 10.3389/fimmu.2022.1053558] [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: 09/25/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023] Open
Abstract
Background Allergic rhinitis (AR) and chronic spontaneous urticaria (CSU) are often concurrent in patients. Changes in DNA methylation affect T cell biological processes, which may explain the occurrence and progression of comorbidity. However, downstream regulatory pathways of DNA methylation in two diseases and the underlying mechanisms have not been fully elucidated. Methods The GSE50101, GSE72541, GSE50222 and OEP002482 were mined for the identification of differentially expressed genes (DEGs) or co-expressed genes and differentially methylated genes (DMGs) in AR and CSU patients. We applied GO analysis and consensus clustering to study the potential functions and signal pathways of selected genes in two diseases. GSVA and logistic regression analysis were used to find the regulatory pathway between DNA methylation and activation patterns of CD4+ T cells. Besides, we used the Illumina 850k chip to detect DNA methylation expression profiles and recognize the differentially methylated CpG positions (DMPs) on corresponding genes. Finally, we annotated the biological process of these genes using GO and KEGG pathway analysis. Result The AR-related DEGs were found closely related to the differentiation and activation of CD4+ T cells. The DEGs or co-expressed genes of CD4+ T cells in AR and CSU patients were also clustered using GO and KEGG analysis and we got 57 co-regulatory pathways. Furthermore, logistic regression analysis showed that the regulation of cellular component size was closely related to the activation of CD4+ T cells regulated by DNA methylation. We got self-tested data using the Illumina 850k chip and identified 98 CpGs that were differentially methylated in patients. Finally, we mapped the DMPs to 15 genes and found that they were mainly enriched in the same CD4+T cell regulating pathway. Conclusion Our study indicated that DNA methylation affected by pollen participated in the activation patterns of CD4 + T cells, providing a novel direction for the symptomatic treatment of the co-occurrence of AR and CSU.
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Affiliation(s)
- Zijiang Yang
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Puqiao Wen
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Jing Chen
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jian Kang
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yaping Xiang
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shu Ding
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lihua Gao
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiaoliang Tong
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Aiyuan Guo
- Department of Dermatology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China,*Correspondence: Aiyuan Guo,
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13
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Klinkhammer H, Staerk C, Maj C, Krawitz PM, Mayr A. A statistical boosting framework for polygenic risk scores based on large-scale genotype data. Front Genet 2023; 13:1076440. [PMID: 36704342 PMCID: PMC9871367 DOI: 10.3389/fgene.2022.1076440] [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: 10/21/2022] [Accepted: 12/20/2022] [Indexed: 01/12/2023] Open
Abstract
Polygenic risk scores (PRS) evaluate the individual genetic liability to a certain trait and are expected to play an increasingly important role in clinical risk stratification. Most often, PRS are estimated based on summary statistics of univariate effects derived from genome-wide association studies. To improve the predictive performance of PRS, it is desirable to fit multivariable models directly on the genetic data. Due to the large and high-dimensional data, a direct application of existing methods is often not feasible and new efficient algorithms are required to overcome the computational burden regarding efficiency and memory demands. We develop an adapted component-wise L 2-boosting algorithm to fit genotype data from large cohort studies to continuous outcomes using linear base-learners for the genetic variants. Similar to the snpnet approach implementing lasso regression, the proposed snpboost approach iteratively works on smaller batches of variants. By restricting the set of possible base-learners in each boosting step to variants most correlated with the residuals from previous iterations, the computational efficiency can be substantially increased without losing prediction accuracy. Furthermore, for large-scale data based on various traits from the UK Biobank we show that our method yields competitive prediction accuracy and computational efficiency compared to the snpnet approach and further commonly used methods. Due to the modular structure of boosting, our framework can be further extended to construct PRS for different outcome data and effect types-we illustrate this for the prediction of binary traits.
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Affiliation(s)
- Hannah Klinkhammer
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Christian Staerk
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
- Center for Human Genetics, University of Marburg, Marburg, Germany
| | - Peter Michael Krawitz
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Bonn, Germany
| | - Andreas Mayr
- Institute for Medical Biometry, Informatics and Epidemiology, Medical Faculty, University of Bonn, Bonn, Germany
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14
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Dapas M, Thompson EE, Wentworth-Sheilds W, Clay S, Visness CM, Calatroni A, Sordillo JE, Gold DR, Wood RA, Makhija M, Khurana Hershey GK, Sherenian MG, Gruchalla RS, Gill MA, Liu AH, Kim H, Kattan M, Bacharier LB, Rastogi D, Altman MC, Busse WW, Becker PM, Nicolae D, O’Connor GT, Gern JE, Jackson DJ, Ober C. Multi-omic association study identifies DNA methylation-mediated genotype and smoking exposure effects on lung function in children living in urban settings. PLoS Genet 2023; 19:e1010594. [PMID: 36638096 PMCID: PMC9879483 DOI: 10.1371/journal.pgen.1010594] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 01/26/2023] [Accepted: 12/23/2022] [Indexed: 01/14/2023] Open
Abstract
Impaired lung function in early life is associated with the subsequent development of chronic respiratory disease. Most genetic associations with lung function have been identified in adults of European descent and therefore may not represent those most relevant to pediatric populations and populations of different ancestries. In this study, we performed genome-wide association analyses of lung function in a multiethnic cohort of children (n = 1,035) living in low-income urban neighborhoods. We identified one novel locus at the TDRD9 gene in chromosome 14q32.33 associated with percent predicted forced expiratory volume in one second (FEV1) (p = 2.4x10-9; βz = -0.31, 95% CI = -0.41- -0.21). Mendelian randomization and mediation analyses revealed that this genetic effect on FEV1 was partially mediated by DNA methylation levels at this locus in airway epithelial cells, which were also associated with environmental tobacco smoke exposure (p = 0.015). Promoter-enhancer interactions in airway epithelial cells revealed chromatin interaction loops between FEV1-associated variants in TDRD9 and the promoter region of the PPP1R13B gene, a stimulator of p53-mediated apoptosis. Expression of PPP1R13B in airway epithelial cells was significantly associated the FEV1 risk alleles (p = 1.3x10-5; β = 0.12, 95% CI = 0.06-0.17). These combined results highlight a potential novel mechanism for reduced lung function in urban youth resulting from both genetics and smoking exposure.
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Affiliation(s)
- Matthew Dapas
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
| | - Emma E. Thompson
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
| | | | - Selene Clay
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
| | | | | | - Joanne E. Sordillo
- Department of Population Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Diane R. Gold
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert A. Wood
- Department of Pediatrics, Johns Hopkins University Medical Center, Baltimore, Maryland, United States of America
| | - Melanie Makhija
- Division of Allergy and Immunology, Ann & Robert H. Lurie Children’s Hospital, Chicago, Illinois, United States of America
| | - Gurjit K. Khurana Hershey
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Michael G. Sherenian
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Rebecca S. Gruchalla
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Michelle A. Gill
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Andrew H. Liu
- Department of Allergy and Immunology, Children’s Hospital Colorado, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Haejin Kim
- Department of Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Meyer Kattan
- Columbia University College of Physicians and Surgeons, New York, New York, United States of America
| | - Leonard B. Bacharier
- Monroe Carell Jr. Children’s Hospital at Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Deepa Rastogi
- Children’s National Health System, Washington, District of Columbia, United States of America
| | - Matthew C. Altman
- Department of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - William W. Busse
- Department of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Patrice M. Becker
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Dan Nicolae
- Department of Statistics, University of Chicago, Chicago, Illinois, United States of America
| | - George T. O’Connor
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - James E. Gern
- Department of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Daniel J. Jackson
- Department of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
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15
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St John AL, Rathore APS, Ginhoux F. New perspectives on the origins and heterogeneity of mast cells. Nat Rev Immunol 2023; 23:55-68. [PMID: 35610312 DOI: 10.1038/s41577-022-00731-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2022] [Indexed: 01/06/2023]
Abstract
Mast cells are immune cells of the haematopoietic lineage that are now thought to have multifaceted functions during homeostasis and in various disease states. Furthermore, while mast cells have been known for a long time to contribute to allergic disease in adults, recent studies, mainly in mice, have highlighted their early origins during fetal development and potential for immune functions, including allergic responses, in early life. Our understanding of the imprinting of mast cells by particular tissues of residence and their potential for regulatory interactions with organ systems such as the peripheral immune, nervous and vascular systems is also rapidly evolving. Here, we discuss the origins of mast cells and their diverse and plastic phenotypes that are influenced by tissue residence. We explore how divergent phenotypes and functions might result from both their hard-wired 'nature' defined by their ontogeny and the 'nurture' they receive within specialized tissue microenvironments.
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Affiliation(s)
- Ashley L St John
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore.
- Department of Pathology, Duke University Medical Center, Durham, NC, USA.
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- SingHealth Duke-NUS Global Health Institute, Singapore, Singapore.
| | - Abhay P S Rathore
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Florent Ginhoux
- Singapore Immunology Network, A*STAR, Singapore, Singapore.
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore.
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16
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Chronic allergic asthma alters m6A epitranscriptomic tagging of mRNAs and lncRNAs in the lung. Biosci Rep 2022; 42:231936. [PMID: 36250525 DOI: 10.1042/bsr20221395] [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: 07/04/2022] [Revised: 10/14/2022] [Accepted: 10/14/2022] [Indexed: 12/14/2022] Open
Abstract
To evaluate the role of m6A methylation of mRNAs and long non-coding RNAs (lncRNAs) in chronic allergic asthma. Transcriptome-wide N6-methyladenosine (m6A) changes in BALB/c mice were profiled using immunoprecipitated methylated RNAs with microarrays in lung with chronic allergic asthma. Gene ontology (GO) and KEGG analyses were conducted. Target genes were verified by methylated RNA immunoprecipitation and real-time polymerase chain reaction (PCR). Specifically, the mRNA levels of m6A writers (METTL3, METTL14, and WTAP), and readers and erasers (FTO and ALKBH5) were estimated by real-time PCR analysis, using the SYBR-green method. IL17RB mRNA was also evaluated by PCR. Hematoxylin and eosin (H&E) staining showed that the airway and lung tissues in mice in the asthma group had extensive infiltration of inflammatory cells around the bronchioles, blood vessels, and alveoli. The lungs of those allergic asthma mice showed altered m6A epitranscriptome, whereby 1369 mRNAs and 176 lncRNAs were hypermethylated, and 197 mRNAs and 30 lncRNAs were hypomethylated (>1.5-fold vs control). Also, compared with the control group, IL17RB mRNA in lung of the asthmatic group was significantly hypermethylated (P<0.01). In the asthma group, the mRNA and the protein level of METTL14 (the key methyltransferase) and ALKBH5 (the major demethyltransferase) were significantly decreased compared with the control group (P<0.01). Chronic allergic asthma alters the lung m6A epitranscriptome, suggesting functional implications in the pathophysiology of refractory asthma. Data support methylated IL17RB mRNA possibly becoming a new therapeutic target for chronic allergic asthma.
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17
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Tong S, Beggs PJ, Davies JM, Jiang F, Kinney PL, Liu S, Yin Y, Ebi KL. Compound impacts of climate change, urbanization and biodiversity loss on allergic disease. Int J Epidemiol 2022:6760684. [PMID: 36228124 DOI: 10.1093/ije/dyac197] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 10/10/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
- Shilu Tong
- Department of Clinical Epidemiology and Biostatistics, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,School of Public Health, Institute of Environment and Population Health, Anhui Medical University, Hefei, China.,Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.,School of Public Health and Social Work, Queensland University of Technology, Brisbane, Australia
| | - Paul J Beggs
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, New South Wales, Australia
| | - Janet M Davies
- School of Biomedical Sciences, Centre Immunology and Infection Control, Queensland University of Technology, Brisbane, Australia
| | - Fan Jiang
- Department of Child Health, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Patrick L Kinney
- Department of Environmental Health, Boston University School of Public Health, Boston, USA
| | - Shijian Liu
- Department of Clinical Epidemiology and Biostatistics, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yong Yin
- Department of Respiratory Disease, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Kristie L Ebi
- Center for Health and the Global Environment, University of Washington, Seattle, USA
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18
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The Role of Systems Biology in Deciphering Asthma Heterogeneity. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101562. [PMID: 36294997 PMCID: PMC9605413 DOI: 10.3390/life12101562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/28/2022] [Accepted: 10/04/2022] [Indexed: 11/17/2022]
Abstract
Asthma is one of the most common and lifelong and chronic inflammatory diseases characterized by inflammation, bronchial hyperresponsiveness, and airway obstruction episodes. It is a heterogeneous disease of varying and overlapping phenotypes with many confounding factors playing a role in disease susceptibility and management. Such multifactorial disorders will benefit from using systems biology as a strategy to elucidate molecular insights from complex, quantitative, massive clinical, and biological data that will help to understand the underlying disease mechanism, early detection, and treatment planning. Systems biology is an approach that uses the comprehensive understanding of living systems through bioinformatics, mathematical, and computational techniques to model diverse high-throughput molecular, cellular, and the physiologic profiling of healthy and diseased populations to define biological processes. The use of systems biology has helped understand and enrich our knowledge of asthma heterogeneity and molecular basis; however, such methods have their limitations. The translational benefits of these studies are few, and it is recommended to reanalyze the different studies and omics in conjugation with one another which may help understand the reasons for this variation and help overcome the limitations of understanding the heterogeneity in asthma pathology. In this review, we aim to show the different factors that play a role in asthma heterogeneity and how systems biology may aid in understanding and deciphering the molecular basis of asthma.
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19
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Liotti A, Ferrara AL, Loffredo S, Galdiero MR, Varricchi G, Di Rella F, Maniscalco GT, Belardo M, Vastano R, Prencipe R, Pignata L, Romano R, Spadaro G, de Candia P, Pezone A, De Rosa V. Epigenetics: an Opportunity to Shape Innate and Adaptive Immune Responses. Immunol Suppl 2022; 167:451-470. [PMID: 36043705 DOI: 10.1111/imm.13571] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 08/09/2022] [Indexed: 12/01/2022]
Abstract
Epigenetics connects genetic and environmental factors: it includes DNA methylation, histone post-translational modifications and the regulation of chromatin accessibility by non-coding RNAs, all of which control constitutive or inducible gene transcription. This plays a key role in harnessing the transcriptional programs of both innate and adaptive immune cells due to its plasticity and environmental-driven nature, piloting myeloid and lymphoid cell fate decision with no change in their genomic sequence. In particular, epigenetic marks at the site of lineage specific transcription factors and maintenance of cell type-specific epigenetic modifications, referred to as "epigenetic memory", dictate cell differentiation, cytokine production and functional capacity following repeated antigenic exposure in memory T cells. Moreover, metabolic and epigenetic reprogramming occurring during a primary innate immune response leads to enhanced responses to secondary challenges, a phenomenon known as "trained immunity". Here we discuss how stable and dynamic epigenetic states control immune cell identity and plasticity in physiological and pathological conditions. Dissecting the regulatory circuits of cell fate determination and maintenance is of paramount importance for understanding the delicate balance between immune cell activation and tolerance, in healthy conditions and in autoimmune diseases. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Antonietta Liotti
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy
| | - Anne Lise Ferrara
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy.,Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Stefania Loffredo
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy.,Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Maria Rosaria Galdiero
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy.,Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Gilda Varricchi
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy.,Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Francesca Di Rella
- Department of Breast and Thoracic Oncology, Istituto Nazionale Tumori IRCCS Fondazione Pascale, Naples, Italy
| | - Giorgia Teresa Maniscalco
- Neurological Clinic and Stroke Unit and Multiple Sclerosis Center "A. Cardarelli" Hospital, Naples, Italy
| | - Martina Belardo
- Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Roberta Vastano
- Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Rosaria Prencipe
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy
| | - Laura Pignata
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Roberta Romano
- Department of Translational Medical Sciences, Pediatric Section, University of Naples "Federico II", Naples, Italy
| | - Giuseppe Spadaro
- Department of Translational Medical Sciences, Center for Basic and Clinical Immunology Research (CISI) and World Allergy Organization (WAO) Center of Excellence, University of Naples "Federico II", Naples, Italy
| | - Paola de Candia
- Department of Molecular Medicine and Medical Biotechnology, University of Naples "Federico II", Naples, Italy
| | - Antonio Pezone
- Department of Biology, University of Naples "Federico II", Naples, Italy
| | - Veronica De Rosa
- Institute of Experimental Endocrinology and Oncology (IEOS), National Research Council, Naples, Italy
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20
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Corona-Rivera J, Peña-Padilla C, Morales-Domínguez GE, Romero-Bolaño YM. [Genetic aspects involved in asthma]. REVISTA ALERGIA MÉXICO 2022; 69:21-30. [PMID: 36927748 DOI: 10.29262/ram.v69i1.1031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 01/03/2022] [Indexed: 11/24/2022] Open
Abstract
Asthma is an etiologically heterogeneous disease resulting from a complex interaction between genetic. The genetic aspects involved in asthma, which were analyzed from the perspective of the traditional model of multifactorial inheritance, were susceptibility, host factors, and environmental exposures. In the present paper, studies on their family aggregation, concordance in twins, and heritability were analized; as well as the current knowledge about candidate genes, genome wide association studies, and epigenomics contributions and other omic studies that have increased our knowledge about their pathophysiology and environmental interactions.
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Affiliation(s)
- Jorge Corona-Rivera
- Universidad de Guadalajara, Centro Universitario de Ciencias de la Salud, Departamento de Biología Mole-cular y Genómica, Instituto de Genética Humana Dr. Enrique Corona-Rivera, Guadalajara, Jalisco, México.
| | - Christian Peña-Padilla
- Hospital Civil de Guadalajara Dr. Juan I. Menchaca, División de Pediatría, Servicio de Genética, Guadalajara, Jalisco, México
| | | | - Yaneris Maibeth Romero-Bolaño
- Hospital Civil de Guadalajara Dr. Juan I. Menchaca, División de Pediatría, Servicio de Genética, Guadalajara, Jalisco, México
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Exploration of the pathogenesis of Sjögren's syndrome via DNA methylation and transcriptome analyses. Clin Rheumatol 2022; 41:2765-2777. [PMID: 35562622 DOI: 10.1007/s10067-022-06200-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/07/2022] [Accepted: 05/03/2022] [Indexed: 11/03/2022]
Abstract
OBJECTIVES Sjögren's syndrome (SS), a systemic autoimmune disorder, is characterized by dry mouth and eyes. However, SS pathogenesis is poorly understood. We performed bioinformatics analysis to investigate the potential targets and molecular pathogenesis of SS. METHODS Gene expression profiles (GSE157159) and methylation data (GSE110007) associated with SS patients were obtained from the Gene Expression Omnibus (GEO) database. Differentially methylated positions (DMPs) and differentially expressed genes (DEGs) were identified by the R package limma. The potential biological functions of DEGs were determined using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Key DMPs were selected by overlap and the shrunken centroid algorithm, and corresponding genes were identified as hub genes, with their diagnostic value assessed by receiver operating characteristic (ROC) curves. The potential molecular mechanisms of hub genes were analyzed by protein-protein interaction (PPI) networks and single-gene gene set enrichment analysis (GSEA). Peripheral blood mononuclear cells (PBMCs) were collected from control and SS patients at The Affiliated Hospital of Southwest Medical University and Dazhou Central Hospital. The mRNA levels of hub genes were verified by quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS We identified 788 DMPs and 2457 DEGs between the two groups. Functional enrichment analysis suggested that the DEGs were significantly enriched in T cell activation, leukocyte cell-cell adhesion, and cytokine-cytokine receptor interaction. TSS200, TSS1500, and 1stExon were identified as highly enriched areas of differentially methylated promoter CpG islands (DMCIs). In total, 61 differentially methylated genes (DMGs) were identified by the overlap of 2457 DEGs and 507 genes related to DMPs (DMPGs), of which 21 genes located near TSS200, TSS1500, and 1stExon were selected. Then, three key DMPs and the corresponding hub genes (RUNX3, HLA-DPA1, and CD6) were screened by the shrunken centroid algorithm and calculated to have areas under the ROC curve of 1.000, 0.931, and 0.986, respectively, indicating good diagnostic value. The GSEA results suggested that all three hub genes were highly associated with the immune response. Finally, positive mRNA expression of the three hub genes in clinical SS samples was verified by qRT-PCR, consistent with the GSE157159 data. CONCLUSIONS The identification of three hub genes provides novel insight into molecular mechanisms and therapeutic targets for SS. Key Points • Hub genes were screened by DNA methylation and transcriptome analyses. • The relative expression of hub genes in peripheral blood samples was verified by qRT-PCR. • HLA-DPA1 was correlated with the pathogenic mechanism of SS.
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Hernandez-Pacheco N, Kere M, Melén E. Gene-environment interactions in childhood asthma revisited; expanding the interaction concept. Pediatr Allergy Immunol 2022; 33:e13780. [PMID: 35616899 PMCID: PMC9325482 DOI: 10.1111/pai.13780] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/13/2022] [Indexed: 01/04/2023]
Abstract
Investigation of gene-environment interactions (GxE) may provide important insights into the gene regulatory framework in response to environmental factors of relevance for childhood asthma. Over the years, different methodological strategies have been applied, more recently using genome-wide approaches. The best example to date is the major asthma locus on the 17q12-21 chromosome region, viral infections, and airway epithelium processes where recent studies have shed much light on mechanisms in childhood asthma. However, there are challenges with the traditional single variant-single exposure interaction models, as they do not encompass the complexity and cumulative effects of multiple exposures or multiple genetic variants. As such, we need to redefine our traditional GxE thinking, and we propose in this review to expand the GxE concept by also evaluating other omics layers, such as epigenetics, transcriptomics, metabolomics, and proteomics. In addition, host factors such as age, gender, and other exposures are very likely to influence GxE effects and need firmly to be considered in future studies.
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Affiliation(s)
- Natalia Hernandez-Pacheco
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.,CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Maura Kere
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Erik Melén
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.,Sachs' Children's Hospital, South General Hospital, Stockholm, Sweden
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Recent Progress in Traditional Chinese Medicines and Their Mechanism in the Treatment of Allergic Rhinitis. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:3594210. [PMID: 35444784 PMCID: PMC9015857 DOI: 10.1155/2022/3594210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 03/17/2022] [Indexed: 02/06/2023]
Abstract
Objective To conduct a systematic review on the mechanism of action and use of traditional Chinese medicines (TCM) in allergic rhinitis treatment. Background Allergic rhinitis (AR) is a type I allergic disease of the immune system induced by immunoglobulin E mediated inflammation and is characterized by sneezing, nasal itching, paroxysmal nasal obstruction, mucosal edema, cough, and rhinorrhea. More than 500 million people have been affected by rhinitis worldwide in the past 20 years, leading to negative effects on health, quality of life, and social relationships. Currently, the trending medicines used in the case of AR include intranasal corticosteroids and oral H1 antihistamines, which are given as combinatorial medicines supplemented with immune therapy. These medications have been found to be very effective in either the short term or long term; however, they have been found to possess some serious side effects. Search Methodology. The information in this article on classical and traditional Chinese medications used to treat AR was derived from original papers and reviews published in Chinese and English language journals. Two Chinese databases (Wanfang and CNKI) and three English databases (Cochrane Library, PubMed, and Embase) were utilized for data gathering. Results Traditional Chinese remedies have been identified to influence the production of cytokines such as IL-5 and IL-6, which are key mediators of eosinophilic inflammation, TNF-α, which stimulates TH2 cells at the site of inflammation, and NF-кB, which is required for cytokine and IgE antibody production. TCM has also been shown to be successful in lowering histamine levels, preserving histological changes by decreasing the thickness of the lamina propria, and downregulating the expression of Orai1, STIM1, and TRYC1, showing low expression of Ca+2 channel proteins. Conclusion In this review, we discussed a series of classical, traditional Chinese medications, including Centipeda minima, Scutellaria baicalensis, licorice root (Glycyrrhiza uralensis), and others, as potential antiallergic agents and investigate their in vivo effect upon the production of cytokines and release of histamines for allergic rhinitis treatment.
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Maiello N, Comberiati P, Giannetti A, Ricci G, Carello R, Galli E. New Directions in Understanding Atopic March Starting from Atopic Dermatitis. CHILDREN (BASEL, SWITZERLAND) 2022; 9:children9040450. [PMID: 35455494 PMCID: PMC9029734 DOI: 10.3390/children9040450] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 01/12/2023]
Abstract
Recent evidence showed that the postulated linear progression of the atopic march, from atopic dermatitis to food and respiratory allergies, does not capture the heterogeneity of allergic phenotypes, which are influenced by complex interactions between environmental, genetic, and psychosocial factors. Indeed, multiple atopic trajectories are possible in addition to the classic atopic march. Nevertheless, atopic dermatitis is often the first manifestation of an atopic march. Improved understanding of atopic dermatitis pathogenesis is warranted as this could represent a turning point in the prevention of atopic march. In this review, we outline the recent findings on the pathogenetic mechanisms leading to atopic dermatitis that could be targeted by intervention strategies for the prevention of atopic march.
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Affiliation(s)
- Nunzia Maiello
- Department of Woman, Child and General and Specialized Surgery, University of Campania “Luigi Vanvitelli”, 81100 Naples, Italy
- Correspondence:
| | - Pasquale Comberiati
- Department of Clinical and Experimental Medicine, Section of Pediatrics, University of Pisa, 56126 Pisa, Italy;
- Department of Clinical Immunology and Allergology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Arianna Giannetti
- Pediatric Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Giampaolo Ricci
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy;
| | - Rossella Carello
- Pediatric Allergic Unit, S.Pietro Hospital FbF Roma, 00189 Rome, Italy; (R.C.); (E.G.)
| | - Elena Galli
- Pediatric Allergic Unit, S.Pietro Hospital FbF Roma, 00189 Rome, Italy; (R.C.); (E.G.)
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Zhou Y, Liang ZS, Jin Y, Ding J, Huang T, Moore JH, Zheng ZJ, Huang J. Shared Genetic Architecture and Causal Relationship Between Asthma and Cardiovascular Diseases: A Large-Scale Cross-Trait Analysis. Front Genet 2022; 12:775591. [PMID: 35126453 PMCID: PMC8811262 DOI: 10.3389/fgene.2021.775591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/08/2021] [Indexed: 12/11/2022] Open
Abstract
Background: Accumulating evidence has suggested that there is a positive association between asthma and cardiovascular diseases (CVDs), implying a common architecture between them. However, the shared genetic architecture and causality of asthma and CVDs remain unclear. Methods: Based on the genome-wide association study (GWAS) summary statistics of recently published studies, our study examined the genetic correlation, shared genetic variants, and causal relationship between asthma (N = 127,669) and CVDs (N = 86,995–521,612). Statistical methods included high-definition likelihood (HDL), cross-trait meta-analyses of large-scale GWAS, transcriptome-wide association studies (TWAS), and Mendelian randomization (MR). Results: First, we observed a significant genetic correlation between asthma and heart failure (HF) (Rg = 0.278, P = 5 × 10−4). Through cross-trait analyses, we identified a total of 145 shared loci between asthma and HF. Fifteen novel loci were not previously reported for association with either asthma or HF. Second, we mapped these 145 loci to a total of 99 genes whose expressions are enriched in a broad spectrum of tissues, including the seminal vesicle, tonsil, appendix, spleen, skin, lymph nodes, breast, cervix and uterus, skeletal muscle, small intestine, lung, prostate, cardiac muscle, and liver. TWAS analysis identified five significant genes shared between asthma and HF in tissues from the hemic and immune system, digestive system, integumentary system, and nervous system. GSDMA, GSDMB, and ORMDL3 are statistically independent genetic effects from all shared TWAS genes between asthma and HF. Third, through MR analysis, genetic liability to asthma was significantly associated with heart failure at the Bonferroni-corrected significance level. The odds ratio (OR) is 1.07 [95% confidence interval (CI): 1.03–1.12; p = 1.31 × 10−3] per one-unit increase in loge odds of asthma. Conclusion: These findings provide strong evidence of genetic correlations and causal relationship between asthma and HF, suggesting a shared genetic architecture for these two diseases.
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Affiliation(s)
- Yi Zhou
- Department of Global Health, School of Public Health, Peking University, Beijing, China
| | - Zhi-Sheng Liang
- Department of Global Health, School of Public Health, Peking University, Beijing, China
| | - Yinzi Jin
- Department of Global Health, School of Public Health, Peking University, Beijing, China
| | - Jiayuan Ding
- College of Arts and Sciences, Boston University, Boston, MA, United States
| | - Tao Huang
- Department of Global Health, School of Public Health, Peking University, Beijing, China
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Jason H. Moore
- Department of Biostatistics, Epidemiology and Informatics, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA, United States
| | - Zhi-Jie Zheng
- Department of Global Health, School of Public Health, Peking University, Beijing, China
- Institute for Global Health and Development, Peking University, Beijing, China
| | - Jie Huang
- Department of Global Health, School of Public Health, Peking University, Beijing, China
- Institute for Global Health and Development, Peking University, Beijing, China
- *Correspondence: Jie Huang,
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Exposure of pigs to glyphosate affects gene-specific DNA methylation and gene expression. Toxicol Rep 2022; 9:298-310. [PMID: 35284244 PMCID: PMC8908043 DOI: 10.1016/j.toxrep.2022.02.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 12/24/2022] Open
Abstract
Glyphosate (N-(phosphonomethyl)glycine) is a broad-spectrum systemic herbicide and crop desiccant. Glyphosate has long been suspected of leading to the development of cancer and of compromising fertility. Herbicides have been increasingly recognized as epigenetic modifiers, and the impact of glyphosate on human and animal health might be mediated by epigenetic modifications. This article presents the results from an animal study where pigs were exposed to glyphosate while feeding. The experimental setup included a control group with no glyphosate added to the feed and two groups of pigs with 20 ppm and 200 ppm of glyphosate added to the feed, respectively. After exposure, the pigs were dissected, and tissues of the small intestine, liver, and kidney were used for DNA methylation and gene expression analyses. No significant change in global DNA methylation was found in the small intestine, kidney, or liver. Methylation status was determined for selected genes involved in various functions such as DNA repair and immune defense. In a CpG island of the promoter for IL18, we observed significantly reduced DNA methylation for certain individual CpG positions. However, this change in DNA methylation had no influence on IL18 mRNA expression. The expression of the DNA methylation enzymes DNMT1, DNMT3A, and DNMT3B was measured in the small intestine, kidney, and liver of pigs exposed to glyphosate. No significant changes in relative gene expression were found for these enzymes following dietary exposure to 20 and 200 ppm glyphosate. In contrast, a significant increase in expression of the enzyme TET3, responsible for demethylation, was observed in kidneys exposed to 200 ppm glyphosate. A large animal study with exposure of pigs to glyphosate is presented here. Pigs were exposed to 20 ppm and 200 ppm in the diet. No significant changes in global DNA methylation was observed. A significantly reduced DNA methylation was found in the porcine IL18 promoter. A significant increase in TET3 expression was seen in porcine kidneys exposed to 200 ppm glyphosate.
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Network Pharmacology-Based Analysis of the Underlying Mechanism of Hyssopus cuspidatus Boriss. for Antiasthma: A Characteristic Medicinal Material in Xinjiang. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:7671247. [PMID: 34880921 PMCID: PMC8648465 DOI: 10.1155/2021/7671247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/26/2021] [Indexed: 12/24/2022]
Abstract
Background Hyssopus cuspidatus Boriss. (Shen Xiang Cao (SXC)), a traditional medicine herb in Xinjiang, has a long history of being used by minorities to treat asthma. However, its active antiasthmatic compounds and underlying mechanism of action are still unknown. The aim of this study was to investigate the bioactive compounds and explore the molecular mechanism of SCX in the treatment of asthma using network pharmacology. Methods The compounds of SCX were collected by a literature search, and Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) and SwissTargetPrediction were used to predict targets and screen active compounds. Moreover, asthma-related targets were obtained based on DisGeNET, Herb, and GeneCards databases, and a protein-protein interaction (PPI) network was built by the STRING database. Furthermore, the topological analysis of the PPI and SXC-compound-target networks were analyzed and established by Cytoscape software. Finally, the RStudio software package was used for carrying out Gene Ontology (GO) function enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. AutoDock tools and AutoDock Vina were used to molecularly dock the active compounds and key targets. Results A total of 8 active compounds and 258 potential targets related to SXC were predicted, and PPI network screened out key targets, including IL-6, JUN, TNF, IL10, and CXCL8. GO enrichment analysis involved cell responses to reactive oxygen species, oxidative stress, chemical stress, etc. In addition, KEGG pathway analysis showed that SXC effectively treated asthma through regulation of mitogen-activated protein kinases (MAPK) signaling pathways, interleukin 17 (IL-17) signaling pathways, toll-like receptor (TLR) signaling pathways, and tumor necrosis factor (TNF) signaling pathways. Conclusion The preliminary study that was based on multiple compounds, multiple targets, and multiple pathways provides a scientific basis for further elucidating the molecules involved and the underlying antiasthma-related mechanisms of SXC.
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Alobaidi A, Alsamarai A, Alsamarai MA. Inflammation in Asthma Pathogenesis: Role of T cells, Macrophages, Epithelial Cells and Type 2 Inflammation. Antiinflamm Antiallergy Agents Med Chem 2021; 20:317-332. [PMID: 34544350 DOI: 10.2174/1871523020666210920100707] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 06/06/2021] [Accepted: 06/15/2021] [Indexed: 11/22/2022]
Abstract
Asthma is a chronic disease with abnormal inflammatory and immunological responses. The disease initiated by antigens in subjects with genetic susceptibility. However, environmental factors play a role in the initiation and exacerbation of asthma attack. Asthma is T helper 2 (Th2)-cell-mediated disease. Recent studies indicated that asthma is not a single disease entity, but it is with multiple phenotypes and endotypes. The pathophysiological changes in asthma included a series of subsequent continuous vicious circle of cellular activation contributed to induction of chemokines and cytokines that potentiate inflammation. The heterogeneity of asthma influenced the treatment response. The asthma pathogenesis driven by varied set of cells such as eosinophils, basophils, neutrophils, mast cells, macrophages, epithelial cells and T cells. In this review the role of T cells, macrophage, and epithelial cells are discussed.
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Affiliation(s)
- Amina Alobaidi
- Kirkuk University College of Veterinary Medicine, Kirkuk. Iraq
| | - Abdulghani Alsamarai
- Aalborg Academy College of Medicine [AACOM], Denmark. Tikrit University College of Medicine, [TUCOM], Tikrit. Iraq
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Chen Y, Kong D, Fu J, Zhang Y, Zhao Y, Liu Y, Chang Z, Liu Y, Liu X, Xu K, Jiang C, Fan Z. Increased hospital admissions for asthma from short-term exposure to cold spells in Beijing, China. Int J Hyg Environ Health 2021; 238:113839. [PMID: 34507107 DOI: 10.1016/j.ijheh.2021.113839] [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: 05/18/2021] [Revised: 08/31/2021] [Accepted: 09/04/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND There is a paucity of studies investigating extreme cold events and asthma exacerbations. This study examined whether an association exists between cold spells and daily hospital admissions for asthma in Beijing, China from 2012 to 2016. METHODS Daily hospital admissions for asthma, meteorological variables and air quality data were collected during 2012-2016 in Beijing. A cold spell was defined as a period of at least two consecutive days with the daily mean temperature below or at the 5th percentile (-7 °C) in cold seasons (November to March) during the study period. We applied a time-series design using quasi-Poisson regression combined with a distributed lag model to estimate the risk of asthma hospital admissions associated with cold spells. Stratified analyses by gender and age groups were conducted to identify the potential susceptible subpopulations to cold spells. We also explored the effect modification by air quality by dividing the daily air quality index (AQI) into two levels (high and low) based on the median value. RESULTS Cold spells increased the risk of asthma hospital admissions, with the maximum cumulative relative risk (CRR) over three weeks (Lag0-21) in the total population. The highest single-day relative risk (RR) was found on the days of cold spells (Lag0) with the RR = 1.059 (95% CI: 1.008-1.113), and the CRR at Lag0-21 was 1.333 (95% CI: 1.049-1.693). Across different gender and age groups, younger people (<65 years) were more sensitive to cold spells. No significant effect modification by AQI was detected. CONCLUSION Short-term exposure to cold spells is associated with an increased risk of hospital admissions for asthma in Beijing. During the cold spells, younger people aged <65 years were at particular risk for asthma exacerbations. Our results suggest that extreme cold events have a significant impact on asthma.
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Affiliation(s)
- Yuxiong Chen
- Department of Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, 100730, China
| | - Dehui Kong
- Department of Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, 100730, China
| | - Jia Fu
- Department of Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, 100730, China
| | - Yongqiao Zhang
- Department of Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, 100730, China
| | - Yakun Zhao
- Department of Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, 100730, China
| | - Yanbo Liu
- Department of Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, 100730, China
| | - Zhen'ge Chang
- Department of Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, 100730, China
| | - Yijie Liu
- Department of Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, 100730, China
| | - Xiaole Liu
- Department of Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, 100730, China
| | - Kaifeng Xu
- Department of Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, 100730, China
| | - Chengyu Jiang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Department of Biochemistry, Peking Union Medical College, Beijing, 100005, China
| | - Zhongjie Fan
- Department of Medicine, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, 100730, China.
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Abstract
Epigenetic modifications are emerging as important regulatory mechanisms of gene expression in lung disease, given that they are influenced by environmental exposures and genetic variants, and that they regulate immune and fibrotic processes. In this review, we introduce these concepts with a focus on the study of DNA methylation and histone modifications and discuss how they have been applied to lung disease, and how they can be applied to sarcoidosis. This information has implications for other exposure and immunologically mediated lung diseases, such as chronic beryllium disease, hypersensitivity pneumonitis, and asbestosis.
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Affiliation(s)
- Iain R Konigsberg
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Lisa A Maier
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Dept of Medicine, National Jewish Health, Denver, CO, USA
- Dept of Environmental and Occupational Health, Colorado School of Public Health, Aurora, CO, USA
| | - Ivana V Yang
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Dept of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
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Fiuza BSD, Fonseca HF, Meirelles PM, Marques CR, da Silva TM, Figueiredo CA. Understanding Asthma and Allergies by the Lens of Biodiversity and Epigenetic Changes. Front Immunol 2021; 12:623737. [PMID: 33732246 PMCID: PMC7957070 DOI: 10.3389/fimmu.2021.623737] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/08/2021] [Indexed: 12/12/2022] Open
Abstract
Exposure to different organisms (bacteria, mold, virus, protozoan, helminths, among others) can induce epigenetic changes affecting the modulation of immune responses and consequently increasing the susceptibility to inflammatory diseases. Epigenomic regulatory features are highly affected during embryonic development and are responsible for the expression or repression of different genes associated with cell development and targeting/conducting immune responses. The well-known, "window of opportunity" that includes maternal and post-natal environmental exposures, which include maternal infections, microbiota, diet, drugs, and pollutant exposures are of fundamental importance to immune modulation and these events are almost always accompanied by epigenetic changes. Recently, it has been shown that these alterations could be involved in both risk and protection of allergic diseases through mechanisms, such as DNA methylation and histone modifications, which can enhance Th2 responses and maintain memory Th2 cells or decrease Treg cells differentiation. In addition, epigenetic changes may differ according to the microbial agent involved and may even influence different asthma or allergy phenotypes. In this review, we discuss how exposure to different organisms, including bacteria, viruses, and helminths can lead to epigenetic modulations and how this correlates with allergic diseases considering different genetic backgrounds of several ancestral populations.
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Affiliation(s)
| | | | - Pedro Milet Meirelles
- Instituto de Biologia, Universidade Federal da Bahia, Salvador, Brazil
- Instituto Nacional de Ciência e Tecnologia em Estudos Interdisciplinares e Transdisciplinares em Ecologia e Evolução (IN-TREE), Salvador, Brazil
| | - Cintia Rodrigues Marques
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, Vitória da Conquista, Brazil
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Acevedo N, Alashkar Alhamwe B, Caraballo L, Ding M, Ferrante A, Garn H, Garssen J, Hii CS, Irvine J, Llinás-Caballero K, López JF, Miethe S, Perveen K, Pogge von Strandmann E, Sokolowska M, Potaczek DP, van Esch BCAM. Perinatal and Early-Life Nutrition, Epigenetics, and Allergy. Nutrients 2021; 13:724. [PMID: 33668787 PMCID: PMC7996340 DOI: 10.3390/nu13030724] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 02/08/2021] [Accepted: 02/12/2021] [Indexed: 02/08/2023] Open
Abstract
Epidemiological studies have shown a dramatic increase in the incidence and the prevalence of allergic diseases over the last several decades. Environmental triggers including risk factors (e.g., pollution), the loss of rural living conditions (e.g., farming conditions), and nutritional status (e.g., maternal, breastfeeding) are considered major contributors to this increase. The influences of these environmental factors are thought to be mediated by epigenetic mechanisms which are heritable, reversible, and biologically relevant biochemical modifications of the chromatin carrying the genetic information without changing the nucleotide sequence of the genome. An important feature characterizing epigenetically-mediated processes is the existence of a time frame where the induced effects are the strongest and therefore most crucial. This period between conception, pregnancy, and the first years of life (e.g., first 1000 days) is considered the optimal time for environmental factors, such as nutrition, to exert their beneficial epigenetic effects. In the current review, we discussed the impact of the exposure to bacteria, viruses, parasites, fungal components, microbiome metabolites, and specific nutritional components (e.g., polyunsaturated fatty acids (PUFA), vitamins, plant- and animal-derived microRNAs, breast milk) on the epigenetic patterns related to allergic manifestations. We gave insight into the epigenetic signature of bioactive milk components and the effects of specific nutrition on neonatal T cell development. Several lines of evidence suggest that atypical metabolic reprogramming induced by extrinsic factors such as allergens, viruses, pollutants, diet, or microbiome might drive cellular metabolic dysfunctions and defective immune responses in allergic disease. Therefore, we described the current knowledge on the relationship between immunometabolism and allergy mediated by epigenetic mechanisms. The knowledge as presented will give insight into epigenetic changes and the potential of maternal and post-natal nutrition on the development of allergic disease.
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Affiliation(s)
- Nathalie Acevedo
- Institute for Immunological Research, University of Cartagena, Cartagena 130014, Colombia; (N.A.); (L.C.); (K.L.-C.); (J.F.L.)
| | - Bilal Alashkar Alhamwe
- Institute of Tumor Immunology, Clinic for Hematology, Oncology and Immunology, Center for Tumor Biology and Immunology, Philipps University Marburg, 35043 Marburg, Germany; (B.A.A.); (E.P.v.S.)
- College of Pharmacy, International University for Science and Technology (IUST), Daraa 15, Syria
| | - Luis Caraballo
- Institute for Immunological Research, University of Cartagena, Cartagena 130014, Colombia; (N.A.); (L.C.); (K.L.-C.); (J.F.L.)
| | - Mei Ding
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, 7265 Davos, Switzerland; (M.D.); (M.S.)
- Christine Kühne-Center for Allergy Research and Education, 7265 Davos, Switzerland
- Department of Allergology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Antonio Ferrante
- Department of Immunopathology, SA Pathology at the Women’s and Children’s Hospital, North Adelaide, SA 5006, Australia; (A.F.); (C.S.H.); (J.I.); (K.P.)
- Adelaide School of Medicine and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Holger Garn
- Translational Inflammation Research Division & Core Facility for Single Cell Multiomics, Medical Faculty, Philipps University Marburg, Member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center, 35043 Marburg, Germany; (H.G.); (S.M.)
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CG Utrecht, The Netherlands;
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands
| | - Charles S. Hii
- Department of Immunopathology, SA Pathology at the Women’s and Children’s Hospital, North Adelaide, SA 5006, Australia; (A.F.); (C.S.H.); (J.I.); (K.P.)
- Adelaide School of Medicine and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - James Irvine
- Department of Immunopathology, SA Pathology at the Women’s and Children’s Hospital, North Adelaide, SA 5006, Australia; (A.F.); (C.S.H.); (J.I.); (K.P.)
- Adelaide School of Medicine and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - Kevin Llinás-Caballero
- Institute for Immunological Research, University of Cartagena, Cartagena 130014, Colombia; (N.A.); (L.C.); (K.L.-C.); (J.F.L.)
| | - Juan Felipe López
- Institute for Immunological Research, University of Cartagena, Cartagena 130014, Colombia; (N.A.); (L.C.); (K.L.-C.); (J.F.L.)
| | - Sarah Miethe
- Translational Inflammation Research Division & Core Facility for Single Cell Multiomics, Medical Faculty, Philipps University Marburg, Member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center, 35043 Marburg, Germany; (H.G.); (S.M.)
| | - Khalida Perveen
- Department of Immunopathology, SA Pathology at the Women’s and Children’s Hospital, North Adelaide, SA 5006, Australia; (A.F.); (C.S.H.); (J.I.); (K.P.)
- Adelaide School of Medicine and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5005, Australia
| | - Elke Pogge von Strandmann
- Institute of Tumor Immunology, Clinic for Hematology, Oncology and Immunology, Center for Tumor Biology and Immunology, Philipps University Marburg, 35043 Marburg, Germany; (B.A.A.); (E.P.v.S.)
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, 7265 Davos, Switzerland; (M.D.); (M.S.)
- Christine Kühne-Center for Allergy Research and Education, 7265 Davos, Switzerland
| | - Daniel P. Potaczek
- Translational Inflammation Research Division & Core Facility for Single Cell Multiomics, Medical Faculty, Philipps University Marburg, Member of the German Center for Lung Research (DZL) and the Universities of Giessen and Marburg Lung Center, 35043 Marburg, Germany; (H.G.); (S.M.)
| | - Betty C. A. M. van Esch
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, 3584 CG Utrecht, The Netherlands;
- Danone Nutricia Research, 3584 CT Utrecht, The Netherlands
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Silva CP, Kamens HM. Cigarette smoke-induced alterations in blood: A review of research on DNA methylation and gene expression. Exp Clin Psychopharmacol 2021; 29:116-135. [PMID: 32658533 PMCID: PMC7854868 DOI: 10.1037/pha0000382] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Worldwide, smoking remains a threat to public health, causing preventable diseases and premature mortality. Cigarette smoke is a powerful inducer of DNA methylation and gene expression alterations, which have been associated with negative health consequences. Here, we review the current knowledge on smoking-related changes in DNA methylation and gene expression in human blood samples. We identified 30 studies focused on the association between active smoking, DNA methylation modifications, and gene expression alterations. Overall, we identified 1,758 genes with differentially methylated sites (DMS) and differentially expressed genes (DEG) between smokers and nonsmokers, of which 261 were detected in multiple studies (≥4). The most frequently (≥10 studies) reported genes were AHRR, GPR15, GFI1, and RARA. Functional enrichment analysis of the 261 genes identified the aryl hydrocarbon receptor repressor and T cell pathways (T helpers 1 and 2) as influenced by smoking status. These results highlight specific genes for future mechanistic and translational research that may be associated with cigarette smoke exposure and smoking-related diseases. (PsycInfo Database Record (c) 2021 APA, all rights reserved).
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Affiliation(s)
- Constanza P. Silva
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States of America
| | - Helen M. Kamens
- Department of Biobehavioral Health, The Pennsylvania State University, University Park, Pennsylvania, 16802, United States of America.,Correspondence concerning this article should be addressed to Helen M. Kamens, 228 Biobehavioral Health Building, The Pennsylvania State University, University Park, PA 16802; ; Phone number: 814-865-1269; Fax number: 814-863-7525
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Feng Z, Wang J, Xie Y, Li J. Effects of exercise-based pulmonary rehabilitation on adults with asthma: a systematic review and meta-analysis. Respir Res 2021; 22:33. [PMID: 33516207 PMCID: PMC7847170 DOI: 10.1186/s12931-021-01627-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 01/18/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Pulmonary rehabilitation (PR) has been proposed as an effective method for many respiratory diseases. However, the effects of exercise-based PR on asthma are currently inconclusive. This review aimed to investigate the effects of exercise-based PR on adults with asthma. METHODS The PubMed, Embase, Cochrane Library, Web of Science, International Clinical Trials Registry Platform and ClinicalTrials.gov databases were searched from inception to 31 July 2019 without language restriction. Randomized controlled trials (RCTs) investigating the effects of exercise-based PR on adults with asthma were included. Study selection, data extraction and risk of bias assessment were performed by two investigators independently. Meta-analysis was conducted by RevMan software (version 5.3). Evidence quality was rated by the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) system. RESULTS Ten literatures from nine studies (n = 418 patients) were identified. Asthma quality of life questionnaire total scores (MD = 0.39, 95% CI: 0.02 to 0.76) improved significantly in the experimental group compared to control group, including activity domain scores (MD = 0.58, 95% CI: 0.21 to 0.94), symptom domain scores (MD = 0.52, 95% CI: 0.19 to 0.85), emotion domain scores (MD = 0.53, 95% CI: - 0.03 to 1.09) and environment domain scores (MD = 0.56, 95% CI: 0.00 to 1.11). Both the 6-min walk distance (MD = 34.09, 95% CI: 2.51 to 65.66) and maximum oxygen uptake (MD = 4.45, 95% CI: 3.32 to 5.58) significantly improved. However, improvements in asthma control questionnaire scores (MD = - 0.25, 95% CI: - 0.51 to 0.02) and asthma symptom-free days (MD = 3.35, 95% CI: - 0.21 to 6.90) were not significant. Moreover, there was no significant improvement (MD = 0.10, 95% CI: - 0.08 to 0.29) in forced expiratory volume in 1 s. Nonetheless, improvements in forced vital capacity (MD = 0.23, 95% CI: 0.08 to 0.38) and peak expiratory flow (MD = 0.39, 95% CI: 0.21 to 0.57) were significant. CONCLUSIONS Exercise-based PR may improve quality of life, exercise tolerance and some aspects of pulmonary function in adults with asthma and can be considered a supplementary therapy. RCTs of high quality and large sample sizes are required. CLINICAL TRIAL REGISTRATION The review was registered with PROSPERO (The website is https://www.crd.york.ac.uk/prospero/ , and the ID is CRD42019147107).
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Affiliation(s)
- Zhenzhen Feng
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China.,Co-Construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases By Henan & Education Ministry of P.R. China, Henan University of Chinese Medicine, 156 Jinshui East Road, Zhengzhou, 450046, China.,Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Jiajia Wang
- Co-Construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases By Henan & Education Ministry of P.R. China, Henan University of Chinese Medicine, 156 Jinshui East Road, Zhengzhou, 450046, China.,Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, Zhengzhou, 450046, China.,Department of Respiratory Diseases, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, 450000, China
| | - Yang Xie
- Co-Construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases By Henan & Education Ministry of P.R. China, Henan University of Chinese Medicine, 156 Jinshui East Road, Zhengzhou, 450046, China.,Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, Zhengzhou, 450046, China.,Department of Respiratory Diseases, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, 450000, China
| | - Jiansheng Li
- Co-Construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases By Henan & Education Ministry of P.R. China, Henan University of Chinese Medicine, 156 Jinshui East Road, Zhengzhou, 450046, China. .,Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Henan University of Chinese Medicine, Zhengzhou, 450046, China. .,Department of Respiratory Diseases, The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, 450000, China.
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Feng J, Pang J, He D, Wu Z, Li Q, Ji P, He C, Zhong Z, Li H, Zhang J. Identification of Genes with Altered Methylation and Its Role in Early Diagnosis of Sepsis-Induced Acute Respiratory Distress Syndrome. Int J Gen Med 2021; 14:243-253. [PMID: 33536775 PMCID: PMC7847772 DOI: 10.2147/ijgm.s287960] [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: 10/21/2020] [Accepted: 01/06/2021] [Indexed: 01/10/2023] Open
Abstract
Purpose Early diagnosis of sepsis-induced acute respiratory distress syndrome (ARDS) is critical for effective treatment. We aimed to identify early stage biomarkers. Materials and Methods Differentially expressed genes were identified in whole blood samples from patients with sepsis or ARDS based on the Gene Expression Omnibus (GEO) datasets GSE32707, GSE54514 and GSE10361. Functional enrichment analysis explored the biological characteristics of differentially expressed genes. Genes with high functional connectivity based on a protein-protein interaction network were marked as hub genes, which were validated using the GEO dataset GSE76293, and a gene set variation analysis index (GSVA) was assigned. Diagnostic and predictive ability of the hub genes were assessed by receiver operating characteristic (ROC) curve analysis. DNA methylation levels of hub genes were quantified using the GEO dataset GSE67530. Results Forty-one differentially expressed genes were shared between sepsis-specific and ARDS-specific datasets. MAP2K2 and IRF7 functional activity was highly connected in sepsis-induced ARDS. Hub genes included RETN, MVP, DEFA4, CTSG, AZU1, FMNL1, RBBP7, POLD4, RIN3, IRF7. ROC curve analysis of the hub gene GSVA index showed good diagnostic ability in sepsis or ARDS. Among genes related to sepsis-induced ARDS, 17 were differentially methylated. Principal component analysis and heatmaps indicated that gene methylation patterns differed significantly between ARDS patients and controls. Conclusion We identified a genetic profile specific to early-stage sepsis-induced ARDS. The abnormal expression of these genes may be caused by hypomethylation, which may serve as a biomarker for early diagnosis of ARDS.
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Affiliation(s)
- Jihua Feng
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, People's Republic of China
| | - Jielong Pang
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, People's Republic of China
| | - Dan He
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, People's Republic of China
| | - Zimeng Wu
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, People's Republic of China
| | - Qian Li
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, People's Republic of China
| | - Pan Ji
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, People's Republic of China
| | - Cuiying He
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, People's Republic of China
| | - Zhimei Zhong
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, People's Republic of China
| | - Hongyuan Li
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, People's Republic of China
| | - Jianfeng Zhang
- Department of Emergency Medicine, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, People's Republic of China
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Caliri AW, Tommasi S, Besaratinia A. Relationships among smoking, oxidative stress, inflammation, macromolecular damage, and cancer. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 787:108365. [PMID: 34083039 PMCID: PMC8287787 DOI: 10.1016/j.mrrev.2021.108365] [Citation(s) in RCA: 201] [Impact Index Per Article: 67.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 02/07/2023]
Abstract
Smoking is a major risk factor for a variety of diseases, including cancer and immune-mediated inflammatory diseases. Tobacco smoke contains a mixture of chemicals, including a host of reactive oxygen- and nitrogen species (ROS and RNS), among others, that can damage cellular and sub-cellular targets, such as lipids, proteins, and nucleic acids. A growing body of evidence supports a key role for smoking-induced ROS and the resulting oxidative stress in inflammation and carcinogenesis. This comprehensive and up-to-date review covers four interrelated topics, including 'smoking', 'oxidative stress', 'inflammation', and 'cancer'. The review discusses each of the four topics, while exploring the intersections among the topics by highlighting the macromolecular damage attributable to ROS. Specifically, oxidative damage to macromolecular targets, such as lipid peroxidation, post-translational modification of proteins, and DNA adduction, as well as enzymatic and non-enzymatic antioxidant defense mechanisms, and the multi-faceted repair pathways of oxidized lesions are described. Also discussed are the biological consequences of oxidative damage to macromolecules if they evade the defense mechanisms and/or are not repaired properly or in time. Emphasis is placed on the genetic- and epigenetic alterations that may lead to transcriptional deregulation of functionally-important genes and disruption of regulatory elements. Smoking-associated oxidative stress also activates the inflammatory response pathway, which triggers a cascade of events of which ROS production is an initial yet indispensable step. The release of ROS at the site of damage and inflammation helps combat foreign pathogens and restores the injured tissue, while simultaneously increasing the burden of oxidative stress. This creates a vicious cycle in which smoking-related oxidative stress causes inflammation, which in turn, results in further generation of ROS, and potentially increased oxidative damage to macromolecular targets that may lead to cancer initiation and/or progression.
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Affiliation(s)
- Andrew W Caliri
- Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, M/C 9603, Los Angeles, CA 90033, USA
| | - Stella Tommasi
- Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, M/C 9603, Los Angeles, CA 90033, USA
| | - Ahmad Besaratinia
- Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, M/C 9603, Los Angeles, CA 90033, USA.
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Watanabe H, Miyake K, Matsuoka T, Kojima R, Sakurai D, Masuyama K, Yamagata Z. LPCAT2 Methylation, a Novel Biomarker for the Severity of Cedar Pollen Allergic Rhinitis in Japan. Am J Rhinol Allergy 2020; 35:631-639. [PMID: 33356413 DOI: 10.1177/1945892420983646] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Recently, the role of the epigenome in allergies has been receiving increasing attention. Although several genes that are methylated in relation to serum immunoglobulin E (IgE) concentration have been reported by epigenome-wide association studies, little is known about the DNA methylation sites associated with the symptoms and severity of cedar pollinosis (CP). OBJECTIVE Our aim was to analyze the association between DNA methylation and the symptoms and severity of CP in peripheral blood mononuclear cells (PBMCs) and nasal mucosa scraping cells (NMSCs). METHODS We recruited 70 participants during the cedar pollen dispersal season. IgE levels were measured by a fluorescence enzyme immunoassay. We analyzed DNA methylation of acyl-CoA thioesterase 7 (ACOT7), mucin 4 (MUC4), schlafen 12 (SLFN12), lysophosphatidylcholine acyltransferase 2 (LPCAT2), and interleukin-4 (IL4) in PBMCs and NMSCs using bisulfite next-generation sequencing; the correlation of DNA methylation with non-specific IgE and cedar pollen-specific IgE levels in peripheral blood samples was also investigated. Symptom severity and DNA methylation were investigated in 15 untreated CP patients. RESULTS Non-specific IgE levels showed a significant negative correlation with average IL4 methylation in PBMCs (r = -0.46, P < 0.0001) but not with methylation of ACOT7, MUC4, SLFN12, and LPCAT2. Cedar pollen-specific IgE levels showed a significant negative correlation with average IL4 and MUC4 methylation in PBMCs (r = -0.31, P = 0.01 and r = -0.241, P = 0.046, respectively) but not with methylation of ACOT7, SLFN12, and LPCAT2. The methylation of some genes in NMSCs was not significantly correlated with IgE levels. The mean methylation of LPCAT2 in NMSCs showed a decreasing trend with increasing severity of CP (P = 0.027). CONCLUSION LPCAT2 methylation in NMSCs may reflect the severity of CP and could be used as a novel biomarker to identify suitable treatment options for CP.
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Affiliation(s)
- Hiroyuki Watanabe
- Department of Otorhinolaryngology, Head and Neck Surgery, Faculty of Medicine, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Kofu, Japan.,Department of Health Sciences, Graduate School of Interdisciplinary Research, University of Yamanashi, Kofu, Japan
| | - Kunio Miyake
- Department of Health Sciences, Graduate School of Interdisciplinary Research, University of Yamanashi, Kofu, Japan
| | - Tomokazu Matsuoka
- Department of Otorhinolaryngology, Head and Neck Surgery, Faculty of Medicine, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Kofu, Japan
| | - Reiji Kojima
- Department of Health Sciences, Graduate School of Interdisciplinary Research, University of Yamanashi, Kofu, Japan
| | - Daiju Sakurai
- Department of Otorhinolaryngology, Head and Neck Surgery, Faculty of Medicine, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Kofu, Japan
| | - Keisuke Masuyama
- Department of Otorhinolaryngology, Head and Neck Surgery, Faculty of Medicine, Graduate Faculty of Interdisciplinary Research, University of Yamanashi, Kofu, Japan.,Department of Otorhinolaryngology, Suwa Central Hospital, Chino, Japan
| | - Zentaro Yamagata
- Department of Health Sciences, Graduate School of Interdisciplinary Research, University of Yamanashi, Kofu, Japan
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Liu T, Sun Y, Bai W. The Role of Epigenetics in the Chronic Sinusitis with Nasal Polyp. Curr Allergy Asthma Rep 2020; 21:1. [PMID: 33236242 DOI: 10.1007/s11882-020-00976-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2020] [Indexed: 12/13/2022]
Abstract
PURPOSE OF REVIEW Chronic rhinosinusitis with nasal polyps (CRSwNP) is a common and heterogeneous inflammatory disease. The underlying epigenetic mechanisms and treatment of CRSwNP are partially understood. Of the different epigenetic changes in CRSwNP, histone deacetylases (HDACs), methylation of DNA, and the levels of miRNA are widely studied. Here, we review the human studies of epigenetic mechanisms in CRSwNP. RECENT FINDINGS The promoters of COL18A1, PTGES, PLAT, and TSLP genes are hypermethylated in CRSwNP compared with those of controls, while the promoters of PGDS, ALOX5AP, LTB4R, IL-8, and FZD5 genes are hypomethylated in CRSwNP. Promoter hypermethylation suppresses the gene expression, while promoter hypomethylation increases the gene expression. Studies have shown the elevation in the levels of HDAC2, HDAC4, and H3K4me3 in CRSwNP. In CRSwNP patients, there is also an upregulation of certain miRNAs including miR-125b, miR-155, miR-19a, miR-142-3p, and miR-21 and downregulation of miR-4492. Epigenetics takes part in the immunology of CRSwNP and may give rise to endotypes of CRSwNP. Both HDAC2 and the miRNA including miR-18a, miR-124a, and miR-142-3p may take function in the regulation of glucocorticoid resistance. HDAC inhibitors and KDM2B have shown effectiveness in decreasing nasal polyp, and DNA methyltransferase (DNMT) or HDAC inhibitors may have a potential efficacy for the treatment of CRSwNP. Recent advances in the epigenetics of CRSwNP have led to the identification of several potential therapeutic targets for this disease. The use of epigenetics may provide novel and effective biomarkers and therapies for the treatment of nasal polyp.
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Affiliation(s)
- Tiancong Liu
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Yang Sun
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Weiliang Bai
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
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Huang J, Hu X, Zheng X, Kuang J, Liu C, Wang X, Tang Y. Effects of STIP1 and GLCCI1 polymorphisms on the risk of childhood asthma and inhaled corticosteroid response in Chinese asthmatic children. BMC Pulm Med 2020; 20:303. [PMID: 33208131 PMCID: PMC7677774 DOI: 10.1186/s12890-020-01332-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 11/02/2020] [Indexed: 12/21/2022] Open
Abstract
Background Asthma is a common chronic lung disease in children. We aimed to determine the associations between stress-induced phosphoprotein 1 (STIP1) and glucocorticoid-induced transcript 1 (GLCCI1) polymorphisms and susceptibility of childhood asthma and inhaled corticosteroid (ICS) response in children. Methods A total of 263 Chinese Han asthmatic children were recruited from the Xiangya Hospital, Central South University. Pulmonary function tests were performed before the treatment and 3 months after the treatment. One hundred fifty non-asthmatic children were recruited. Each participant’s DNA was extracted from the peripheral blood and Method of MassARRAY was used to genotype the single-nucleotide polymorphisms (SNPs). Results STIP1 rs2236647 wild-type homozygote (CC) was associated with increased asthma risk of children (OR = 1.858, 95% CI:1.205–2.864), but not associated with the ICS response. GLCCI1 rs37969, rs37972 and rs37973 polymorphisms were not associated with the risk of childhood asthma. However, rs37969 mutant genotypes (TT/GT) were significantly associated with less improvement in PD20 (p = 0.028). We also found significant associations between rs37969, rs37972 and rs37973 mutant genotypes and less improvement in maximal midexpiratory flow (MMEF) after ICS treatment for 3 months (p = 0.036, p = 0.010 and p = 0.003, respectively). Conclusions STIP1 rs2236647 was associated with asthma risk of children and GLCCI1 rs37969 mutant genotypes were associated with less improvement in airway hyper-responsiveness. GLCCI1 rs37969, rs37972 and rs37973 polymorphisms might be associated with pulmonary function in childhood asthma patients after ICS treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-020-01332-2.
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Affiliation(s)
- Juan Huang
- Department of Pediatric, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Pediatric, The First Hospital of Changsha, Changsha, Hunan, China
| | - Xiaolei Hu
- National Institution of Drug Clinical Trial, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiangrong Zheng
- Department of Pediatric, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Jian Kuang
- Department of Pediatric, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chentao Liu
- Department of Pediatric, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xia Wang
- Department of Pediatric, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yongjun Tang
- Department of Pediatric, Xiangya Hospital, Central South University, Changsha, Hunan, China
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Groth EE, Weber M, Bahmer T, Pedersen F, Kirsten A, Börnigen D, Rabe KF, Watz H, Ammerpohl O, Goldmann T. Exploration of the sputum methylome and omics deconvolution by quadratic programming in molecular profiling of asthma and COPD: the road to sputum omics 2.0. Respir Res 2020; 21:274. [PMID: 33076907 PMCID: PMC7574293 DOI: 10.1186/s12931-020-01544-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/11/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND To date, most studies involving high-throughput analyses of sputum in asthma and COPD have focused on identifying transcriptomic signatures of disease. No whole-genome methylation analysis of sputum cells has been performed yet. In this context, the highly variable cellular composition of sputum has potential to confound the molecular analyses. METHODS Whole-genome transcription (Agilent Human 4 × 44 k array) and methylation (Illumina 450 k BeadChip) analyses were performed on sputum samples of 9 asthmatics, 10 healthy and 10 COPD subjects. RNA integrity was checked by capillary electrophoresis and used to correct in silico for bias conferred by RNA degradation during biobank sample storage. Estimates of cell type-specific molecular profiles were derived via regression by quadratic programming based on sputum differential cell counts. All analyses were conducted using the open-source R/Bioconductor software framework. RESULTS A linear regression step was found to perform well in removing RNA degradation-related bias among the main principal components of the gene expression data, increasing the number of genes detectable as differentially expressed in asthma and COPD sputa (compared to controls). We observed a strong influence of the cellular composition on the results of mixed-cell sputum analyses. Exemplarily, upregulated genes derived from mixed-cell data in asthma were dominated by genes predominantly expressed in eosinophils after deconvolution. The deconvolution, however, allowed to perform differential expression and methylation analyses on the level of individual cell types and, though we only analyzed a limited number of biological replicates, was found to provide good estimates compared to previously published data about gene expression in lung eosinophils in asthma. Analysis of the sputum methylome indicated presence of differential methylation in genomic regions of interest, e.g. mapping to a number of human leukocyte antigen (HLA) genes related to both major histocompatibility complex (MHC) class I and II molecules in asthma and COPD macrophages. Furthermore, we found the SMAD3 (SMAD family member 3) gene, among others, to lie within differentially methylated regions which has been previously reported in the context of asthma. CONCLUSIONS In this methodology-oriented study, we show that methylation profiling can be easily integrated into sputum analysis workflows and exhibits a strong potential to contribute to the profiling and understanding of pulmonary inflammation. Wherever RNA degradation is of concern, in silico correction can be effective in improving both sensitivity and specificity of downstream analyses. We suggest that deconvolution methods should be integrated in sputum omics analysis workflows whenever possible in order to facilitate the unbiased discovery and interpretation of molecular patterns of inflammation.
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Affiliation(s)
- Espen E Groth
- LungenClinic Grosshansdorf, Großhansdorf, Germany. .,Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Großhansdorf, Germany. .,Department of Internal Medicine I, Pneumology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany. .,Department of Oncology, Hematology and BMT with Section Pneumology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Melanie Weber
- Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ, USA
| | - Thomas Bahmer
- LungenClinic Grosshansdorf, Großhansdorf, Germany.,Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Großhansdorf, Germany.,Department of Internal Medicine I, Pneumology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Frauke Pedersen
- LungenClinic Grosshansdorf, Großhansdorf, Germany.,Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Großhansdorf, Germany.,Pulmonary Research Institute at LungenClinic Grosshansdorf, Großhansdorf, Germany
| | - Anne Kirsten
- Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Großhansdorf, Germany.,Pulmonary Research Institute at LungenClinic Grosshansdorf, Großhansdorf, Germany
| | - Daniela Börnigen
- Bioinformatics Core Unit, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus F Rabe
- LungenClinic Grosshansdorf, Großhansdorf, Germany.,Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Großhansdorf, Germany
| | - Henrik Watz
- Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Großhansdorf, Germany.,Pulmonary Research Institute at LungenClinic Grosshansdorf, Großhansdorf, Germany
| | - Ole Ammerpohl
- Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Großhansdorf, Germany.,Institute of Human Genetics, University Medical Center Ulm, Ulm, Germany
| | - Torsten Goldmann
- Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Großhansdorf, Germany.,Research Center Borstel, Pathology, Borstel, Germany
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Li YL, Xing XQ, Xiao Y, Liu YH, Zhou YS, Zhuang M, Li CQ. Correlation between DNA methylation and Thymic Stromal Lymphopoietin expression in asthmatic airway epithelial cells. Genes Genomics 2020; 42:1399-1406. [PMID: 33040302 DOI: 10.1007/s13258-020-01000-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 09/15/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND The overexpression of TSLP and DNA methylation in asthma were both risk factors the relationship was not clear. OBJECTIVE This study aimed to investigate the relationship between methylation status of TSLP promoter and mRNA/protein expression in asthmatic airway epithelial cells. METHODS Human bronchial epithelial cells were cultured in vitro and divided into: Control group, treated with PBS, model group, sensitized with LPS (10 μg/mL) for 12 h (37 °C, 5% CO2). Other groups were cultured with the pCMV3 plasmid (M + NC/pCMV), pGPH1 plasmid (M + NC/pGPH), DNMT1/pCMV3 plasmid (M + DNMT1/pCMV), and DNMT1/pGPH1 plasmid (M + DNMT1/pGPH) for 48 h. The expression of DNA methyltransferase 1 and TSLP were measured using real-time PCR and western blotting. RESULTS Compared with the control group, TSLP mRNA (1.00 ± 0.00 vs. 2.82 ± 0.81 vs. 1, P < 0.001) and protein (1.07 ± 0.04 vs. 1.46 ± 0.11, P < 0.01) were significantly greater, and the methylation of promoter was lower (92.75 ± 1.26 vs. 58.57 ± 3.34, P < 0.05) in the model group. Compared with the model group, TSLP mRNA (2.82 ± 0.81 vs. 1.17 ± 0.10, P < 0.001) decreased, but TSLP promoter methylation increased (58.57 ± 3.34 vs. 92.58 ± 7.30, P < 0.05) in M + DNMT1/pCMV. TSLP mRNA and protein were higher (2.82 ± 0.81 vs. 5.32 ± 0.21, P < 0.001; 1.46 ± 0.11 vs. 1.94 ± 0.11, respectively, P < 0.01), TSLP promoter methylation was lower (58.57 ± 3.34 vs. 33.57 ± 4.29, P < 0.05) in M + DNMT1/pGPH. CONCLUSIONS Overexpression of TSLP in asthmatic airway epithelial cells may be regulated by DNA demethylation.
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Affiliation(s)
- Yan-Li Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Qingxiu District, Nanning, 530021, Guangxi, People's Republic of China.,First Department of Pulmonary and Critical Care Medicine, Yan'An Hospital Affiliated to Kunming Medical University, Kunming, 650051, Yunnan, People's Republic of China
| | - Xi-Qian Xing
- First Department of Pulmonary and Critical Care Medicine, Yan'An Hospital Affiliated to Kunming Medical University, Kunming, 650051, Yunnan, People's Republic of China
| | - Yi Xiao
- First Department of Pulmonary and Critical Care Medicine, Yan'An Hospital Affiliated to Kunming Medical University, Kunming, 650051, Yunnan, People's Republic of China
| | - Yan-Hong Liu
- First Department of Pulmonary and Critical Care Medicine, Yan'An Hospital Affiliated to Kunming Medical University, Kunming, 650051, Yunnan, People's Republic of China
| | - Yu-Shan Zhou
- First Department of Pulmonary and Critical Care Medicine, Yan'An Hospital Affiliated to Kunming Medical University, Kunming, 650051, Yunnan, People's Republic of China
| | - Min Zhuang
- First Department of Pulmonary and Critical Care Medicine, Yan'An Hospital Affiliated to Kunming Medical University, Kunming, 650051, Yunnan, People's Republic of China
| | - Chao-Qian Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Qingxiu District, Nanning, 530021, Guangxi, People's Republic of China.
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Men S, Yu Y. Prospects for Use of Single-Cell Sequencing to Assess DNA Methylation in Asthma. Med Sci Monit 2020; 26:e925514. [PMID: 33009362 PMCID: PMC7539641 DOI: 10.12659/msm.925514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Asthma is a complex disease with an increasing prevalence rate caused by the interaction of multiple genetically inherited and environmental factors. Epigenetics link genetic susceptibility and environmental factors. DNA methylation is an epigenetic modification that plays a crucial role in the regulation of growth and development, gene expression, and disease. Relatively little is known about DNA methylation in asthma, with few studies to date using single-cell sequencing to analyze the molecular mechanism by which DNA methylation regulates asthma. Cells with similar phenotypes may be heterogeneous in function and transcription, as may their genetic information. Although multi-omics methods, such as studies of the genome, transcriptome, and epigenome, can be used to evaluate biological processes, these methods are applicable only to groups of cells or tissues and provide averages that may obscure direct correlations among multiple layers of data. Single-cell sequencing technology can clarify the methylation and expression of genes in different populations of cells, in contrast to traditional multi-omics sequencing, which can determine only average values of cell populations. Single-cell sequence can therefore better reflect the pathogenesis of asthma, as it can clarify the function and regulatory mechanism of DNA methylation in asthma, and detect new genes and molecular markers that may become therapeutic targets in this disease.
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Affiliation(s)
- Shuai Men
- Pediatric Asthma Department, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China (mainland)
| | - Yanyan Yu
- Pediatric Asthma Department, Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China (mainland)
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Decoding Susceptibility to Respiratory Viral Infections and Asthma Inception in Children. Int J Mol Sci 2020; 21:ijms21176372. [PMID: 32887352 PMCID: PMC7503410 DOI: 10.3390/ijms21176372] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 01/19/2023] Open
Abstract
Human Respiratory Syncytial Virus and Human Rhinovirus are the most frequent cause of respiratory tract infections in infants and children and are major triggers of acute viral bronchiolitis, wheezing and asthma exacerbations. Here, we will discuss the application of the powerful tools of systems biology to decode the molecular mechanisms that determine risk for infection and subsequent asthma. An important conceptual advance is the understanding that the innate immune system is governed by a Bow-tie architecture, where diverse input signals converge onto a few core pathways (e.g., IRF7), which in turn generate diverse outputs that orchestrate effector and regulatory functions. Molecular profiling studies in children with severe exacerbations of asthma/wheeze have identified two major immunological phenotypes. The IRF7hi phenotype is characterised by robust upregulation of antiviral response networks, and the IRF7lo phenotype is characterised by upregulation of markers of TGFβ signalling and type 2 inflammation. Similar phenotypes have been identified in infants and children with severe viral bronchiolitis. Notably, genome-wide association studies supported by experimental validation have identified key pathways that increase susceptibility to HRV infection (ORMDL3 and CHDR3) and modulate TGFβ signalling (GSDMB, TGFBR1, and SMAD3). Moreover, functional deficiencies in the activation of type I and III interferon responses are already evident at birth in children at risk of developing febrile lower respiratory tract infections and persistent asthma/wheeze, suggesting that the trajectory to asthma begins at birth or in utero. Finally, exposure to microbes and their products reprograms innate immunity and provides protection from the development of allergies and asthma in children, and therefore microbial products are logical candidates for the primary prevention of asthma.
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Heijink IH, Kuchibhotla VNS, Roffel MP, Maes T, Knight DA, Sayers I, Nawijn MC. Epithelial cell dysfunction, a major driver of asthma development. Allergy 2020; 75:1902-1917. [PMID: 32460363 PMCID: PMC7496351 DOI: 10.1111/all.14421] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 05/04/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022]
Abstract
Airway epithelial barrier dysfunction is frequently observed in asthma and may have important implications. The physical barrier function of the airway epithelium is tightly interwoven with its immunomodulatory actions, while abnormal epithelial repair responses may contribute to remodelling of the airway wall. We propose that abnormalities in the airway epithelial barrier play a crucial role in the sensitization to allergens and pathogenesis of asthma. Many of the identified susceptibility genes for asthma are expressed in the airway epithelium, supporting the notion that events at the airway epithelial surface are critical for the development of the disease. However, the exact mechanisms by which the expression of epithelial susceptibility genes translates into a functionally altered response to environmental risk factors of asthma are still unknown. Interactions between genetic factors and epigenetic regulatory mechanisms may be crucial for asthma susceptibility. Understanding these mechanisms may lead to identification of novel targets for asthma intervention by targeting the airway epithelium. Moreover, exciting new insights have come from recent studies using single‐cell RNA sequencing (scRNA‐Seq) to study the airway epithelium in asthma. This review focuses on the role of airway epithelial barrier function in the susceptibility to develop asthma and novel insights in the modulation of epithelial cell dysfunction in asthma.
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Affiliation(s)
- Irene H. Heijink
- Department of Pathology & Medical Biology GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen The Netherlands
- Department of Pulmonology University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Virinchi N. S. Kuchibhotla
- Department of Pathology & Medical Biology GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen The Netherlands
- School of Biomedical Sciences and Pharmacy University of Newcastle Callaghan NSW Australia
| | - Mirjam P. Roffel
- Department of Pathology & Medical Biology GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen The Netherlands
- Department of Respiratory Medicine Laboratory for Translational Research in Obstructive Pulmonary Diseases Ghent University Hospital Ghent University Ghent Belgium
| | - Tania Maes
- Department of Respiratory Medicine Laboratory for Translational Research in Obstructive Pulmonary Diseases Ghent University Hospital Ghent University Ghent Belgium
| | - Darryl A. Knight
- School of Biomedical Sciences and Pharmacy University of Newcastle Callaghan NSW Australia
- UBC Providence Health Care Research Institute Vancouver BC Canada
- Department of Anesthesiology, Pharmacology and Therapeutics University of British Columbia Vancouver BC Canada
| | - Ian Sayers
- Division of Respiratory Medicine National Institute for Health Research Nottingham Biomedical Research Centre University of Nottingham Biodiscovery Institute University of Nottingham Nottingham UK
| | - Martijn C. Nawijn
- Department of Pathology & Medical Biology GRIAC Research Institute University Medical Center Groningen University of Groningen Groningen The Netherlands
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Krempski JW, Dant C, Nadeau KC. The origins of allergy from a systems approach. Ann Allergy Asthma Immunol 2020; 125:507-516. [PMID: 32702411 DOI: 10.1016/j.anai.2020.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/10/2020] [Accepted: 07/14/2020] [Indexed: 12/24/2022]
Abstract
OBJECTIVE The origins of allergic diseases have traditionally been explained by immunoglobulin E-mediated immune responses to account for asthma, atopic dermatitis, atopic rhinitis, and food allergy. Research insights into disease origins support a broader array of factors that predispose, initiate, or exacerbate altered immunity in allergic diseases, such as (1) inherent epithelial barrier dysfunction; (2) loss of immune tolerance; (3) disturbances in the gut; and (4) organ-specific microbiomes, diet, and age. Here, we discuss these influences that together form a better understanding of allergy as a systems disease. DATA SOURCES We summarize recent advances in epithelial dysfunction, environmental influences, inflammation, infection, alterations in the specific microbiome, and inherent genetic predisposition. STUDY SELECTIONS We performed a literature search targeting primary and review articles. RESULTS We explored microbial-epithelial-immune interactions underlying the early-life origins of allergic disorders and evaluated immune mechanisms suggesting novel disease prevention or intervention strategies. Damage to epithelial surfaces lies at the origin of various manifestations of allergic disease. As a sensor of environmental stimuli, the epithelium of the lungs, gut, and skin is affected by an altered microbiome, air pollution, food allergens in a changed diet, and chemicals in modern detergents. This collectively leads to alterations of lung, skin, or gut epithelial surfaces, driving a type 2 immune response that underlies atopic diseases. Treatment and prevention of allergic diseases include biologics, oral desensitization, targeted gut microbiome alterations, and changes in behavior. CONCLUSION Understanding the spectrum of allergy as a systems disease will allow us to better define the mechanisms of allergic disorders and improve their treatment.
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Affiliation(s)
- James Walter Krempski
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, California
| | - Christopher Dant
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, California
| | - Kari C Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, California; Department of Medicine, Stanford University School of Medicine, Stanford, California.
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Genome‑wide analysis of DNA methylation and gene expression changes in an ovalbumin‑induced asthma mouse model. Mol Med Rep 2020; 22:1709-1716. [PMID: 32705270 PMCID: PMC7411290 DOI: 10.3892/mmr.2020.11245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 02/04/2020] [Indexed: 12/12/2022] Open
Abstract
The aim of the present study was to establish an integrated network of DNA methylation and RNA expression in an ovalbumin (OVA)-induced asthma model, and to investigate the epigenetically-regulated genes involved in asthma development. Genome-wide CpG-DNA methylation profiling was conducted through the use of a methylated DNA immunoprecipitation microarray and RNA sequencing was performed using three lung samples from mice with OVA-induced asthma. A total of 35,401 differentially methylated regions (DMRs) were identified between mice with OVA-induced asthma and control mice. Of these, 3,060 were located in promoter regions and 370 of the genes containing these DMRs demonstrated an inverse correlation between methylation and gene expression. Kyoto Encyclopedia of Genes and Genomes pathway analysis identified that 368 genes were upregulated or downregulated in OVA-induced asthma samples, including genes involved in ‘chemokine signalling pathway’, ‘focal adhesion’, ‘leukocyte transendothelial migration’ and ‘vascular smooth muscle contraction signaling’ pathways. Integrated network analysis identified four hub genes, consisting of three upregulated genes [forkhead box O1 (FOXO1), SP1 transcription factor (SP1) and amyloid β precursor protein (APP)], and one downregulated gene [RUNX family transcription factor 1 (RUNX1)], all of which demonstrated an association between DNA methylation and gene expression. These genes were highly interconnected nodes in the Ingenuity Pathway Analysis module and were functionally significant. A total of four interconnected hub genes, FOXO1, RUNX1, SP1 and APP, were identified from the integrated DNA methylation and gene expression networks involved in asthma development. These results suggested that modulating these four genes could effectively control the development of asthma.
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Sugita K, Soyka MB, Wawrzyniak P, Rinaldi AO, Mitamura Y, Akdis M, Akdis CA. Outside-in hypothesis revisited: The role of microbial, epithelial, and immune interactions. Ann Allergy Asthma Immunol 2020; 125:517-527. [PMID: 32454094 DOI: 10.1016/j.anai.2020.05.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/14/2020] [Accepted: 05/17/2020] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Our understanding of the origin of allergic diseases has increased in recent years, highlighting the importance of microbial dysbiosis and epithelial barrier dysfunction in affected tissues. Exploring the microbial-epithelial-immune crosstalk underlying the mechanisms of allergic diseases will allow the development of novel prevention and treatment strategies for allergic diseases. DATA SOURCES This review summarizes the recent advances in microbial, epithelial, and immune interactions in atopic dermatitis, allergic rhinitis, chronic rhinosinusitis, and asthma. STUDY SELECTIONS We performed a literature search, identifying relevant recent primary articles and review articles. RESULTS Dynamic crosstalk between the environmental factors and microbial, epithelial, and immune cells in the development of atopic dermatitis, allergic rhinitis, chronic rhinosinusitis, and asthma underlies the pathogenesis of these diseases. There is substantial evidence in the literature suggesting that environmental factors directly affect barrier function of the epithelium. In addition, T-helper 2 (TH2) cells, type 2 innate lymphoid cells, and their cytokine interleukin 13 (IL-13) damage skin and lung barriers. The effects of environmental factors may at least in part be mediated by epigenetic mechanisms. Histone deacetylase activation by type 2 immune response has a major effect on leaky barriers and blocking of histone deacetylase activity corrects the defective barrier in human air-liquid interface cultures and mouse models of allergic asthma with rhinitis. We also present and discuss a novel device to detect and monitor skin barrier dysfunction, which provides an opportunity to rapidly and robustly assess disease severity. CONCLUSION A complex interplay between environmental factors, epithelium, and the immune system is involved in the development of systemic allergic diseases.
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Affiliation(s)
- Kazunari Sugita
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland; Christine Kühne-Center for Allergy Research and Education, Davos, Switzerland; Division of Dermatology, Department of Medicine of Sensory and Motor Organs, Faculty of Medicine, Tottori University, Yonago, Japan.
| | - Michael B Soyka
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland; Department of Otorhinolaryngology, Head and Neck Surgery, University and University Hospital of Zurich, Zurich, Switzerland
| | - Paulina Wawrzyniak
- Division of Clinical Chemistry and Biochemistry and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Arturo O Rinaldi
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Yasutaka Mitamura
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland; Christine Kühne-Center for Allergy Research and Education, Davos, Switzerland
| | - Mübeccel Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland
| | - Cezmi A Akdis
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland; Christine Kühne-Center for Allergy Research and Education, Davos, Switzerland
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48
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Leveraging -omics for asthma endotyping. J Allergy Clin Immunol 2020; 144:13-23. [PMID: 31277743 DOI: 10.1016/j.jaci.2019.05.015] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 05/08/2019] [Accepted: 05/09/2019] [Indexed: 12/13/2022]
Abstract
Asthma is a highly heterogeneous disease, often manifesting with wheeze, dyspnea, chest tightness, and cough as prominent symptoms. The eliciting factors, natural history, underlying molecular biology, and clinical management of asthma vary highly among affected subjects. Because of this variation, many efforts have gone into subtyping asthma. Endotypes are subtypes of disease based on distinct pathophysiologic mechanisms. Endotypes can be clinically useful because they organize our mechanistic understanding of heterogeneous diseases and can direct treatment toward modalities that are likely to be the most effective. Asthma endotyping can be shaped by clinical features, laboratory parameters, and/or -omics approaches. We discuss the application of -omics approaches, including transcriptomics, epigenomics, microbiomics, metabolomics, and proteomics, to asthma endotyping. -Omics approaches have provided supporting evidence for many existing endotyping paradigms and also suggested novel ways to conceptualize asthma endotypes. Although endotypes based on single -omics approaches are relatively common, their integrated multi-omics application to asthma endotyping has been more limited thus far. We discuss paths forward to integrate multi-omics with clinical features and laboratory parameters to achieve the goal of precise asthma endotypes.
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Jiang XH, Li CQ, Feng GY, Luo MJ, Sun QX, Huang J. Mycobacterium vaccae nebulization protects Balb/c mice against bronchial asthma through neural mechanisms. J Asthma 2020; 58:1003-1012. [PMID: 32329381 DOI: 10.1080/02770903.2020.1761381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVES Bronchial asthma can be effectively controlled but not be cured, its etiology and pathogenesis are still unclear, and there are no effective preventive measures. The key characteristic of asthma is chronic airway inflammation, and recent research has found that airway neurogenic inflammation plays an important role in asthma. We previously found that Mycobacterium vaccae nebulization protects against asthma. Therefore, this objective of this study is to explore the effect of M. vaccae nebulization on asthmatic neural mechanisms. METHODS A total 18 of female Balb/c mice were randomized into normal, asthma control, and M. vaccae nebulization (Neb.group) groups, and mice in the Neb.group were nebulized with M. vaccae one month before the asthmatic model was established. Then, 1 month later, the mice were sensitized and challenged with ovalbumin. Twenty-four hours after the last challenge, mouse airway responsiveness; pulmonary brain-derived neurotropic factor (BDNF), neurofilament-medium length (NF-M, using NF09 antibody), and acetylcholine expression; and nerve growth factor (NGF) mRNA level were determined. RESULTS We found that the BDNF, NF09, acetylcholine expression, and NGF mRNA level were decreased in the Neb.group compared with levels in the asthma control group. CONCLUSION M. vaccae nebulization may protected in Balb/c mice against bronchial asthma through neural mechanisms.
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Affiliation(s)
- Xiao-Hong Jiang
- Department of Geriatric Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Chao-Qian Li
- Department of Geriatric Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Guang-Yi Feng
- Department of Geriatric Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Ming-Jie Luo
- Department of Respiratory Medicine, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, Guangxi, China
| | - Qi-Xiang Sun
- The Graduate School, Guangxi Medical University, Nanning, Guangxi, China
| | - Jianlin Huang
- The Graduate School, Guangxi Medical University, Nanning, Guangxi, China
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50
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Nafea OE, El-Korashi LA, Gehad MH, Yousif YM, Zake LG. Association between blood aluminum and beta-2 receptor gene methylation with childhood asthma control. Hum Exp Toxicol 2020; 39:1301-1309. [PMID: 32351130 DOI: 10.1177/0960327120921436] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Previous studies have shown that environmental exposure to heavy metals has been related to epigenetic changes, such as DNA methylation in receptors involved in pathogenesis of asthma. One of these receptors is beta-2 adrenergic receptor (ADRB2). We conducted this study to examine the association between blood aluminum concentration, blood ADRB2 5' untranslated region (5'-UTR) methylation level, and childhood asthma control level. Our results showed a significant positive association between high blood aluminum concentration (odds ratio, 16, 95% confidence interval (CI) [3.57 to 71.76], p < 0.001) and high blood ADRB2 5'-UTR methylation level (odds ratio, 4.75, 95% CI [1.39 to 16.2], p = 0.013), and risk of uncontrolled asthma. Multivariable logistic regression revealed that higher blood aluminum concentration was independently associated with increased risk of uncontrolled bronchial asthma (odds ratio, 9.10, 95% CI [2.38 to 34.85], p = 0.0013], after controlling for age, sex, and blood ADRB2 5'-UTR methylation level. In addition, blood ADRB2 5'-UTR methylation level significantly correlated with whole blood aluminum concentration in asthmatic children (r = 0.480, p < 0.001). We concluded that increasing blood aluminum concentration is an important independent correlate of risk for uncontrolled bronchial asthma as well as increased blood aluminum concentration caused ADRB2 5'-UTR hyper-methylation with increasing risk of uncontrolled bronchial asthma.
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Affiliation(s)
- O E Nafea
- Department of Forensic Medicine and Clinical Toxicology, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - L A El-Korashi
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - M H Gehad
- Department of Pediatrics, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Y M Yousif
- Department of Pediatrics, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - L G Zake
- Department of Pulmonology, Faculty of Medicine, Zagazig University, Zagazig, Egypt
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