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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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Sheikhpour M, Maleki M, Ebrahimi Vargoorani M, Amiri V. A review of epigenetic changes in asthma: methylation and acetylation. Clin Epigenetics 2021; 13:65. [PMID: 33781317 PMCID: PMC8008616 DOI: 10.1186/s13148-021-01049-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/04/2021] [Indexed: 12/30/2022] Open
Abstract
Several studies show that childhood and adulthood asthma and its symptoms can be modulated through epigenetic modifications. Epigenetic changes are inheritable modifications that can modify the gene expression without changing the DNA sequence. The most common epigenetic alternations consist of DNA methylation and histone modifications. How these changes lead to asthmatic phenotype or promote the asthma features, in particular by immune pathways regulation, is an understudied topic. Since external effects, like exposure to tobacco smoke, air pollution, and drugs, influence both asthma development and the epigenome, elucidating the role of epigenetic changes in asthma is of great importance. This review presents available evidence on the epigenetic process that drives asthma genes and pathways, with a particular focus on DNA methylation, histone methylation, and acetylation. We gathered and assessed studies conducted in this field over the past two decades. Our study examined asthma in different aspects and also shed light on the limitations and the important factors involved in the outcomes of the studies. To date, most of the studies in this area have been carried out on DNA methylation. Therefore, the need for diagnostic and therapeutic applications through this molecular process calls for more research on the histone modifications in this disease.
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Affiliation(s)
- Mojgan Sheikhpour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.
- Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| | - Mobina Maleki
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Maryam Ebrahimi Vargoorani
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
- Department of Microbiology, College of Basic Sciences, Tehran North Branch, Islamic Azad University, Tehran, Iran
| | - Vahid Amiri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
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Braun M, Klingelhöfer D, Oremek GM, Quarcoo D, Groneberg DA. Influence of Second-Hand Smoke and Prenatal Tobacco Smoke Exposure on Biomarkers, Genetics and Physiological Processes in Children-An Overview in Research Insights of the Last Few Years. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E3212. [PMID: 32380770 PMCID: PMC7246681 DOI: 10.3390/ijerph17093212] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/16/2020] [Accepted: 04/29/2020] [Indexed: 02/07/2023]
Abstract
Children are commonly exposed to second-hand smoke (SHS) in the domestic environment or inside vehicles of smokers. Unfortunately, prenatal tobacco smoke (PTS) exposure is still common, too. SHS is hazardous to the health of smokers and non-smokers, but especially to that of children. SHS and PTS increase the risk for children to develop cancers and can trigger or worsen asthma and allergies, modulate the immune status, and is harmful to lung, heart and blood vessels. Smoking during pregnancy can cause pregnancy complications and poor birth outcomes as well as changes in the development of the foetus. Lately, some of the molecular and genetic mechanisms that cause adverse health effects in children have been identified. In this review, some of the current insights are discussed. In this regard, it has been found in children that SHS and PTS exposure is associated with changes in levels of enzymes, hormones, and expression of genes, micro RNAs, and proteins. PTS and SHS exposure are major elicitors of mechanisms of oxidative stress. Genetic predisposition can compound the health effects of PTS and SHS exposure. Epigenetic effects might influence in utero gene expression and disease susceptibility. Hence, the limitation of domestic and public exposure to SHS as well as PTS exposure has to be in the focus of policymakers and the public in order to save the health of children at an early age. Global substantial smoke-free policies, health communication campaigns, and behavioural interventions are useful and should be mandatory.
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Affiliation(s)
- Markus Braun
- Institute of Occupational Medicine, Social Medicine and Environmental Medicine, Goethe University Frankfurt, D-60590 Frankfurt, Germany; (D.K.); (G.M.O.); (D.Q.); (D.A.G.)
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Kogan V, Millstein J, London SJ, Ober C, White SR, Naureckas ET, Gauderman WJ, Jackson DJ, Barraza-Villarreal A, Romieu I, Raby BA, Breton CV. Genetic-Epigenetic Interactions in Asthma Revealed by a Genome-Wide Gene-Centric Search. Hum Hered 2019; 83:130-152. [PMID: 30669148 PMCID: PMC7365350 DOI: 10.1159/000489765] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES There is evidence to suggest that asthma pathogenesis is affected by both genetic and epigenetic variation independently, and there is some evidence to suggest that genetic-epigenetic interactions affect risk of asthma. However, little research has been done to identify such interactions on a genome-wide scale. The aim of this studies was to identify genes with genetic-epigenetic interactions associated with asthma. METHODS Using asthma case-control data, we applied a novel nonparametric gene-centric approach to test for interactions between multiple SNPs and CpG sites simultaneously in the vicinities of 18,178 genes across the genome. RESULTS Twelve genes, PF4, ATF3, TPRA1, HOPX, SCARNA18, STC1, OR10K1, UPK1B, LOC101928523, LHX6, CHMP4B, and LANCL1, exhibited statistically significant SNP-CpG interactions (false discovery rate = 0.05). Of these, three have previously been implicated in asthma risk (PF4, ATF3, and TPRA1). Follow-up analysis revealed statistically significant pairwise SNP-CpG interactions for several of these genes, including SCARNA18, LHX6, and LOC101928523 (p = 1.33E-04, 8.21E-04, 1.11E-03, respectively). CONCLUSIONS Joint effects of genetic and epigenetic variation may play an important role in asthma pathogenesis. Statistical methods that simultaneously account for multiple variations across chromosomal regions may be needed to detect these types of effects on a genome-wide scale.
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Affiliation(s)
- Vladimir Kogan
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Joshua Millstein
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA,
| | - Stephanie J London
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, RTP, Research Triangle Park, North Carolina, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
| | - Steven R White
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | | | - W James Gauderman
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Daniel J Jackson
- University of Wisconsin School of Medicine and Public Health, Madison, Illinois, USA
| | - Albino Barraza-Villarreal
- Department of Environmental Health, Population Health Center, National Institute of Public Health of Mexico, Cuernavaca, Mexico
| | - Isabelle Romieu
- International Agency for Research on Cancer, Section of Nutrition and Metabolism, Lyon, France
| | - Benjamin A Raby
- Department of Medicine, Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Carrie V Breton
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
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Meyer KF, Verkaik-Schakel RN, Timens W, Kobzik L, Plösch T, Hylkema MN. The fetal programming effect of prenatal smoking on Igf1r and Igf1 methylation is organ- and sex-specific. Epigenetics 2018; 12:1076-1091. [PMID: 29160127 PMCID: PMC5810788 DOI: 10.1080/15592294.2017.1403691] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The impact of prenatal smoke exposure (PSE) on DNA methylation has been demonstrated in blood samples from children of smoking mothers, but evidence for sex-dependent smoke-induced effects is limited. As the identified differentially methylated genes can be associated with developmental processes, and insulin-like growth factors (IGFs) play a critical role in prenatal tissue growth, we hypothesized that PSE induces fetal programming of Igf1r and Igf1. Using a mouse model of smoking during pregnancy, we show that PSE alters promoter methylation of Igf1r and Igf1 and deregulates their gene expression in lung and liver of fetal (E17.5) and neonatal (D3) mouse offspring. By further comparing female versus male, lung versus liver, or fetal versus neonatal time point, our results demonstrate that CpG site-specific aberrant methylation patterns sex-dependently vary per organ and time point. Moreover, PSE reduces gene expression of Igf1r and Igf1, dependent on organ, sex, and offspring's age. Our results indicate that PSE may be a source of organ-specific rather than general systemic fetal programming. This is exemplified here by gene promoter methylation and mRNA levels of Igf1r and Igf1, together with a sex- and organ-specific naturally established correlation of both parameters that is affected by prenatal smoke exposure. Moreover, the comparison of fetuses with neonates suggests a CpG site-dependent reversibility/persistence of PSE-induced differential methylation patterns.
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Affiliation(s)
- Karolin F Meyer
- a Department of Pathology and Medical Biology , University of Groningen, University Medical Center Groningen , Hanzeplein 1, EA10, 9713 GZ , Groningen , The Netherlands.,b University of Groningen , University Medical Center Groningen , GRIAC Research Institute , Hanzeplein 1, EA10, 9713 GZ , Groningen , The Netherlands
| | - Rikst Nynke Verkaik-Schakel
- c Department of Obstetrics and Gynaecology , University of Groningen , University Medical Center Groningen , Hanzeplein 1, 9713 GZ , Groningen , The Netherlands
| | - Wim Timens
- a Department of Pathology and Medical Biology , University of Groningen, University Medical Center Groningen , Hanzeplein 1, EA10, 9713 GZ , Groningen , The Netherlands.,b University of Groningen , University Medical Center Groningen , GRIAC Research Institute , Hanzeplein 1, EA10, 9713 GZ , Groningen , The Netherlands
| | - Lester Kobzik
- d Molecular and Integrative Physiological Sciences Program, Department of Environmental Health , Harvard T. H. Chan School of Public Health , Building II Room 221, 655 Huntington Avenue, Boston , MA 02115 , USA
| | - Torsten Plösch
- c Department of Obstetrics and Gynaecology , University of Groningen , University Medical Center Groningen , Hanzeplein 1, 9713 GZ , Groningen , The Netherlands
| | - Machteld N Hylkema
- a Department of Pathology and Medical Biology , University of Groningen, University Medical Center Groningen , Hanzeplein 1, EA10, 9713 GZ , Groningen , The Netherlands.,b University of Groningen , University Medical Center Groningen , GRIAC Research Institute , Hanzeplein 1, EA10, 9713 GZ , Groningen , The Netherlands
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Hu WP, Zeng YY, Zuo YH, Zhang J. Identification of novel candidate genes involved in the progression of emphysema by bioinformatic methods. Int J Chron Obstruct Pulmon Dis 2018; 13:3733-3747. [PMID: 30532529 PMCID: PMC6241693 DOI: 10.2147/copd.s183100] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Purpose By reanalyzing the gene expression profile GSE76925 in the Gene Expression Omnibus database using bioinformatic methods, we attempted to identify novel candidate genes promoting the development of emphysema in patients with COPD. Patients and methods According to the Quantitative CT data in GSE76925, patients were divided into mild emphysema group (%LAA-950<20%, n=12) and severe emphysema group (%LAA-950>50%, n=11). Differentially expressed genes (DEGs) were identified using Agilent GeneSpring GX v11.5 (corrected P-value <0.05 and |Fold Change|>1.3). Known driver genes of COPD were acquired by mining literatures and retrieving databases. Direct protein–protein interaction network (PPi) of DEGs and known driver genes was constructed by STRING.org to screen the DEGs directly interacting with driver genes. In addition, we used STRING.org to obtain the first-layer proteins interacting with DEGs’ products and constructed the indirect PPi of these interaction proteins. By merging the indirect PPi with driver genes’ PPi using Cytoscape v3.6.1, we attempted to discover potential pathways promoting emphysema’s development. Results All the patients had COPD with severe airflow limitation (age=62±8, FEV1%=28±12). A total of 57 DEGs (including 12 pseudogenes) and 135 known driving genes were identified. Direct PPi suggested that GPR65, GNB4, P2RY13, NPSR1, BCR, BAG4, and IMPDH2 were potential pathogenic genes. GPR65 could regulate the response of immune cells to the acidic microenvironment, and NPSR1’s expression on eosinophils was associated with asthma’s severity and IgE level. Indirect merging PPi demonstrated that the interacting network of TP53, IL8, CCR2, HSPA1A, ELANE, PIK3CA was associated with the development of emphysema. IL8, ELANE, and PIK3CA were molecules involved in the pathological mechanisms of emphysema, which also in return proved the role of TP53 in emphysema. Conclusion Candidate genes such as GPR65, NPSR1, and TP53 may be involved in the progression of emphysema.
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Affiliation(s)
- Wei-Ping Hu
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China,
| | - Ying-Ying Zeng
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China,
| | - Yi-Hui Zuo
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China,
| | - Jing Zhang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China,
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Langie SAS, Moisse M, Szarc Vel Szic K, Van Der Plas E, Koppen G, De Prins S, Louwies T, Nelen V, Van Camp G, Lambrechts D, Schoeters G, Vanden Berghe W, De Boever P. GLI2 promoter hypermethylation in saliva of children with a respiratory allergy. Clin Epigenetics 2018; 10:50. [PMID: 29682088 PMCID: PMC5896137 DOI: 10.1186/s13148-018-0484-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 03/27/2018] [Indexed: 12/13/2022] Open
Abstract
Background The prevalence of respiratory allergy in children is increasing. Epigenetic DNA methylation changes are plausible underlying molecular mechanisms. Results Saliva samples collected in substudies of two longitudinal birth cohorts in Belgium (FLEHS1 & FLEHS2) were used to discover and confirm DNA methylation signatures that can differentiate individuals with respiratory allergy from healthy subjects. Genome-wide analysis with Illumina Methylation 450K BeadChips revealed 23 differentially methylated gene regions (DMRs) in saliva from 11y old allergic children (N=26) vs. controls (N=20) in FLEHS1. A subset of 7 DMRs was selected for confirmation by iPLEX MassArray analysis. First, iPLEX analysis was performed in the same 46 FLEHS1 samples for analytical confirmation of the findings obtained during the discovery phase. iPLEX results correlated significantly with the 450K array data (P <0.0001) and confirmed 4 out of the 7 DMRs. Aiming for additional biological confirmation, the 7 DMRs were analyzed using iPLEX in a substudy of an independent birth cohort (FLEHS2; N=19 cases vs. 20 controls, aged 5 years). One DMR in the GLI2 promoter region showed a consistent statistically significant hypermethylation in individuals with respiratory allergy across the two birth cohorts and technologies. In addition to its involvement in TGF-β signaling and T-helper differentiation, GLI2 has a regulating role in lung development. Conclusion GLI2 is considered an interesting candidate DNA methylation marker for respiratory allergy. Electronic supplementary material The online version of this article (10.1186/s13148-018-0484-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sabine A S Langie
- 1VITO- Sustainable Health, Boeretang 200, 2400 Mol, Belgium.,2Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Matthieu Moisse
- 3Laboratory for Translational Genetics, Center for Cancer Biology, VIB and KU Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Katarzyna Szarc Vel Szic
- 1VITO- Sustainable Health, Boeretang 200, 2400 Mol, Belgium.,4Proteinchemistry, Proteomics & Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Ellen Van Der Plas
- 1VITO- Sustainable Health, Boeretang 200, 2400 Mol, Belgium.,7Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Gudrun Koppen
- 1VITO- Sustainable Health, Boeretang 200, 2400 Mol, Belgium
| | - Sofie De Prins
- 1VITO- Sustainable Health, Boeretang 200, 2400 Mol, Belgium
| | - Tijs Louwies
- 1VITO- Sustainable Health, Boeretang 200, 2400 Mol, Belgium
| | - Vera Nelen
- Environment and Health unit, Provincial Institute of Hygiene, Antwerp, Belgium
| | - Guy Van Camp
- 6Center for Medical Genetics, University of Antwerp and Antwerp University hospital, Antwerp, Belgium
| | - Diether Lambrechts
- 3Laboratory for Translational Genetics, Center for Cancer Biology, VIB and KU Leuven, Campus Gasthuisberg, Leuven, Belgium
| | - Greet Schoeters
- 1VITO- Sustainable Health, Boeretang 200, 2400 Mol, Belgium.,7Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium.,8Department of Environmental Medicine, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | - Wim Vanden Berghe
- 4Proteinchemistry, Proteomics & Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium
| | - Patrick De Boever
- 1VITO- Sustainable Health, Boeretang 200, 2400 Mol, Belgium.,2Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
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Hill SY, Rompala G, Homanics GE, Zezza N. Cross-generational effects of alcohol dependence in humans on HRAS and TP53 methylation in offspring. Epigenomics 2017; 9:1189-1203. [PMID: 28799801 DOI: 10.2217/epi-2017-0052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
AIM We hypothesized that cross-generational effects of alcohol exposure could alter DNA methylation and expression of the HRAS oncogene and TP53 tumor suppressor gene that drive cancer development. METHODS DNA methylation of the HRAS and TP53 genes was tested in samples from young participants (Mean age of 13.4 years). RESULTS Controlling for both personal use and maternal use of substances during pregnancy, familial alcohol dependence was associated with hypomethylation of CpG sites in the HRAS promoter region and hypermethylation of the TP53 gene. CONCLUSION The results suggest that ancestral exposure to alcohol can have enduring effects that impact epigenetic processes such as DNA methylation that controls expression of genes that drive cancer development such as HRAS and TP53.
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Affiliation(s)
- Shirley Y Hill
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Gregory Rompala
- Center for Neuroscience, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Gregg E Homanics
- Departments of Anesthesiology & Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Nicholas Zezza
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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Potaczek DP, Harb H, Michel S, Alhamwe BA, Renz H, Tost J. Epigenetics and allergy: from basic mechanisms to clinical applications. Epigenomics 2017; 9:539-571. [PMID: 28322581 DOI: 10.2217/epi-2016-0162] [Citation(s) in RCA: 191] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Allergic diseases are on the rise in the Western world and well-known allergy-protecting and -driving factors such as microbial and dietary exposure, pollution and smoking mediate their influence through alterations of the epigenetic landscape. Here, we review key facts on the involvement of epigenetic modifications in allergic diseases and summarize and critically evaluate the lessons learned from epigenome-wide association studies. We show the potential of epigenetic changes for various clinical applications: as diagnostic tools, to assess tolerance following immunotherapy or possibly predict the success of therapy at an early time point. Furthermore, new technological advances such as epigenome editing and DNAzymes will allow targeted alterations of the epigenome in the future and provide novel therapeutic tools.
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Affiliation(s)
- Daniel P Potaczek
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps-Universität Marburg, Marburg, Germany.,International Inflammation (in-FLAME) Network, Worldwide Universities Network (WUN).,German Centre for Lung Research (DZL).,John Paul II Hospital, Krakow, Poland
| | - Hani Harb
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps-Universität Marburg, Marburg, Germany.,International Inflammation (in-FLAME) Network, Worldwide Universities Network (WUN).,German Centre for Lung Research (DZL)
| | - Sven Michel
- Secarna Pharmaceuticals GmbH & Co KG, Planegg, Germany
| | - Bilal Alashkar Alhamwe
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps-Universität Marburg, Marburg, Germany
| | - Harald Renz
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, Philipps-Universität Marburg, Marburg, Germany.,International Inflammation (in-FLAME) Network, Worldwide Universities Network (WUN).,German Centre for Lung Research (DZL)
| | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Génotypage, CEA-Institut de Génomique, Evry, France
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Abstract
Tremendous efforts have been invested in research to (1) discover risk factors, biomarkers, and clinical characteristics; (2) understand the pathophysiology and treatment response variability in severe asthma; and (3) design new therapies. However, to combat severe asthma, many questions concerning the pathogenesis of severe asthma, including its natural history, genetic and environmental risk factors, and disease mechanisms, must be answered. In this article we highlight some of the major discoveries concerning the pathogenesis of severe asthma and its therapeutic development. We conclude that discoveries on numerous fronts of severe asthma, from disease heterogeneity, features of airway remodeling, cytokine mediators and signaling pathways underlying disease pathogenesis, disease mechanisms, potential biomarkers, to new therapeutic targets, demonstrate that progress has been made in understanding and developing more effective treatments for this difficult-to-treat disease.
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Abstract
PURPOSE OF REVIEW The goal of this review was to systematically analyze recent studies updating our knowledge on the role of epigenetic mechanisms in childhood asthma. RECENT FINDINGS A systematic literature search was conducted that identified 23 fresh articles published within the last 5 years reporting the results of human studies on the relationships between epigenetic modifications and childhood asthma or its/related phenotypes. In almost all these studies, meaningful associations between levels of epigenetic marks (DNA methylation and/or histone modifications) and pediatric asthma or its/related phenotypes have been observed. In addition, many studies identified by our screening analyzed those associations in the context of environmental factors, such as pollution, tobacco smoke, farming, or diet, showing in a huge majority a modifying effect of those exposures. SUMMARY The results of our systematic literature search provide a strong support for the role of epigenetic mechanisms in (mediating the effects of environmental exposure on) pediatric asthma. This knowledge may possibly be translated into diagnostic and/or therapeutic approaches.
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DNA methylation: conducting the orchestra from exposure to phenotype? Clin Epigenetics 2016; 8:92. [PMID: 27602172 PMCID: PMC5012062 DOI: 10.1186/s13148-016-0256-8] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/22/2016] [Indexed: 01/02/2023] Open
Abstract
DNA methylation, through 5-methyl- and 5-hydroxymethylcytosine (5mC and 5hmC), is considered to be one of the principal interfaces between the genome and our environment, and it helps explain phenotypic variations in human populations. Initial reports of large differences in methylation level in genomic regulatory regions, coupled with clear gene expression data in both imprinted genes and malignant diseases, provided easily dissected molecular mechanisms for switching genes on or off. However, a more subtle process is becoming evident, where small (<10 %) changes to intermediate methylation levels are associated with complex disease phenotypes. This has resulted in two clear methylation paradigms. The latter “subtle change” paradigm is rapidly becoming the epigenetic hallmark of complex disease phenotypes, although we are currently hampered by a lack of data addressing the true biological significance and meaning of these small differences. Our initial expectation of rapidly identifying mechanisms linking environmental exposure to a disease phenotype led to numerous observational/association studies being performed. Although this expectation remains unmet, there is now a growing body of literature on specific genes, suggesting wide ranging transcriptional and translational consequences of such subtle methylation changes. Data from the glucocorticoid receptor (NR3C1) has shown that a complex interplay between DNA methylation, extensive 5′UTR splicing, and microvariability gives rise to the overall level and relative distribution of total and N-terminal protein isoforms generated. Additionally, the presence of multiple AUG translation initiation codons throughout the complete, processed mRNA enables translation variability, hereby enhancing the translational isoforms and the resulting protein isoform diversity, providing a clear link between small changes in DNA methylation and significant changes in protein isoforms and cellular locations. Methylation changes in the NR3C1 CpG island alters the NR3C1 transcription and eventually protein isoforms in the tissues, resulting in subtle but visible physiological variability. This review addresses the current pathophysiological and clinical associations of such characteristically small DNA methylation changes, the ever-growing roles of DNA methylation and the evidence available, particularly from the glucocorticoid receptor of the cascade of events initiated by such subtle methylation changes, as well as addressing the underlying question as to what represents a genuine biologically significant difference in methylation.
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Sabar MF, Ghani MU, Shahid M, Sumrin A, Ali A, Akram M, Tariq MA, Bano I. Genetic variants of ADAM33 are associated with asthma susceptibility in the Punjabi population of Pakistan. J Asthma 2016. [DOI: https://doi.org/10.3109/02770903.2015.1124441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Sabar MF, Ghani MU, Shahid M, Sumrin A, Ali A, Akram M, Tariq MA, Bano I. Genetic variants of ADAM33 are associated with asthma susceptibility in the Punjabi population of Pakistan. J Asthma 2016; 53:341-348. [PMID: 26666372 DOI: 10.3109/02770903.2015.1124441] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
OBJECTIVE A disintegrin and metalloproteinase 33 (ADAM33) gene has been considered as an asthma susceptibility gene due to its possible role in airway remodeling, abnormal cell proliferation, and differentiation. Association of this gene with asthma has been reported in several genetic studies on various populations. The current study aims to evaluate the association of ADAM33 gene polymorphisms with the risk of asthma in the Punjabi population of Pakistan. METHOD A total of 101 asthma patients and 102 age-matched healthy controls from Lahore, a city in Punjab, were recruited. ADAM33 single nucleotide polymorphisms (SNPs) T + 1[rs2280089], T2[rs2280090], T1[rs2280091], ST + 5[rs597980], ST + 4[rs44707], S2[rs528557], Q - 1[rs612709], and F + 1[rs511898] were genotyped in both patients and controls using single base extension and capillary electrophoresis-based genetic analyzer. The basic allelic and genotypic model was analyzed for association of the SNPs with asthma using SHEsis software. Haploview software was used to calculate pairwise linkage disequilibrium (LD) among six of the genotyped SNPs. RESULTS Of the 8 SNPs genotyped, only S2[rs528557] showed significant association with asthma (Allele p = 0.0189, Genotype p = 0.021). SNPs T + 1[rs2280089], T2[rs2280090], T1[rs2280091], ST + 4[rs44707], S2[rs528557], and Q - 1[rs612709] were found to be in moderate to strong LD. The significantly higher frequency of haplotype "AAGTCG" in healthy controls suggests a protective effect against asthma risk in the studied population (p = 0.0059). CONCLUSION These findings suggest that genetic variants of ADAM33 gene may play important roles in asthma susceptibility in the Punjabi population of Pakistan.
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Affiliation(s)
- Muhammad Farooq Sabar
- a Centre for Applied Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Muhammad Usman Ghani
- a Centre for Applied Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Mariam Shahid
- a Centre for Applied Molecular Biology, University of the Punjab , Lahore , Pakistan
- b Centre of Excellence in Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Aleena Sumrin
- a Centre for Applied Molecular Biology, University of the Punjab , Lahore , Pakistan
| | - Amjad Ali
- c Allied Health Sciences, The University of Lahore , Lahore , Pakistan , and
| | - Muhammad Akram
- a Centre for Applied Molecular Biology, University of the Punjab , Lahore , Pakistan
| | | | - Iqbal Bano
- d Pediatric Pulmonology, The Children's Hospital & The Institute of Child Health , Lahore , Pakistan
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Sabounchi S, Bollyky J, Nadeau K. Review of Environmental Impact on the Epigenetic Regulation of Atopic Diseases. Curr Allergy Asthma Rep 2015; 15:33. [PMID: 26141578 DOI: 10.1007/s11882-015-0533-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
There has been significant increase in the prevalence of atopy over the past decade that cannot be explained by genetic predisposition. Environmental factors including nutrition, the uterine environment, and lifestyle factors are known to play a role in gene expression through epigenetic modifications. In this article, we review the literature on the environmental impact on epigenetic modulation of atopic diseases including asthma, food allergy, eczema, and allergic rhinitis. Recent public release of epigenomic data for hundreds of human tissues provides a powerful resource for further investigation of the molecular basis of atopic diseases.
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Affiliation(s)
- Saman Sabounchi
- Department of Pediatrics, Division of Allergy, Immunology, and Rheumatology, Stanford University School of Medicine, 269 Campus Drive, CCSR Suite 3215, Stanford, CA, 94305, USA
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16
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Berenguer AG. I feel you-monitoring environmental variables related to asthma in an integrated real-time frame. BMC Res Notes 2015; 8:431. [PMID: 26361763 PMCID: PMC4566483 DOI: 10.1186/s13104-015-1421-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 09/07/2015] [Indexed: 11/10/2022] Open
Abstract
The study of asthma and other complex diseases has proven to be a "moving target" for researchers due to its complex aetiology, difficulty in definition, and immeasurable environmental effects. A large number of studies regarding the contribution of both genetic and environmental factors often result in contradictory results, in part due to the highly heterogeneous nature of asthma. Recent literature has focused on the epigenetic signatures of asthma caused by environmental factors, highlighting the importance of environment. However, unlike the genetic techniques, environmental assessment still lacks accuracy. A plausible solution for this problem would be an individual-based environmental exposure assessment, relying on new technologies such as personal real-time environmental sensors. This could prove to enable the assessment of the whole environmental exposure-or exposome-matching in terms of precision the genome that is emphasized in most studies so far. In addition, the measurement of the whole array of biological molecules, in response to the environment action, could help understand the context of the disease. The current perspective comprises a beyond-genetics integrated vision of omics technology coupled with real-time environmental measures targeting to enhance our comprehension of the disease genesis.
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Affiliation(s)
- Anabela Gonçalves Berenguer
- Human Genetics Laboratory, University of Madeira, 9000-390, Funchal, Portugal. .,Department of Computer Science and Engineering, University of Oulu, PL 4500, 90014, Oulu, Finland.
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17
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Gagné-Ouellet V, Guay SP, Boucher-Lafleur AM, Bouchard L, Laprise C. DNA methylation signature of interleukin 1 receptor type II in asthma. Clin Epigenetics 2015; 7:80. [PMID: 26246860 PMCID: PMC4526162 DOI: 10.1186/s13148-015-0114-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/13/2015] [Indexed: 12/25/2022] Open
Abstract
Interleukin 1 and its receptors are associated with allergic diseases such as asthma. In the present study, we measured DNA methylation at the IL1R1 and IL1R2 gene loci and assessed for associations with asthma-related phenotypes and gene expressions. We found that asthmatic and atopic individuals have higher IL1R2 promoter DNA methylation than control subjects. Additionally, we observed a negative correlation between DNA methylation at the IL1R2 promoter and IL1R2 mRNA expression. These results suggest for the first time that IL1R2 promoter DNA methylation is associated with its gene repression in allergic diseases such as asthma.
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Affiliation(s)
- Valérie Gagné-Ouellet
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC Canada
| | - Simon-Pierre Guay
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC Canada ; ECOGENE-21 and Lipid Clinic, Hôpital de Chicoutimi, Saguenay, QC Canada
| | | | - Luigi Bouchard
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC Canada ; ECOGENE-21 and Lipid Clinic, Hôpital de Chicoutimi, Saguenay, QC Canada
| | - Catherine Laprise
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, QC Canada
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18
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Selective breeding for high anxiety introduces a synonymous SNP that increases neuropeptide S receptor activity. J Neurosci 2015; 35:4599-613. [PMID: 25788677 DOI: 10.1523/jneurosci.4764-13.2015] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Neuropeptide S (NPS) has generated substantial interest due to its anxiolytic and fear-attenuating effects in rodents, while a corresponding receptor polymorphism associated with increased NPS receptor (NPSR1) surface expression and efficacy has been implicated in an increased risk of panic disorder in humans. To gain insight into this paradox, we examined the NPS system in rats and mice bred for high anxiety-related behavior (HAB) versus low anxiety-related behavior, and, thereafter, determined the effect of central NPS administration on anxiety- and fear-related behavior. The HAB phenotype was accompanied by lower basal NPS receptor (Npsr1) expression, which we could confirm via in vitro dual luciferase promoter assays. Assessment of shorter Npsr1 promoter constructs containing a sequence mutation that introduces a glucocorticoid receptor transcription factor binding site, confirmed via oligonucleotide pull-down assays, revealed increased HAB promoter activity-an effect that was prevented by dexamethasone. Analogous to the human NPSR1 risk isoform, functional analysis of a synonymous single nucleotide polymorphism in the coding region of HAB rodents revealed that it caused a higher cAMP response to NPS stimulation. Assessment of the behavioral consequence of these differences revealed that intracerebroventricular NPS reversed the hyperanxiety of HAB rodents as well as the impaired cued-fear extinction in HAB rats and the enhanced fear expression in HAB mice, respectively. These results suggest that alterations in the NPS system, conserved across rodents and humans, contribute to innate anxiety and fear, and that HAB rodents are particularly suited to resolve the apparent discrepancy between the preclinical and clinical findings to date.
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Krauss-Etschmann S, Meyer KF, Dehmel S, Hylkema MN. Inter- and transgenerational epigenetic inheritance: evidence in asthma and COPD? Clin Epigenetics 2015; 7:53. [PMID: 26052354 PMCID: PMC4456695 DOI: 10.1186/s13148-015-0085-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 04/09/2015] [Indexed: 12/21/2022] Open
Abstract
Evidence is now emerging that early life environment can have lifelong effects on metabolic, cardiovascular, and pulmonary function in offspring, a concept also known as fetal or developmental programming. In mammals, developmental programming is thought to occur mainly via epigenetic mechanisms, which include DNA methylation, histone modifications, and expression of non-coding RNAs. The effects of developmental programming can be induced by the intrauterine environment, leading to intergenerational epigenetic effects from one generation to the next. Transgenerational epigenetic inheritance may be considered when developmental programming is transmitted across generations that were not exposed to the initial environment which triggered the change. So far, inter- and transgenerational programming has been mainly described for cardiovascular and metabolic disease risk. In this review, we discuss available evidence that epigenetic inheritance also occurs in respiratory diseases, using asthma and chronic obstructive pulmonary disease (COPD) as examples. While multiple epidemiological as well as animal studies demonstrate effects of 'toxic' intrauterine exposure on various asthma-related phenotypes in the offspring, only few studies link epigenetic marks to the observed phenotypes. As epigenetic marks may distinguish individuals most at risk of later disease at early age, it will enable early intervention strategies to reduce such risks. To achieve this goal further, well designed experimental and human studies are needed.
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Affiliation(s)
- Susanne Krauss-Etschmann
- />Comprehensive Pneumology Center, Helmholtz Center Munich and Children’s Hospital of Ludwig-Maximilians University, Max-Lebsche-Platz 31, 81377 Munich, Germany
- />Priority Area Asthma & Allergy, Leibniz Center for Medicine and Biosciences, Research Center Borstel and Christian Albrechts University Kiel, Airway Research Center North, Member of the German Center for Lung Research, Parkallee 1-40, Borstel, Germany
| | - Karolin F Meyer
- />Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen, The Netherlands
- />University of Groningen, GRIAC Research Institute, University Medical Center Groningen, Hanzeplein 1, Groningen, The Netherlands
| | - Stefan Dehmel
- />Comprehensive Pneumology Center, Helmholtz Center Munich and Children’s Hospital of Ludwig-Maximilians University, Max-Lebsche-Platz 31, 81377 Munich, Germany
| | - Machteld N Hylkema
- />Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen, The Netherlands
- />University of Groningen, GRIAC Research Institute, University Medical Center Groningen, Hanzeplein 1, Groningen, The Netherlands
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20
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Abstract
It is generally agreed that environmental factors trigger the onset and cause flares of inflammatory bowel disease. Although we have learned much about genetic susceptibility factors of inflammatory bowel disease in recent years, our knowledge on these environmental factors is limited. The sum of all environmental factors a human is exposed to during lifetime has been termed the exposome. The challenge of investigating the exposome is discussed in this overview. The environmental exposure of a subject causes changes in the intestinal microbiota and subsequently changes the epigenetic imprinting of the mucosa and the associated immune system. Some relevant environmental factors have been investigated in recent years in inflammatory bowel disease and other (auto)inflammatory disease. These factors can be categorized in air pollution, diet, drugs, stress, infections, water pollution, food additives, and lifestyle. Examples from those categories and their potential pathophysiological mechanism are discussed.
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21
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Gruzieva O, Merid SK, Melén E. An update on epigenetics and childhood respiratory diseases. Paediatr Respir Rev 2014; 15:348-54. [PMID: 25151612 DOI: 10.1016/j.prrv.2014.07.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 07/24/2014] [Indexed: 01/28/2023]
Abstract
Epigenetic mechanisms, defined as changes in phenotype or gene expression caused by mechanisms other than changes in the underlying DNA sequence, have been proposed to constitute a link between genetic and environmental factors that affect complex diseases. Recent studies show that DNA methylation, one of the key epigenetic mechanisms, is altered in children exposed to air pollutants and environmental tobacco smoke early in life. Several candidate gene studies on epigenetics have been published to date, but it is only recently that global methylation analyses have been performed for respiratory disorders such as asthma and chronic obstructive pulmonary disease. However, large-scale studies with adequate power are yet to be presented in children, and implications for clinical use remain to be evaluated. In this review, we summarize the recent advances in epigenetics and respiratory disorders in children, with a main focus on methodological challenges and analyses related to phenotype and exposure using global methylation approaches.
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Affiliation(s)
- Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Simon Kebede Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Sachs' Children's Hospital, Stockholm, Sweden.
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22
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Interaction of NPSR1 genotypes and probiotics in the manifestation of atopic eczema in early childhood. Allergol Immunopathol (Madr) 2014; 42:560-7. [PMID: 24439655 DOI: 10.1016/j.aller.2013.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 10/09/2013] [Accepted: 10/29/2013] [Indexed: 11/21/2022]
Abstract
BACKGROUND Neuropeptide S Receptor (NPSR1) gene has been associated with multiple allergic phenotypes in several patient populations. OBJECTIVE We analysed the effect of the NPSR1 genotypes in the development of asthma, rhinitis, eczema, or food allergy in children randomly receiving either probiotic or placebo treatment. METHODS 796 children born to families at high risk for allergic diseases were examined by a paediatrician at the age of three months, six months, two years, and five years. Asthma, rhinitis, eczema, and food allergy were diagnosed according to international guidelines. Treatment with probiotics (double-blinded and placebo controlled) was begun with mothers at 35 weeks of gestation age and continued after the birth of infants up to the age of six months. Association and additive inheritance models were used in genetic analyses. RESULTS Distribution of the hopo546333 was suggestive in the group of patients with atopic eczema at two years. The hopo546333_G was found more often in those with eczema in the placebo group (p=0.048, after Bonferroni correction) and the hopo546333_A was found more often in those with eczema and probiotics compared to those with eczema and placebo treatment. None of the NPSR1 tagging SNPs was associated with asthma, IgE-mediated asthma, or sensitisation. Allergic disease in both parents doubled the risk for IgE-mediated allergic disease (OR 2.1). CONCLUSIONS The NPSR1 gene SNP hopo546333 showed a suggestive association for high IgE-associated atopic eczema at two years.
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23
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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: 1.7] [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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24
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Henström M, Zucchelli M, Söderhäll C, Bergström A, Kere J, Melén E, Olén O, D'Amato M. NPSR1 polymorphisms influence recurrent abdominal pain in children: a population-based study. Neurogastroenterol Motil 2014; 26:1417-25. [PMID: 25091462 DOI: 10.1111/nmo.12401] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/23/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND Recurrent abdominal pain (RAP) occurs frequently among children and is one of the cardinal symptoms of functional gastrointestinal disorders (FGID). The mechanisms of visceral pain and RAP are not fully understood. A heritable component has been demonstrated and a few candidate genes proposed. NPSR1 encodes the receptor for neuropeptide S (NPS) and NPS-NPSR1 signaling is involved in anxiety, inflammation, and nociception. NPSR1 polymorphisms are associated with asthma and chronic inflammatory diseases, but also with IBS-related intermediate phenotypes such as colonic transit time and rectal sensory ratings. Here, we sought to determine whether genetic variability in the NPSR1 gene influences the presence of RAP in children. METHODS Twenty-eight single-nucleotide polymorphisms (SNPs) in the NPSR1 gene region were successfully genotyped in 1744 children from the Swedish birth cohort BAMSE. Questionnaire information was used to define RAP as episodes of abdominal pain occurring at least once a month in 12-year-olds. KEY RESULTS The prevalence of RAP was 9% in BAMSE. Association with RAP was observed for seven NPSR1 SNPs, five of which withstood false discovery rate (FDR) correction for multiple testing (best p = 0.00054, OR: 1.55 for SNP rs2530566). The associated SNPs all map in a putative regulatory region upstream NPSR1, where they may exert their genetic effects through the modulation of gene expression. CONCLUSIONS & INFERENCES Genetic variation at the NPSR1 locus impacts children's predisposition to RAP episodes in a Swedish population.
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Affiliation(s)
- M Henström
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
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25
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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: 5.5] [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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26
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Hong X, Wang X. Epigenetics and development of food allergy (FA) in early childhood. Curr Allergy Asthma Rep 2014; 14:460. [PMID: 25096861 DOI: 10.1007/s11882-014-0460-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review aims to highlight the latest advance on epigenetics in the development of food allergy (FA) and to offer future perspectives. FA, a condition caused by an immunoglobulin (Ig) E-mediated hypersensitivity reaction to food, has emerged as a major clinical and public health problem worldwide in light of its increasing prevalence, potential fatality, and significant medical and economic impact. Current evidence supports that epigenetic mechanisms are involved in immune regulation and that the epigenome may represent a key "missing piece" of the etiological puzzle for FA. There are a growing number of population-based epigenetic studies on allergy-related phenotypes, mostly focused on DNA methylation. Previous studies mostly applied candidate-gene approaches and have demonstrated that epigenetic marks are associated with multiple allergic diseases and/or with early-life exposures relevant to allergy development (such as early-life smoking exposure, air pollution, farming environment, and dietary fat). Rapid technological advancements have made unbiased genome-wide DNA methylation studies highly feasible, although there are substantial challenge in study design, data analyses, and interpretation of findings. In conclusion, epigenetics represents both an important knowledge gap and a promising research area for FA. Due to the early onset of FA, epigenetic studies of FA in prospective birth cohorts have the potential to better understand gene-environment interactions and underlying biological mechanisms in FA during critical developmental windows (preconception, in utero, and early childhood) and may lead to new paradigms in the diagnosis, prevention, and management of FA and provide novel targets for future drug discovery and therapies for FA.
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Affiliation(s)
- Xiumei Hong
- Center on the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe Street, E4132, Baltimore, MD, 21205-2179, 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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28
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Bégin P, Nadeau KC. Epigenetic regulation of asthma and allergic disease. Allergy Asthma Clin Immunol 2014; 10:27. [PMID: 24932182 PMCID: PMC4057652 DOI: 10.1186/1710-1492-10-27] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 05/18/2014] [Indexed: 01/18/2023] Open
Abstract
Epigenetics of asthma and allergic disease is a field that has expanded greatly in the last decade. Previously thought only in terms of cell differentiation, it is now evident the epigenetics regulate many processes. With T cell activation, commitment toward an allergic phenotype is tightly regulated by DNA methylation and histone modifications at the Th2 locus control region. When normal epigenetic control is disturbed, either experimentally or by environmental exposures, Th1/Th2 balance can be affected. Epigenetic marks are not only transferred to daughter cells with cell replication but they can also be inherited through generations. In animal models, with constant environmental pressure, epigenetically determined phenotypes are amplified through generations and can last up to 2 generations after the environment is back to normal. In this review on the epigenetic regulation of asthma and allergic diseases we review basic epigenetic mechanisms and discuss the epigenetic control of Th2 cells. We then cover the transgenerational inheritance model of epigenetic traits and discuss how this could relate the amplification of asthma and allergic disease prevalence and severity through the last decades. Finally, we discuss recent epigenetic association studies for allergic phenotypes and related environmental risk factors as well as potential underlying mechanisms for these associations.
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Affiliation(s)
- Philippe Bégin
- Allergy, Immunology, and Rheumatology Division, Stanford University, 269 Campus Drive, Stanford, California, USA
| | - Kari C Nadeau
- Allergy, Immunology, and Rheumatology Division, Stanford University, 269 Campus Drive, Stanford, California, USA
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29
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Mazzio EA, Soliman KFA. Epigenetics and nutritional environmental signals. Integr Comp Biol 2014; 54:21-30. [PMID: 24861811 DOI: 10.1093/icb/icu049] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
All terrestrial life is influenced by multi-directional flows of information about its environment, enabling malleable phenotypic change through signals, chemical processes, or various forms of energy that facilitate acclimatization. Billions of biological co-inhabitants of the earth, including all plants and animals, collectively make up a genetic/epigenetic ecosystem by which adaptation/survival (inputs and outputs) are highly interdependent on one another. As an ecosystem, the solar system, rotation of the planets, changes in sunlight, and gravitational pull influence cyclic epigenetic transitions and chromatin remodeling that constitute biological circadian rhythms controlling senescence. In humans, adverse environmental conditions such as poverty, stress, alcohol, malnutrition, exposure to pollutants generated from industrialization, man-made chemicals, and use of synthetic drugs can lead to maladaptive epigenetic-related illnesses with disease-specific genes being atypically activated or silenced. Nutrition and dietary practices are one of the largest facets in epigenetic-related metabolism, where specific "epi-nutrients" can stabilize the genome, given established roles in DNA methylation, histone modification, and chromatin remodeling. Moreover, food-based "epi-bioactive" constituents may reverse maladaptive epigenetic patterns, not only prior to conception and during fetal/early postnatal development but also through adulthood. In summary, in contrast to a static genomic DNA structure, epigenetic changes are potentially reversible, raising the hope for therapeutic and/or dietary interventions that can reverse deleterious epigenetic programing as a means to prevent or treat major illnesses.
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Affiliation(s)
- Elizabeth A Mazzio
- Florida A&M University, College of Pharmacy & Pharmaceutical Sciences, 1520 S MLK Jr. Blvd Tallahassee, FL 32307, USA
| | - Karam F A Soliman
- Florida A&M University, College of Pharmacy & Pharmaceutical Sciences, 1520 S MLK Jr. Blvd Tallahassee, FL 32307, USA
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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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