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Liao Y, Cavalcante R, Waller J, Deng F, Scruggs A, Huang Y, Atasoy U, Chen Y, Huang S. Differences in the DNA Methylome of T cells in Adults With Asthma of Varying Severity. RESEARCH SQUARE 2024:rs.3.rs-4476948. [PMID: 38946998 PMCID: PMC11213176 DOI: 10.21203/rs.3.rs-4476948/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Background DNA methylation plays a critical role in asthma development, but differences in DNA methylation among adults with varying asthma severity or asthma endotypes are less well-defined. Objective To examine how DNA methylomic patterns differ among adults with asthma based on asthma severity and airway inflammation. Methods Peripheral blood T cells from 35 adults with asthma in Beijing, China were serially collected over time (130 samples total) and analyzed for global DNA methylation using the Illumina MethylationEPIC Array. Differential methylation was compared among subjects with varying airway inflammation and severity, as measured by fraction of exhaled nitric oxide, forced expiratory volume in one second (FEV1), and Asthma Control Test (ACT) scores. Results Significant differences in DNA methylation were noted among subjects with different degrees of airway inflammation and asthma severity. These differences in DNA methylation were annotated to genes that were enriched in pathways related to asthma or T cell function and included gene ontology categories related to MHC class II assembly, T cell activation, interleukin (IL)-1, and IL-12. Genes related to P450 drug metabolism, glutathione metabolism, and developmental pathways were also differentially methylated in comparisons between subjects with high vs low FEV1 and ACT. Notable genes that were differentially methylated based on asthma severity included RUNX3, several members of the HLA family, AGT, PTPRC, PTPRJ, and several genes downstream of the JAK2 and TNF signaling pathway. Conclusion These findings demonstrate how adults with asthma of varying severity possess differences in peripheral blood T cell DNA methylation that contribute to the phenotype and severity of their overall disease.
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Wang Z, Wang L, Dai L, Wang Y, Li E, An S, Wang F, Liu D, Pan W. Identification of candidate aberrant differentially methylated/expressed genes in asthma. Allergy Asthma Clin Immunol 2022; 18:108. [PMID: 36550577 PMCID: PMC9784293 DOI: 10.1186/s13223-022-00744-5] [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: 08/04/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Asthma is an important non-communicable disease worldwide. DNA methylation is associated with the occurrence and development of asthma. We are aimed at assuring differential expressed genes (DEGs) modified by aberrantly methylated genes (DMGs) and pathways related to asthma by integrating bioinformatics analysis. METHODS One mRNA dataset (GSE64913) and one gene methylation dataset (GSE137716) were selected from the Gene Expression Omnibus (GEO) database. Functional enrichment analysis was performed using GeneCodies 4.0 database. All gene expression matrices were analyzed by Gene set enrichment analysis (GSEA) software. STRING was applied to construct a protein-protein interaction (PPI) network to find the hub genes. Then, electronic validation was performed to verify the hub genes, followed by the evaluation of diagnostic value. Eventually, quantitative real-time polymerase chain reaction (qRT-PCR) was utilized to detect the expression of hub genes. RESULTS In total, 14 hypomethylated/high-expression genes and 10 hypermethylated/low-expression genes were obtained in asthma. Among them, 10 hub genes were identified in the PPI network. Functional analysis demonstrated that the differentially methylated/expressed genes were primarily associated with the lung development, cytosol and protein binding. Notably, HLA-DOA was enriched in asthma. FKBP5, WNT5A, TM4SF1, PDK4, EPAS1 and GMPR had potential diagnostic value for asthma. CONCLUSION The project explored the pathogenesis of asthma, which may provide a research basis for the prediction and the drug development of asthma.
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Affiliation(s)
- Zongling Wang
- Department of internal medicine, Qingdao Fuwai Cardiovascular Hospital, 18th Floor north, 201 Nanjing Road, 266034 Qingdao, Shandong China
| | - Lizhi Wang
- Department of internal medicine, Qingdao Fuwai Cardiovascular Hospital, 18th Floor north, 201 Nanjing Road, 266034 Qingdao, Shandong China
| | - Lina Dai
- Department of internal medicine, Qingdao Fuwai Cardiovascular Hospital, 18th Floor north, 201 Nanjing Road, 266034 Qingdao, Shandong China
| | - Yanan Wang
- Department of internal medicine, Qingdao Fuwai Cardiovascular Hospital, 18th Floor north, 201 Nanjing Road, 266034 Qingdao, Shandong China
| | - Erhong Li
- Department of internal medicine, Qingdao Fuwai Cardiovascular Hospital, 18th Floor north, 201 Nanjing Road, 266034 Qingdao, Shandong China
| | - Shuyuan An
- Department of internal medicine, Qingdao Fuwai Cardiovascular Hospital, 18th Floor north, 201 Nanjing Road, 266034 Qingdao, Shandong China
| | - Fengliang Wang
- Department of internal medicine, Qingdao Fuwai Cardiovascular Hospital, 18th Floor north, 201 Nanjing Road, 266034 Qingdao, Shandong China
| | - Dan Liu
- Clinical laboratory, Qingdao Fuwai Cardiovascular Hospital, Qingdao, China
| | - Wen Pan
- Department of internal medicine, Qingdao Fuwai Cardiovascular Hospital, 18th Floor north, 201 Nanjing Road, 266034 Qingdao, Shandong China
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IL-13 Augments Histone Demethylase JMJD2B/KDM4B Expression Levels, Activity, and Nuclear Translocation in Airway Fibroblasts in Asthma. J Immunol Res 2021; 2021:6629844. [PMID: 33688506 PMCID: PMC7920726 DOI: 10.1155/2021/6629844] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/08/2021] [Accepted: 02/12/2021] [Indexed: 01/10/2023] Open
Abstract
Purpose Asthma is one of the most common obstructive pulmonary diseases worldwide. Epigenetic alterations, including DNA methylation and histone modifications, have been reported to contribute to asthma pathogenesis. Since the inflammation mediator and remodeling trigger, IL-13, is known to play a central role in the pathophysiology of asthma, this study was aimed to identify novel IL-13-regulated epigenetic modifiers in asthma that may contribute to subepithelial fibrosis. Methods Publicly available transcriptomic datasets from Gene Expression Omnibus (GEO) were used to identify differentially expressed genes on an epigenetic level upon IL-13 exposure in lung fibroblasts. Bronchial fibroblasts isolated from healthy and asthmatic individuals were assessed for the gene and protein expression levels of the identified gene at baseline and upon IL-13 treatment using qRT-PCR and western blotting, respectively. Its subcellular localization and tissue distribution were examined in bronchial fibroblasts as well as bronchial biopsies by immunofluorescence and immunohistochemical analysis, respectively. Results Bioinformatic analysis revealed the differential expression of the histone demethylase JMJD2B/KDM4B, a well-known epigenetic modulator that leads to the demethylation of different lysine residues on histones, in IL-13-treated lung fibroblasts. The baseline expression levels of JMJD2B were higher in asthmatic fibroblasts and in bronchial biopsies in comparison to healthy ones. There was also an increase in JMJD2B activity as evidenced by the demethylation of its downstream target, H3K36me3. Furthermore, IL-13 stimulation induced JMJD2B expression and further demethylation of H3K36me3 in asthmatic fibroblasts. This was accompanied by increased translocation of JMJD2B into the nucleus. Conclusion This study highlights the novel pathological involvement of the histone demethylase JMJD2B/KDM4B in asthmatic airway fibroblasts that are regulated by IL-13. Clinical implications. Given that there is no single therapeutic medicine to effectively treat the various subtypes of asthma, this study provides promising insights into JMJD2B as a new therapeutic target that could potentially improve the treatment and management of asthma.
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Rathod A, Duan J, Zhang H, Holloway JW, Ewart S, Arshad SH, Karmaus W. Interweaving Between Genetic and Epigenetic Studies on Childhood Asthma. Epigenet Insights 2020; 13:2516865720923395. [PMID: 32754683 PMCID: PMC7378715 DOI: 10.1177/2516865720923395] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/08/2020] [Indexed: 12/16/2022] Open
Abstract
The cause and underlying mechanisms that contribute to asthma pathogenesis are
not well known. Both genome- and epigenome-wide association studies have
identified genes associated with asthma risk. It is unknown to what extent genes
identified in these two types of studies overlap. Based on existing literature
and the DisGeNET database, we extracted overlapping genes identified in genetic
and epigenetic studies of childhood asthma. Through analyses of variance, we
assessed whether DNA methylation (DNAm) at 5′-C-phosphate-G-3′ (CpGs) on the
overlapping genes was associated with neighboring single-nucleotide
polymorphisms (SNPs) within 1M base pairs (bps) and with low linkage
disequilibrium (r2 < 0.2) in the
childhood asthma-related genes. In total, 285 genes from genetic studies and 226
genes from epigenetic studies were shown to be associated with asthma risk, of
which six overlap. Of the six genes, 79 CpGs and 8229 unique neighboring SNPs
(1M bps) were included in methylation quantitative loci (methQTL) assessment
analyses. We tested the association of DNAm at each of the 79 CpG sites with its
neighboring SNPs. After adjusting for multiple testing by controlling the false
discovery rate to 0.05 when testing methQTL for each CpG site, we found
statistically significant associations in three genes with their neighboring
SNPs and identified 34 unique methQTLs. The rather limited overlap in genes
between genetic and epigenetic studies on asthma and the absence of methQTL in
some of the overlapping genes highlight a need to jointly, rather than
independently, examine genetic and epigenetic effects on asthma risk to improve
our understanding of the underlying mechanisms of asthma.
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Affiliation(s)
- Aniruddha Rathod
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, The University of Memphis, Memphis, TN, USA
| | - Jiasong Duan
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, The University of Memphis, Memphis, TN, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, The University of Memphis, Memphis, TN, USA
| | - John W Holloway
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - S Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,The David Hide Asthma & Allergy Research Centre, Isle of Wight, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, The University of Memphis, Memphis, TN, USA
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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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Fang L, Sun Q, Roth M. Immunologic and Non-Immunologic Mechanisms Leading to Airway Remodeling in Asthma. Int J Mol Sci 2020; 21:ijms21030757. [PMID: 31979396 PMCID: PMC7037330 DOI: 10.3390/ijms21030757] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 01/18/2020] [Accepted: 01/20/2020] [Indexed: 02/07/2023] Open
Abstract
Asthma increases worldwide without any definite reason and patient numbers double every 10 years. Drugs used for asthma therapy relax the muscles and reduce inflammation, but none of them inhibited airway wall remodeling in clinical studies. Airway wall remodeling can either be induced through pro-inflammatory cytokines released by immune cells, or direct binding of IgE to smooth muscle cells, or non-immunological stimuli. Increasing evidence suggests that airway wall remodeling is initiated early in life by epigenetic events that lead to cell type specific pathologies, and modulate the interaction between epithelial and sub-epithelial cells. Animal models are only available for remodeling in allergic asthma, but none for non-allergic asthma. In human asthma, the mechanisms leading to airway wall remodeling are not well understood. In order to improve the understanding of this asthma pathology, the definition of “remodeling” needs to be better specified as it summarizes a wide range of tissue structural changes. Second, it needs to be assessed if specific remodeling patterns occur in specific asthma pheno- or endo-types. Third, the interaction of the immune cells with tissue forming cells needs to be assessed in both directions; e.g., do immune cells always stimulate tissue cells or are inflamed tissue cells calling immune cells to the rescue? This review aims to provide an overview on immunologic and non-immunologic mechanisms controlling airway wall remodeling in asthma.
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Affiliation(s)
- Lei Fang
- Pulmonary Cell Research & Pneumology, University Hospital & University of Basel, Petersgraben 4, CH-4031 Basel, Switzerland;
| | - Qinzhu Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, Shaanxi, China;
| | - Michael Roth
- Pulmonary Cell Research & Pneumology, University Hospital & University of Basel, Petersgraben 4, CH-4031 Basel, Switzerland;
- Correspondence: ; Tel.: +41-61-265-2337
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Biswas S. Role of PCDH 1 Gene in the Development of Childhood Asthma and Other Related Phenotypes: A Literature Review. Cureus 2018; 10:e3360. [PMID: 30510870 PMCID: PMC6257625 DOI: 10.7759/cureus.3360] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The asthma gene PCDH 1, encoding protocadherin-1, is a cellular adhesion molecule which plays an important role in epithelial barrier formation and repair. PCDH 1 is a novel susceptible gene not only in childhood asthma but also in eczema and other atopic phenotypes. In this article, we reviewed relevant articles from PubMed, Google Scholar, Science Direct and included all available significant pieces of information about the PCDH 1 association with asthma and other atopic or non-atopic phenotypes. It is very interesting that cigarette smoking can induce changes in PCDH 1 expression but how the changes in PCDH 1 induce asthma is still not clear. PCDH 1 gene polymorphism also sometimes plays role in asthma and bronchial hyperresponsiveness (BHR) pathogenesis as well as in allergic dermatitis.
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Affiliation(s)
- Sharmi Biswas
- Pediatrics, California Institute of Behavioral Neurosciences & Psychology, Fairfield, USA
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8
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Brugha R, Lowe R, Henderson AJ, Holloway JW, Rakyan V, Wozniak E, Mahmud N, Seymour K, Grigg J, Shaheen SO. DNA methylation profiles between airway epithelium and proxy tissues in children. Acta Paediatr 2017; 106:2011-2016. [PMID: 28833606 DOI: 10.1111/apa.14027] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/24/2017] [Accepted: 08/15/2017] [Indexed: 12/14/2022]
Abstract
AIM Epidemiological studies of deoxyribonucleic acid (DNA) methylation in airway disease have largely been conducted using blood or buccal samples. However, given tissue specificity of DNA methylation, these surrogate tissues may not allow reliable inferences about methylation in the lung. We sought to compare the pattern of DNA methylation in blood, buccal and nasal epithelial cells to that in airway epithelial cells from children. METHODS Samples of blood, and buccal, nasal and airway epithelium were obtained from six children undergoing elective anaesthesia for adenotonsillectomy. DNA methylation was assessed at 450 000 5'-C-phosphate-G-3' (CpG) sites using the Illumina HumanMethylation450 array. RESULTS Eighteen samples from all sites were suitable for analysis. Hierarchical clustering demonstrated that the methylation profile in nasal epithelium was most representative of that in airway epithelium; the profile in buccal cells was moderately similar and that in blood was least similar. CONCLUSION DNA methylation in blood poorly reflects methylation in airway epithelium. Future epidemiological studies of DNA methylation and airway diseases should consider measurement of methylation either in buccal cells or, preferably, in nasal epithelial cells.
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Affiliation(s)
- Rossa Brugha
- National Heart and Lung Institute; Imperial College London; London UK
| | - Robert Lowe
- Blizard Institute; Barts and The London School of Medicine and Dentistry; Queen Mary University of London; London UK
| | - A. John Henderson
- School of Social and Community Medicine; University of Bristol; Bristol UK
| | - John W. Holloway
- Human Development and Health; Faculty of Medicine; University of Southampton; Southampton UK
| | - Vardhman Rakyan
- Blizard Institute; Barts and The London School of Medicine and Dentistry; Queen Mary University of London; London UK
| | - Eva Wozniak
- Genome Centre; Barts and The London School of Medicine and Dentistry; London UK
| | - Nadiya Mahmud
- Genome Centre; Barts and The London School of Medicine and Dentistry; London UK
| | - Kay Seymour
- Ear, Nose and Throat Surgery; Barts Health NHS Trust; London UK
| | - Jonathan Grigg
- Blizard Institute; Barts and The London School of Medicine and Dentistry; Queen Mary University of London; London UK
| | - Seif O. Shaheen
- Blizard Institute; Barts and The London School of Medicine and Dentistry; Queen Mary University of London; London UK
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Christensen S, Jaffar Z, Cole E, Porter V, Ferrini M, Postma B, Pinkerton KE, Yang M, Kim YJ, Montrose L, Roberts K, Holian A, Cho YH. Prenatal environmental tobacco smoke exposure increases allergic asthma risk with methylation changes in mice. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:423-433. [PMID: 28543436 PMCID: PMC5513771 DOI: 10.1002/em.22097] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 03/01/2017] [Accepted: 04/22/2017] [Indexed: 05/28/2023]
Abstract
Allergic asthma remains an inadequately understood disease. In utero exposure to environmental tobacco smoke (ETS) has been identified as an environmental exposure that can increase an individual's asthma risk. To improve our understanding of asthma onset and development, we examined the effect of in utero ETS exposure on allergic disease susceptibility in an asthmatic phenotype using a house dust mite (HDM) allergen-induced murine model. Pregnant C57BL/6 mice were exposed to either filtered air or ETS during gestation, and their offspring were further exposed to HDM at 6-7 weeks old to induce allergic inflammation. Methylation in the promoter regions of allergic inflammation-related genes and genomic DNA was quantified. Exposure to HDM resulted in the onset of allergic lung inflammation, with an increased presence of inflammatory cells, Th2 cytokines (IL-4, IL-5, and IL-13), and airway remodeling. These asthmatic phenotypes were significantly enhanced when the mice had been exposed to in utero ETS. Furthermore, prenatal ETS exposure and subsequent HDM (ETS/HDM)-induced asthmatic phenotypes agree with methylation changes in the selected asthma-related genes, including IL-4, IL-5, IL-13, INF-γ, and FOXP3. Global DNA methylation was significantly lower in ETS/HDM-exposed mice than that of controls, which coincides with the results observed in lung, spleen, and blood DNAs. Prenatal ETS exposure resulted in a severe increase in allergic inflammatory responses after an HDM challenge, with corresponding methylation changes. Prenatal ETS exposure may influence developmental plasticity and result in altered epigenetic programming, leading to an increased susceptibility to asthma. Environ. Mol. Mutagen. 58:423-433, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Sonja Christensen
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences, University of Montana , Missoula, MT USA
| | - Zeina Jaffar
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences, University of Montana , Missoula, MT USA
| | - Elizabeth Cole
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences, University of Montana , Missoula, MT USA
| | - Virginia Porter
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences, University of Montana , Missoula, MT USA
| | - Maria Ferrini
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences, University of Montana , Missoula, MT USA
| | - Britten Postma
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences, University of Montana , Missoula, MT USA
| | - Kent E. Pinkerton
- Center for Health and the Environment, Department of Anatomy, Physiology and Cell Biology, University of California, Davis, CA, USA
| | - Mihi Yang
- Research Center for Cell Fate Control, Department of Toxicology, Sookmyung Women's University, Seoul, Korea
| | - Yang Jee Kim
- Da Vinci College of General Education, Chung-Ang University, Seoul, Korea
| | - Luke Montrose
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences, University of Montana , Missoula, MT USA
| | - Kevan Roberts
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences, University of Montana , Missoula, MT USA
| | - Andrij Holian
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences, University of Montana , Missoula, MT USA
| | - Yoon Hee Cho
- Center for Environmental Health Sciences, Department of Biomedical and Pharmaceutical Sciences, University of Montana , Missoula, MT USA
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Lockett GA, Soto-Ramírez N, Ray MA, Everson TM, Xu CJ, Patil VK, Terry W, Kaushal A, Rezwan FI, Ewart SL, Gehring U, Postma DS, Koppelman GH, Arshad SH, Zhang H, Karmaus W, Holloway JW. Association of season of birth with DNA methylation and allergic disease. Allergy 2016; 71:1314-24. [PMID: 26973132 PMCID: PMC5639882 DOI: 10.1111/all.12882] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2016] [Indexed: 12/31/2022]
Abstract
BACKGROUND Season of birth influences allergy risk; however, the biological mechanisms underlying this observation are unclear. The environment affects DNA methylation, with potentially long-lasting effects on gene expression and disease. This study examined whether DNA methylation could underlie the association between season of birth and allergy. METHODS In a subset of 18-year-old participants from the Isle of Wight (IoW) birth cohort (n = 367), the risks of birth season on allergic outcomes were estimated. Whole blood epigenome-wide DNA methylation was measured, and season-associated CpGs detected using a training-and-testing-based technique. Validation method examined the 8-year-old Prevention and Incidence of Asthma and Mite Allergy (PIAMA) cohort. The relationships between DNA methylation, season of birth and allergy were examined. CpGs were analysed in IoW third-generation cohort newborns. RESULTS Autumn birth increased risk of eczema, relative to spring birth. Methylation at 92 CpGs showed association with season of birth in the epigenome-wide association study. In validation, significantly more CpGs had the same directionality than expected by chance, and four were statistically significant. Season-associated methylation was enriched among networks relating to development, the cell cycle and apoptosis. Twenty CpGs were nominally associated with allergic outcomes. Two CpGs were marginally on the causal pathway to allergy. Season-associated methylation was largely absent in newborns, suggesting it arises post-natally. CONCLUSIONS This study demonstrates that DNA methylation in adulthood is associated with season of birth, supporting the hypothesis that DNA methylation could mechanistically underlie the effect of season of birth on allergy, although other mechanisms are also likely to be involved.
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Affiliation(s)
- Gabrielle A. Lockett
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Nelís Soto-Ramírez
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Meredith A. Ray
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Todd M. Everson
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Cheng-Jian Xu
- Department of Pulmonology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Veeresh K. Patil
- The David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - William Terry
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Akhilesh Kaushal
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Faisal I. Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Susan L. Ewart
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI, USA
| | - Ulrike Gehring
- Institute for Risk Assessment Sciences, Division of Environmental Epidemiology, Utrecht University, The Netherlands
| | - Dirkje S. Postma
- Department of Pulmonary Medicine and Tuberculosis, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gerard H. Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Beatrix Children’s Hospital, Groningen, The Netherlands
| | - S. Hasan Arshad
- The David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - John W. Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
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Macy E. Practical Management of Patients with a History of Immediate Hypersensitivity to Common non-Beta-Lactam Drugs. Curr Allergy Asthma Rep 2016; 16:4. [PMID: 26714689 DOI: 10.1007/s11882-015-0584-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Immediate hypersensitivity reactions to medications are among the most feared adverse drug reactions, because of their close association with anaphylaxis. This review discusses a practical management approach for patients with a history of an immediate hypersensitivity to a non-beta-lactam medication, where reexposure to the implicated, or similar, medication is clinically necessary. Mechanisms associated with severe immediate hypersensitivity reactions include IgE-mediated mast cell activation, complement-mediated mast cell activation, and direct mast cell activation. Immediate hypersensitivity reactions may also be mediated by vasodilators, other pharmacologic mechanisms, or be secondary to underlying patient-specific biochemical abnormalities such as endocrine tumors or chronic spontaneous urticaria. The key features in the reaction history and the biochemistry of the implicated medication are discussed. Most individuals with a history of immediate hypersensitivity to a medication, who require reuse of that drug, can be safely retreated with a therapeutic course of the implicated drug after a full-dose challenge, graded challenge, or desensitization, with or without premedication and/or any preliminary diagnostic testing, depending on the specific situation.
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Affiliation(s)
- Eric Macy
- Kaiser Permanente, Department of Allergy, 7060 Clairemont Mesa Blvd, San Diego, CA, 92111, USA.
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Mukherjee N, Lockett GA, Merid SK, Melén E, Pershagen G, Holloway JW, Arshad SH, Ewart S, Zhang H, Karmaus W. DNA methylation and genetic polymorphisms of the Leptin gene interact to influence lung function outcomes and asthma at 18 years of age. INTERNATIONAL JOURNAL OF MOLECULAR EPIDEMIOLOGY AND GENETICS 2016; 7:1-17. [PMID: 27186323 PMCID: PMC4858611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 02/28/2016] [Indexed: 06/05/2023]
Abstract
The leptin gene (LEP) plays a regulatory role in satiety, inflammation, and allergy. Prior findings linking leptin to asthma motivated us to investigate whether DNA methylation (DNA-M) of CpG (cytosine-phosphate-guanine) sites in concert with single nucleotide polymorphisms (SNPs) of LEP can explain the risk of asthma and lung function. Methylation of CpG sites was assessed using the Illumina Infinium Human Methylation 450 beadchip in blood samples collected from 10- and 18-year-old boys and girls from the Isle of Wight (IOW) birth cohort (UK). Four LEP SNPs were genotyped. Linear and log linear models were used for the analysis, adjusting for false discovery rate (FDR). The analyses were repeated in the BAMSE cohort (Sweden). In the IOW study, the interaction of cg00666422 and rs11763517 (CT vs TT and CC) was associated with FEV1 (FDR-adjusted p-value: 0.03), FEV1/FVC ratio (FDR-adjusted p-value: 0.0096), and FEF25-75% (FDR-adjusted p-value: 0.00048) such that they decreased with increasing DNA-M. The interaction of the same CpG-SNP pair was also associated with increased risk of asthma at age 18. We replicated the findings for FEV1/FVC and FEF25-75% in a smaller sample of 34 participants at age 10. Regarding the BAMSE cohort, although, the interaction of cg00666422 and rs11763517 on lung function were not significant, the direction of the effect was the same as in IOW cohort. Thus, penetrance of LEP genotype seems to be modified by methylation at cg00666422 and is linked to airway obstruction and asthma.
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Affiliation(s)
- Nandini Mukherjee
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of MemphisMemphis, TN, USA
| | - Gabrielle A Lockett
- Human Development and Health, Faculty of Medicine, University of SouthamptonUK
| | - Simon K Merid
- Institute of Environmental Medicine, Karolinska InstitutetBox 210 171 77 Stockholm, Sweden
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska InstitutetBox 210 171 77 Stockholm, Sweden
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska InstitutetBox 210 171 77 Stockholm, Sweden
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of SouthamptonUK
- Clinical and Experimental Sciences, Faculty of Medicine, University of SouthamptonUK
- NIHR Respiratory Biomedical Research Unit, University Hospital SouthamptonUK
| | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of SouthamptonUK
- NIHR Respiratory Biomedical Research Unit, University Hospital SouthamptonUK
- The David Hide Asthma and Allergy Research CentreIsle of Wight, UK
| | - Susan Ewart
- Department of Large Animal Clinical Sciences, Michigan State UniversityEast Lansing, MI, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of MemphisMemphis, TN, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of MemphisMemphis, TN, USA
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Establishing a birth cohort to investigate the course and aetiology of asthma and allergies across three generations - rationale, design, and methods of the ACROSSOLAR study. BMC Public Health 2015; 15:1210. [PMID: 26637409 PMCID: PMC4670515 DOI: 10.1186/s12889-015-2555-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 12/01/2015] [Indexed: 01/12/2023] Open
Abstract
Background Atopic diseases are a major burden of disease on a global scale. Regarding their aetiology, the early years of life are assumed to play a crucial role. In addition, there is growing evidence that elucidating the impact of cross-generational effects and epigenetic mechanisms such as DNA methylation can substantially widen the scientific knowledge of the occurrence and progression of these diseases. We are thus aiming at following the course of asthma, allergies, and potential risk factors for their occurrence across three generations by establishing a birth cohort in the offspring of an existing population-based cohort. Methods/Design 2051 young adults who have been recruited in 1995 for Phase II of the International Study of Asthma and Allergies in Childhood (ISAAC) and who have subsequently been followed-up by the Study on Occupational Allergy Risks (SOLAR) are asked bi-annually since 2009 if they conceived a child in the meantime. If parenthood is reported, parents are invited to enrol along with their children in the ACROSSOLAR cohort. Participation involves completing a questionnaire assessing general and health-related information about the course of the pregnancy and the first year of life of their children. Subsequently, the children are followed up until primary school age when asthma and allergies can be diagnosed reliably. In addition, DNA for epigenetic analysis will be collected and analysed. Longitudinal data analysis techniques will then be used to assess potential associations between early-life exposures and onset of childhood asthma and allergies taking into account epigenetics. Discussion Birth cohorts are especially suited to elucidate the impact of genetic predisposition, epigenetics, exposures during the first years of life, and gene-environment interactions on the occurrence and progression of asthma and allergies. By building upon an existing cohort, ACROSSOLAR offers a unique and cost-effective opportunity to investigate the aetiology of atopic disease in a prospective and cross-generational way.
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Terry W, Zhang H, Maity A, Arshad H, Karmaus W. Unified variable selection in semi-parametric models. Stat Methods Med Res 2015; 26:2821-2831. [PMID: 26489906 DOI: 10.1177/0962280215610928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We propose a Bayesian variable selection method in semi-parametric models with applications to genetic and epigenetic data (e.g., single nucleotide polymorphisms and DNA methylation, respectively). The data are individually standardized to reduce heterogeneity and facilitate simultaneous selection of categorical (single nucleotide polymorphisms) and continuous (DNA methylation) variables. The Gaussian reproducing kernel is applied to the transformed data to evaluate joint effect of the variables, which may include complex interactions between, e.g., single nucleotide polymorphisms and DNA methylation. Indicator variables are introduced to the model for the purpose of variable selection. The method is demonstrated and evaluated using simulations under different scenarios. We apply the method to identify informative DNA methylation sites and single nucleotide polymorphisms in a set of genes based on their joint effect on allergic sensitization. The selected single nucleotide polymorphisms and methylation sites have the potential to serve as early markers for allergy prediction, and consequently benefit medical and clinical research to prevent allergy before its manifestation.
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Affiliation(s)
- William Terry
- 1 Department of Mathematical Sciences, University of Memphis, Memphis, USA
| | - Hongmei Zhang
- 2 Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Arnab Maity
- 3 Department of Statistics, North Carolina State University, Raleigh, USA
| | - Hasan Arshad
- 4 Allergy and Clinical Immunology, University of Southampton, Southampton, UK. The David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - Wilfried Karmaus
- 2 Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
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Lockett GA, Patil VK, Soto-Ramírez N, Ziyab AH, Holloway JW, Karmaus W. Epigenomics and allergic disease. Epigenomics 2014; 5:685-99. [PMID: 24283882 DOI: 10.2217/epi.13.68] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Allergic disease development is affected by both genes and the environment, and epigenetic mechanisms are hypothesized to mediate these environmental effects. In this article, we discuss the link between the environment, DNA methylation and allergic disease, as well as questions of causality inherent to analyses of DNA methylation. From the practical side, we describe characteristics of allergic phenotypes and contrast different epidemiologic study designs used in epigenetic research. We examine methodological considerations, how best to conduct preprocessing and analysis of DNA methylation data sets, and the latest methods, technologies and discoveries in this rapidly advancing field. DNA methylation and other epigenetic marks are firmly entwined with allergic disease, a link that may hold the basis for future allergic disease diagnosis and treatment.
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Affiliation(s)
- Gabrielle A Lockett
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, UK
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Acevedo N, Reinius LE, Greco D, Gref A, Orsmark-Pietras C, Persson H, Pershagen G, Hedlin G, Melén E, Scheynius A, Kere J, Söderhäll C. Risk of childhood asthma is associated with CpG-site polymorphisms, regional DNA methylation and mRNA levels at the GSDMB/ORMDL3 locus. Hum Mol Genet 2014; 24:875-90. [PMID: 25256354 PMCID: PMC4291244 DOI: 10.1093/hmg/ddu479] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Single-nucleotide polymorphisms (SNPs) in GSDMB (Gasdermin B) and ORMDL3 (ORMDL sphingolipid biosynthesis regulator 3) are strongly associated with childhood asthma, but the molecular alterations contributing to disease remain unknown. We investigated the effects of asthma-associated SNPs on DNA methylation and mRNA levels of GSDMB and ORMDL3. Genetic association between GSDMB/ORMDL3 and physician-diagnosed childhood asthma was confirmed in the Swedish birth-cohort BAMSE. CpG-site SNPs (rs7216389 and rs4065275) showed differences in DNA methylation depending on carrier status of the risk alleles, and were significantly associated with methylation levels in two CpG sites in the 5′ UTR (untranslated region) of ORMDL3. In the Swedish Search study, we found significant differences in DNA methylation between asthmatics and controls in five CpG sites; after adjusting for lymphocyte and neutrophil cell counts, three remained significant: one in IKZF3 [IKAROS family zinc finger 3 (Aiolos); cg16293631] and two in the CpG island (CGI) of ORMDL3 (cg02305874 and cg16638648). Also, cg16293631 and cg02305874 correlated with mRNA levels of ORMDL3. The association between methylation and asthma was independent of the genotype in rs7216389, rs4065275 and rs12603332. Both SNPs and CpG sites showed significant associations with ORMDL3 mRNA levels. SNPs influenced expression independently of methylation, and the residual association between methylation and expression was not mediated by these SNPs. We found a differentially methylated region in the CGI shore of ORMDL3 with six CpG sites less methylated in CD8+ T-cells. In summary, this study supports that there are differences in DNA methylation at this locus between asthmatics and controls; and both SNPs and CpG sites are independently associated with ORMDL3 expression.
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Affiliation(s)
- Nathalie Acevedo
- Department of Biosciences and Nutrition, and Center for Innovative Medicine (CIMED), Karolinska Institutet, Stockholm 141 83, Sweden Department of Medicine Solna, Translational Immunology Unit, Karolinska Institutet and University Hospital, Stockholm 171 77, Sweden
| | - Lovisa E Reinius
- Department of Biosciences and Nutrition, and Center for Innovative Medicine (CIMED), Karolinska Institutet, Stockholm 141 83, Sweden
| | - Dario Greco
- Systems Toxicology Team, Finnish Institute of Occupational Health, Helsinki 00250, Finland
| | | | - Christina Orsmark-Pietras
- Department of Biosciences and Nutrition, and Center for Innovative Medicine (CIMED), Karolinska Institutet, Stockholm 141 83, Sweden
| | - Helena Persson
- Department of Biosciences and Nutrition, and Center for Innovative Medicine (CIMED), Karolinska Institutet, Stockholm 141 83, Sweden
| | | | - Gunilla Hedlin
- Department of Women's and Children's Health Centre of Allergy Research, Karolinska Institutet, Stockholm 171 77, Sweden Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm 171 64, Sweden
| | - Erik Melén
- Institute of Environmental Medicine Centre of Allergy Research, Karolinska Institutet, Stockholm 171 77, Sweden Sachs' Children's Hospital, Södersjukhuset, Stockholm 118 83, Sweden and
| | - Annika Scheynius
- Department of Medicine Solna, Translational Immunology Unit, Karolinska Institutet and University Hospital, Stockholm 171 77, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, and Center for Innovative Medicine (CIMED), Karolinska Institutet, Stockholm 141 83, Sweden Folkhälsan Institute of Genetics, Helsinki, and Research Programs Unit, University of Helsinki, Helsinki 00014, Finland
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, and Center for Innovative Medicine (CIMED), Karolinska Institutet, Stockholm 141 83, Sweden Centre of Allergy Research, Karolinska Institutet, Stockholm 171 77, Sweden
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17
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Guthikonda K, Zhang H, Nolan VG, Soto-Ramírez N, Ziyab AH, Ewart S, Arshad HS, Patil V, Holloway JW, Lockett GA, Karmaus W. Oral contraceptives modify the effect of GATA3 polymorphisms on the risk of asthma at the age of 18 years via DNA methylation. Clin Epigenetics 2014; 6:17. [PMID: 25250096 PMCID: PMC4171400 DOI: 10.1186/1868-7083-6-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 09/10/2014] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The prevalence of asthma in girls increases after puberty. Previous studies have detected associations between sex hormones and asthma, as well as between sex hormones and T helper 2 (Th2) asthma-typical immune responses. Therefore, we hypothesized that exogenous or endogenous sex hormone exposure (represented by oral contraceptive pill (OCP) use and early menarche, respectively) are associated with DNA methylation (DNA-M) of the Th2 transcription factor gene, GATA3, in turn affecting the risk of asthma in girls, possibly in interaction with genetic variants. Blood samples were collected from 245 female participants aged 18 years randomly selected for methylation analysis from the Isle of Wight birth cohort, UK. Information on use of OCPs, age at menarche, and concurrent asthma were assessed by questionnaire. Genome-wide DNA-M was determined using the Illumina Infinium HumanMethylation450 beadchip. In a first stage, we tested the interaction between sex hormone exposure and genetic variants on DNA-M of specific cytosine-phosphate-guanine (CpG) sites. In a second stage, we determined whether these CpG sites interact with genetic variants in GATA3 to explain the risk of asthma. RESULTS Interactions between OCP use and seven single nucleotide polymorphisms (SNPs) of GATA3 were analyzed for 14 CpG sites (stage 1). The interaction between OCP use and SNP rs1269486 was found to be associated with the methylation level of cg17124583 (P = 0.002, false discovery rate (FDR) adjusted P = 0.04). DNA-M of this same CpG site was also influenced by the interaction between age at menarche and rs1269486 (P = 0.0017). In stage 2, we found that cg17124583 modified the association of SNP rs422628 with asthma risk at the age of 18 years (P = 0.006, FDR adjusted P = 0.04). Subjects with genotype AG showed an increase in average risk ratio (RR) from 0.31 (95% CI: 0.10 to 0.8) to 11.65 (95% CI: 1.71 to 79.5) when methylation level increased from 0.02 to 0.12, relative to genotype AA. CONCLUSION A two-stage model consisting of genetic variants in the GATA3 gene, OCP use, age at menarche, and DNA-M may explain how sex hormones in women can increase the asthma prevalence after puberty.
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Affiliation(s)
- Kranthi Guthikonda
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Vikki G Nolan
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Nelís Soto-Ramírez
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Ali H Ziyab
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Susan Ewart
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI, USA
| | - Hasan S Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, and NIHR Respiratory Biomedical Research Unit, University of Southampton, Southampton, UK
- The David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - Veeresh Patil
- Clinical and Experimental Sciences, Faculty of Medicine, and NIHR Respiratory Biomedical Research Unit, University of Southampton, Southampton, UK
- The David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - John W Holloway
- Clinical and Experimental Sciences, Faculty of Medicine, and NIHR Respiratory Biomedical Research Unit, University of Southampton, Southampton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Gabrielle A Lockett
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
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Abstract
Immune-mediated pulmonary diseases are a group of diseases that resulted from immune imbalance initiated by allergens or of unknown causes. Inflammatory responses without restrictions cause tissue damage and remodeling, which leads to airway hyperactivity, destruction of alveolar architecture, and a resultant loss of lung function. Epigenetic mechanisms have been demonstrated to be involved in inflammation, autoimmunity, and cancer. Recent studies have identified that epigenetic changes also regulate molecular pathways in immune-mediated lung diseases. Aberrant DNA methylation status, dysregulation of histone modifications, as well as altered microRNAs expression could change transcription activity of genes involved in the development of immune-mediated pulmonary diseases, which contributes to skewed differentiation of T cells and proliferation and activation of myofibroblasts, leading to overproduction of inflammatory cytokines and excessive accumulation of extracellular matrix, respectively. Aside from this, epigenetics also explains how environmental exposure influence on gene transcription without genetic changes. It acts as a mediator of the interaction between environmental factors and genetic factors. Identification of the abnormal epigenetic marks in diseases provides novel biomarkers for prediction and diagnosis and affords novel therapeutic targets for those difficult clinical problems, such as steroid-resistance and rapidly progressing fibrosis. In this review, we summarized the latest experimental and translational epigenetic studies in immune-mediated pulmonary diseases, including asthma, idiopathic pulmonary fibrosis, tuberculosis, sarcoidosis, and silicosis.
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19
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Myles IA. Fast food fever: reviewing the impacts of the Western diet on immunity. Nutr J 2014; 13:61. [PMID: 24939238 PMCID: PMC4074336 DOI: 10.1186/1475-2891-13-61] [Citation(s) in RCA: 186] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 05/23/2014] [Indexed: 02/08/2023] Open
Abstract
While numerous changes in human lifestyle constitute modern life, our diet has been gaining attention as a potential contributor to the increase in immune-mediated diseases. The Western diet is characterized by an over consumption and reduced variety of refined sugars, salt, and saturated fat. Herein our objective is to detail the mechanisms for the Western diet's impact on immune function. The manuscript reviews the impacts and mechanisms of harm for our over-indulgence in sugar, salt, and fat, as well as the data outlining the impacts of artificial sweeteners, gluten, and genetically modified foods; attention is given to revealing where the literature on the immune impacts of macronutrients is limited to either animal or in vitro models versus where human trials exist. Detailed attention is given to the dietary impact on the gut microbiome and the mechanisms by which our poor dietary choices are encoded into our gut, our genes, and are passed to our offspring. While today's modern diet may provide beneficial protection from micro- and macronutrient deficiencies, our over abundance of calories and the macronutrients that compose our diet may all lead to increased inflammation, reduced control of infection, increased rates of cancer, and increased risk for allergic and auto-inflammatory disease.
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Affiliation(s)
- Ian A Myles
- Bacterial Pathogenesis Unit, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike Building 33, Room 2W10A, Bethesda, MD, 20892, Maryland.
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20
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Meyers DA, Bleecker ER, Holloway JW, Holgate ST. Asthma genetics and personalised medicine. THE LANCET. RESPIRATORY MEDICINE 2014; 2:405-15. [PMID: 24794577 PMCID: PMC4768462 DOI: 10.1016/s2213-2600(14)70012-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Unbiased genetic approaches, especially genome-wide association studies, have identified novel genetic targets in the pathogenesis of asthma, but so far these targets account for only a small proportion of the heritability of asthma. Recognition of the importance of disease heterogeneity, the need for improved disease phenotyping, and the fact that genes involved in the inception of asthma are likely to be different from those involved in severity widens the scope of asthma genetics. The identification of genes implicated in several causal pathways suggests that genetic scores could be used to capture the effect of genetic variations on individuals. Gene-environment interaction adds another layer of complexity, which is being successfully explored by epigenetic approaches. Pharmacogenetics is one example of how gene-environment interactions are already being taken into account in the identification of drug responders and non-responders, and patients most susceptible to adverse effects. Such applications represent one component of personalised medicine, an approach that places the individual at the centre of health care.
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Affiliation(s)
- Deborah A Meyers
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Eugene R Bleecker
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - John W Holloway
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Stephen T Holgate
- Human Development and Health, and Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK.
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21
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Sharma S, Litonjua A. Asthma, allergy, and responses to methyl donor supplements and nutrients. J Allergy Clin Immunol 2014; 133:1246-54. [PMID: 24360248 PMCID: PMC4004707 DOI: 10.1016/j.jaci.2013.10.039] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 10/17/2013] [Accepted: 10/22/2013] [Indexed: 01/14/2023]
Abstract
After a brief period of stabilization, recent data have shown that the prevalence of asthma and allergic diseases continues to increase. Atopic diseases are major public health problems resulting in significant disability and resource use globally. Although environmental factors influence the development of atopic disease, dietary changes might partially explain the high burden of atopic disease. Potential mechanisms through which diet is suspected to effect asthma and allergy susceptibility are through epigenetic changes, including DNA methylation. Dietary methyl donors are important in the one-carbon metabolic pathway that is essential for DNA methylation. Findings from both observational studies and interventional trials of dietary methyl donor supplementation on the development and treatment of asthma and allergy have produced mixed results. Although issues related to the differences in study design partially explain the heterogeneous results, 2 other issues have been largely overlooked in these studies. First, these nutrients affect one of many pathways and occur in many of the same foods. Second, it is now becoming clear that the human intestinal microbiome is involved in the metabolism and production of the B vitamins and other methyl donor nutrients. Future studies will need to account for both the interrelationships between these nutrients and the effects of the microbiome.
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Affiliation(s)
- Sunita Sharma
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Mass; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Mass.
| | - Augusto Litonjua
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, Mass; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Mass
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22
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Genome-wide association studies in asthma; perhaps, the end of the beginning. Curr Opin Allergy Clin Immunol 2014; 13:463-9. [PMID: 23945178 DOI: 10.1097/aci.0b013e328364ea5f] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
PURPOSE OF REVIEW A large number of genetic loci contribute towards an individual's susceptibility to asthma and other complex diseases. Genome-wide association studies (GWASs) have provided us with a wealth of loci associated with asthma susceptibility, asthma endotypes and responsiveness to asthma medications. The reproducibility of these genetic loci across different studies highlights the interplay of general and population-specific risk alleles in asthma. Although GWASs have been successful in identifying disease-associated loci, there is still large potential for such studies to provide further insights into asthma pathogenesis. RECENT FINDINGS GWASs over the past year have extended study design well beyond the simple case-control and continuous phenotype association formats, for example, including interactions with environmental factors, integrating GWAS data with epigenetic data and GWASs in animal models, incorporating pathway analyses and utilising emerging sequencing technologies. SUMMARY Moving beyond traditional GWAS formats is likely to significantly enhance our understanding of the genetic basis for asthma. This review discusses where we are after half a decade of asthma GWASs, and focuses on advances over the past year that show where the GWAS field is headed in the future.
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Guerrero-Bosagna C, Skinner MK. Environmental epigenetics and effects on male fertility. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 791:67-81. [PMID: 23955673 DOI: 10.1007/978-1-4614-7783-9_5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Environmental exposures to factors such as toxicants or nutrition can have impacts on testis biology and male fertility. The ability of these factors to influence epigenetic mechanisms in early life exposures or from ancestral exposures will be reviewed. A growing number of examples suggest environmental epigenetics will be a critical factor to consider in male reproduction.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
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24
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Patil VK, Holloway JW, Zhang H, Soto-Ramirez N, Ewart S, Arshad SH, Karmaus W. Interaction of prenatal maternal smoking, interleukin 13 genetic variants and DNA methylation influencing airflow and airway reactivity. Clin Epigenetics 2013; 5:22. [PMID: 24314122 PMCID: PMC3892084 DOI: 10.1186/1868-7083-5-22] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 11/01/2013] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Asthma is characterized by airflow limitation and airway reactivity (AR). Interleukin-13 (IL-13) is involved in the pathogenesis of asthma. Two functional SNPs, rs20541 and rs1800925, of the IL-13 gene (IL13) have been frequently associated with asthma-related lung functions. However, genetic variation alone does not fully explain asthma risk. DNA-methylation (DNA-M) is an epigenetic mechanism that regulates gene expression and can be influenced by both environment and genetic variants. To explore the interplay of prenatal maternal smoking, genetic variants and DNA-M, we used a two-stage model: (1) identifying cytosine phosphate guanine (CpG) sites where DNA-M is influenced by the interaction between genetic variants and maternal smoking during pregnancy (conditional methQTL (methylation quantitative trait loci)); and (2) determining the effect of the interaction between DNA-M of CpG (from stage 1) and SNPs (modifying genetic variants; modGV) on airflow limitation and AR in 245 female participants of the Isle of Wight birth cohort. DNA-M was assessed using the Illumina Infinium HumanMethylation450 BeadChip. FINDINGS Six CpG sites were analyzed in stage 1. DNA-M at cg13566430 was influenced by interaction of maternal smoking during pregnancy and rs20541. In stage 2, genotype at rs1800925 interacted with DNA-M at cg13566430 significantly affecting airflow limitation (P = 0.042) and AR (P = 0.01). CONCLUSION Both genetic variants and environment affect DNA-M. This study supports the proposed two-stage model (methQTL and modGV) to study genetic variants, environment and DNA-M interactions in asthma-related lung function.
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Affiliation(s)
- Veeresh K Patil
- David Hide Asthma and Allergy Research Centre, St Mary’s Hospital, Newport, Isle of Wight PO30 5TG, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - John W Holloway
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Nelis Soto-Ramirez
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Susan Ewart
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI, USA
| | - S Hasan Arshad
- David Hide Asthma and Allergy Research Centre, St Mary’s Hospital, Newport, Isle of Wight PO30 5TG, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
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Alexander M, Karmaus W, Holloway JW, Zhang H, Roberts G, Kurukulaaratchy RJ, Arshad SH, Ewart S. Effect of GSTM2-5 polymorphisms in relation to tobacco smoke exposures on lung function growth: a birth cohort study. BMC Pulm Med 2013; 13:56. [PMID: 24004509 PMCID: PMC3846453 DOI: 10.1186/1471-2466-13-56] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 08/20/2013] [Indexed: 02/07/2023] Open
Abstract
Background Genetic variation within GSTM2-5 genes may interfere with detoxification of environmental compounds, thereby having a detrimental effect on lung function following exposures such as tobacco smoke. We aim to investigate the influence of variants and associated methylation in the GSTM gene cluster with changes in lung function growth during adolescence. Methods Growth in forced expiratory volume (FEV1), forced vital capacity (FVC), and change in FEV1/FVC ratio measures were obtained from children in the Isle of Wight birth cohort at ages 10 and 18. Illumina GoldenGate assays were used to genotype 10 tagging polymorphisms from GSTM2 (rs574344 and rs12024479), GSTM3 (rs1537236, rs7483, and rs10735234), GSTM4 (rs668413, rs560018, and rs506008), and GSTM5 (rs929166 and rs11807) genes. Diplotypes were generated in the software Phase 3.0.2. DNA methylation was measured in over 450,000 CpG sites using the Infinium HumanMethylation450 BeadChip (Illumina 450K) in a subsample of 245 18-year olds from the Isle of Wight birth cohort. Gender, age, in utero smoke exposure, secondhand smoke exposure (SHS), and current smoking status were assessed via questionnaire; smoke exposures were validated with urine cotinine. We used linear mixed models to estimate the effect of GSTM diplotypes on lung function across time and examine interactions with tobacco smoke. Results 1,121 (77%) out of 1,456 children had information on lung function at ages 10 or 18. After adjustment for false discovery rate, one diplotype in GSTM3 had a detrimental effect on changes in FEV1 (p=0.03), and another diplotype in GSTM3 reduced FVC (p=0.02) over time. No significant interactions with smoking were identified. SHS significantly modified the relationship between diplotypes and methylation levels in one GSTM2 CpG site; however, this site did not predict lung function outcomes at age 18. Joint effects of GSTM loci and CpG sites located within these loci on adolescent lung growth were detected. Conclusions Diplotypes within GSTM2-5 genes are associated with lung function growth across adolescence, but do not appear to modify the effect of tobacco smoke exposures on adolescent lung growth. Interactions between DNA methylation and diplotypes should be taken into account to gain further understanding on lung function in adolescence.
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Affiliation(s)
- Melannie Alexander
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, 236A Robison Hall, Memphis, TN 38152, USA.
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Yousefi M, Karmaus W, Zhang H, Ewart S, Arshad H, Holloway JW. The methylation of the LEPR/LEPROT genotype at the promoter and body regions influence concentrations of leptin in girls and BMI at age 18 years if their mother smoked during pregnancy. INTERNATIONAL JOURNAL OF MOLECULAR EPIDEMIOLOGY AND GENETICS 2013; 4:86-100. [PMID: 23875062 PMCID: PMC3709113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 06/15/2013] [Indexed: 06/02/2023]
Abstract
To determine whether DNA methylation (DNA-M) of the leptin receptor genotype (LEPR/LEPROT) links gestational smoking and leptin serum levels and BMI later in life, we focused on female offspring, 18 years of age, from the Isle of Wight Birth Cohort (IOWBC). Leptin binds to the leptin receptor encoded by the LEPR/LEPROT genotype. Using general linear models, we tested a two-stage model. First, we investigated whether single nucleotide polymorphisms (SNPs) acting as methylation quantitative trait loci (methQTLs) depending on gestational smoking were related to differentially methylated cytosine-phosphate-guanine (CpG) sites. In stage 2, we tested whether the selected CpG sites, in interaction with other SNPs (modifiable genetic variants, modGV), are associated with serum leptin and BMI (stage 2). Children from the IOWBC were followed from birth to age 18. Information on gestational smoking was gathered upon delivery. SNPs tagging LEPR and LEPROT genes were genotyped. Data on LEPR/LEPROTDNA-M and leptin were obtained from blood samples drawn at age 18; to determine BMI, height and weight were ascertained. Blood samples were provided by 238 girls. Of the 21 CpG sites, interactions between gestational smoking and SNPs were detected for 16 CpGs. Methylation of seven of the 16 CpGs were, in interaction with modGVs, associated with leptin levels at age 18 years. Two CpGs survived a multiple testing penalty and were also associated with BMI. This two-stage model may explain why maternal smoking has a long-term effect on leptin levels and BMI in girls at age 18 years.
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Affiliation(s)
- Mitra Yousefi
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South CarolinaColumbia, SC, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of MemphisMemphis, USA
| | - Hongmei Zhang
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South CarolinaColumbia, SC, USA
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State UniversityEast Lansing, MI, 48824, USA
| | - Hasan Arshad
- The David Hide Asthma and Allergy Research Centre, St Mary’s HospitalNewport, Isle of Wight, UK
- Clinical & Experimental Sciences, and Human Development & Health, Faculty of Medicine, University of SouthamptonSouthampton, UK
| | - John W Holloway
- Clinical & Experimental Sciences, and Human Development & Health, Faculty of Medicine, University of SouthamptonSouthampton, UK
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Berenguer AG, Rosa A, Brehm A. Asthma-snapshot or motion picture? Front Genet 2013; 4:73. [PMID: 23641254 PMCID: PMC3639421 DOI: 10.3389/fgene.2013.00073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 04/15/2013] [Indexed: 01/27/2023] Open
Affiliation(s)
| | - Alexandra Rosa
- Human Genetics Laboratory, University of MadeiraFunchal, Portugal
- Medical Sciences Unit, Life Sciences Center, University of MadeiraFunchal, Portugal
| | - António Brehm
- Human Genetics Laboratory, University of MadeiraFunchal, Portugal
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Sex- and age-dependent DNA methylation at the 17q12-q21 locus associated with childhood asthma. Hum Genet 2013; 132:811-22. [PMID: 23546690 DOI: 10.1007/s00439-013-1298-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 03/18/2013] [Indexed: 12/31/2022]
Abstract
Chromosomal region 17q12-q21 is one of the best-replicated genome-wide association study (GWAS) hits and associated with childhood-onset asthma. However, the mechanism by which the genetic association is restricted to childhood-onset disease is unclear. During childhood, more boys than girls develop asthma. Therefore, we tested the hypothesis that the 17q12-q21 genetic association was sex-specific. Indeed, a TDT test showed that in the Saguenay-Lac-Saint-Jean familial collection, the 17q12-q21 association was significant among male, but not among female asthmatic subjects. We next hypothesized that the bias in the genetic association resulted from sex-specific and/or age-dependent DNA methylation at regulatory regions and determined the methylation profiles of five 17q12-q21 gene promoters using the bisulfite sequencing methylation assay. We identified a single regulatory region within the zona pellucida binding protein 2 (ZPBP2) gene, which showed statistically significant differences between males and females with respect to DNA methylation. DNA methylation also varied with age and was higher in adult males compared to boys. We have recently identified two functionally important polymorphisms, both within the ZPBP2 gene that influence expression levels of neighboring genes. Combined with the results of the present work, these data converge pointing to the same 5 kb region within the ZPBP2 gene as a critical region for both gene expression regulation and predisposition to asthma. Our data show that sex- and age-dependent DNA methylation may act as a modifier of genetic effects and influence the results of genetic association studies.
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Lloyd CM, Saglani S. T cells in asthma: influences of genetics, environment, and T-cell plasticity. J Allergy Clin Immunol 2013; 131:1267-74; quiz 1275. [PMID: 23541326 DOI: 10.1016/j.jaci.2013.02.016] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/11/2013] [Accepted: 02/15/2013] [Indexed: 12/11/2022]
Abstract
Asthma is classically considered the archetypal T(H)2 disease, with increased circulating IgE levels and eosinophilic inflammation being caused by increased levels of T(H)2-type cytokines. However, this paradigm has been challenged because of the realization that strategies designed to suppress T(H)2 function are not effective for all patients. The clinical phenotype of asthma is notoriously heterogeneous and is affected by genetic and environmental exposures in addition to interactions between airway structural cells, including epithelial cells, and the immune system, as well as contributions from cells other than T(H)2 cells. A combination of genetic and environmental factors is thought to influence whether inflammation resolves or progresses, and the pulmonary epithelium is increasingly recognized to play a key role in this process. This complex interplay has made it increasingly apparent that immune responses are tailored to the individual patient and determined by the weight of each influence, and thus the label of asthma as a T(H)2 disease is too conservative. Indeed, an important concept that needs to be addressed, both in animal models and clinically, is that of T-cell plasticity and how lymphocytic responses are determined by environmental influences.
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Affiliation(s)
- Clare M Lloyd
- National Heart and Lung Institute, Sir Alexander Fleming Building, Faculty of Medicine, Imperial College, London, United Kingdom.
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