51
|
Shoshi A, Hofestädt R, Zolotareva O, Friedrichs M, Maier A, Ivanisenko VA, Dosenko VE, Bragina EY. GenCoNet - A Graph Database for the Analysis of Comorbidities by Gene Networks. J Integr Bioinform 2018; 15:/j/jib.2018.15.issue-4/jib-2018-0049/jib-2018-0049.xml. [PMID: 30864352 PMCID: PMC6348742 DOI: 10.1515/jib-2018-0049] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 10/31/2018] [Indexed: 12/11/2022] Open
Abstract
The prevalence of comorbid diseases poses a major health issue for millions of people worldwide and an enormous socio-economic burden for society. The molecular mechanisms for the development of comorbidities need to be investigated. For this purpose, a workflow system was developed to aggregate data on biomedical entities from heterogeneous data sources. The process of integrating and merging all data sources of the workflow system was implemented as a semi-automatic pipeline that provides the import, fusion, and analysis of the highly connected biomedical data in a Neo4j database GenCoNet. As a starting point, data on the common comorbid diseases essential hypertension and bronchial asthma was integrated. GenCoNet (https://genconet.kalis-amts.de) is a curated database that provides a better understanding of hereditary bases of comorbidities.
Collapse
Affiliation(s)
- Alban Shoshi
- Bielefeld University, Bioinformatics/Medical Informatics Department, Bielefeld, Germany
| | - Ralf Hofestädt
- Bielefeld University, Bioinformatics/Medical Informatics Department, Bielefeld, Germany
| | - Olga Zolotareva
- Bielefeld University, Bioinformatics/Medical Informatics Department, Bielefeld, Germany.,Bielefeld University, International Research Group "Computational Methods for the Analysis of the Diversity and Dynamics of Genomes", Bielefeld, Germany
| | - Marcel Friedrichs
- Bielefeld University, Bioinformatics/Medical Informatics Department, Bielefeld, Germany
| | - Alex Maier
- Bielefeld University, Bioinformatics/Medical Informatics Department, Bielefeld, Germany
| | - Vladimir A Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | | | - Elena Yu Bragina
- Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia
| |
Collapse
|
52
|
Verhein KC, Vellers HL, Kleeberger SR. Inter-individual variation in health and disease associated with pulmonary infectious agents. Mamm Genome 2018; 29:38-47. [PMID: 29353387 PMCID: PMC5851710 DOI: 10.1007/s00335-018-9733-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Respiratory infectious diseases resulting from bacterial or viral pathogens such as Mycobacterium tuberculosis, Streptococcus pneumoniae, respiratory syncytial virus (RSV), or influenza, are major global public health concerns. Lower respiratory tract infections are leading causes of morbidity and mortality, only behind ischemic heart disease and stroke (GBD 2015 LRI Collaborators in Lancet Infect Dis 17(11):1133–1161, 2017). Developing countries are particularly impacted by these diseases. However, while many are infected with viruses such as RSV (> 90% of all individuals are infected by age 2), only sub-populations develop severe disease. Many factors may contribute to the inter-individual variation in response to respiratory infections, including gender, age, socioeconomic status, nutrition, and genetic background. Association studies with functional single nucleotide polymorphisms in biologically plausible gene candidates have been performed in human populations to provide insight to the molecular genetic contribution to pulmonary infections and disease severity. In vitro cell models and genome-wide association studies in animal models of genetic susceptibility to respiratory infections have also identified novel candidate susceptibility genes, some of which have also been found to contribute to disease susceptibility in human populations. Genetic background may also contribute to differential efficacy of vaccines against respiratory infections. Development of new genetic mouse models such as the collaborative cross and diversity outbred mice should provide additional insight to the mechanisms of genetic susceptibility to respiratory infections. Continued investigation of susceptibility factors should provide insight to novel strategies to prevent and treat disease that contributes to global morbidity and mortality attributed to respiratory infections.
Collapse
Affiliation(s)
- Kirsten C Verhein
- Inflammation, Immunity, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
- Inflammation, Immunity, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 T.W. Alexander Dr., Building 101, Rm. D240, Research Triangle Park, NC, 27709, USA.
| | - Heather L Vellers
- Inflammation, Immunity, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Steven R Kleeberger
- Inflammation, Immunity, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| |
Collapse
|
53
|
Grigg J, Barben J, Everard ML, Hall G, Karadag B, Moeller A, Nenna R, Priftis KN, Rottier RJ, Terheggen-Lagro SWJ, Midulla F. Key paediatric messages from the 2017 European Respiratory Society International Congress. ERJ Open Res 2018; 4:00165-2017. [PMID: 29850468 PMCID: PMC5968195 DOI: 10.1183/23120541.00165-2017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 04/08/2018] [Indexed: 12/31/2022] Open
Abstract
In this article, the group chairs of the Paediatric Assembly of the European Respiratory Society (ERS) highlight some of the most interesting findings presented at the 2017 ERS International Congress, which was held in Milan, Italy.
Collapse
Affiliation(s)
- Jonathan Grigg
- Centre for Child Health, The Blizard Institute, Queen Mary University of London, London, UK
| | - Jürg Barben
- Division of Paediatric Pulmonology, Children's Hospitals of Eastern Switzerland, St Gallen, Switzerland
| | - Mark L Everard
- Princess Margaret Hospital for Children School of Paediatric and Child Health, University of Western Australia, Perth, Australia
| | - Graham Hall
- Telethon Kids Institute and Curtin University, Perth, Australia
| | - Bülent Karadag
- Division of Pediatric Pulmonology, Marmara University, School of Medicine, Istanbul, Turkey
| | - Alexander Moeller
- Division of Respiratory Medicine, University Children's Hospital Zurich, Zurich, Switzerland
| | - Raffaella Nenna
- Dept of Paediatrics, Sapienza University of Rome, Rome, Italy
| | - Kostas N Priftis
- 3rd Dept of Paediatrics, National and Kapodistrian University of Athens, Medical School, Attikon University General Hospital, Athens, Greece
| | | | | | - Fabio Midulla
- Dept of Paediatrics, Sapienza University of Rome, Rome, Italy
| |
Collapse
|
54
|
Vijverberg SJH, Farzan N, Slob EMA, Neerincx AH, Maitland-van der Zee AH. Treatment response heterogeneity in asthma: the role of genetic variation. Expert Rev Respir Med 2017; 12:55-65. [PMID: 29115880 DOI: 10.1080/17476348.2018.1403318] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Asthmatic patients show a large heterogeneity in response to asthma medication. Rapidly evolving genotyping technologies have led to the identification of various genetic variants associated with treatment outcomes. Areas covered: This review focuses on the current knowledge of genetic variants influencing treatment response to the most commonly used asthma medicines: short- and long-acting beta-2 agonists (SABA/LABA), inhaled corticosteroids (ICS) and leukotriene modifiers. This review shows that various genetic variants have been identified, but none are currently used to guide asthma treatment. One of the most promising genetic variants is the Arg16 variant in the ADRB2 gene to guide LABA treatment in asthmatic children. Expert commentary: Poor replication of initially promising results and the low fraction of variability accounted for by single genetic variants inhibit pharmacogenetic findings to reach the asthma clinic. Nevertheless, the identification of genetic variation influencing treatment response does provide more insights in the complex processes underlying response and might identify novel targets for treatment. There is a need to report measures of clinical validity, to perform precision-medicine guided trials, as well as to understand how genetic variation interacts with environmental factors. In addition, systems biology approaches might be able to show a more complete picture of these complex interactions.
Collapse
Affiliation(s)
- Susanne J H Vijverberg
- a Department of Respiratory Medicine, Academic Medical Center (AMC) , University of Amsterdam , Amsterdam , The Netherlands
| | - Niloufar Farzan
- a Department of Respiratory Medicine, Academic Medical Center (AMC) , University of Amsterdam , Amsterdam , The Netherlands
| | - Elise M A Slob
- a Department of Respiratory Medicine, Academic Medical Center (AMC) , University of Amsterdam , Amsterdam , The Netherlands
| | - Anne H Neerincx
- a Department of Respiratory Medicine, Academic Medical Center (AMC) , University of Amsterdam , Amsterdam , The Netherlands
| | - Anke H Maitland-van der Zee
- a Department of Respiratory Medicine, Academic Medical Center (AMC) , University of Amsterdam , Amsterdam , The Netherlands
| |
Collapse
|
55
|
Crespi B, Read S, Hurd P. The SETDB2 locus: evidence for a genetic link between handedness and atopic disease. Heredity (Edinb) 2017; 120:77-82. [PMID: 29234167 DOI: 10.1038/s41437-017-0004-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 12/13/2022] Open
Abstract
The gene SETDB2, which mediates aspects of laterality in animal model systems, has recently been linked with human handedness as measured continuously on a scale from strong left to strong right. By contrast, it was marginally associated with a left-right dichotomous measure, and it showed no evidence of association with absolute handedness strength independent of direction. We genotyped the SETDB2 handedness-associated single nucleotide polymorphism, rs4942830, in a large healthy population likewise phenotyped for continuous, absolute, and dichotomous handedness variables. Our results demonstrated significant effects of rs4942830 genotype on continuous handedness, and weaker, marginal effects on dichotomous handedness, but no effects on absolute handedness. These results help to establish the locus marked by the SNP rs4942830 as a strong candidate for mediating human handedness. Intriguingly, rs4942830 is also in complete linkage disequilibrium with rs386770867, a polymorphism recently shown to affect human serum levels of IgE production and other atopic phenotypes. These findings implicate this locus in the longstanding links of handedness with asthma and other atopic diseases.
Collapse
Affiliation(s)
- Bernard Crespi
- Department of Biological Sciences, 8888 University Drive, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada.
| | - Silven Read
- Department of Biological Sciences, 8888 University Drive, Simon Fraser University, Burnaby, British Columbia, V5A 1S6, Canada
| | - Peter Hurd
- Department of Psychology and Centre for Neuroscience, University of Alberta, Edmonton, T6G 2R3, Canada
| |
Collapse
|
56
|
Amat F, Louha M, Benet M, Guiddir T, Bourgoin-Heck M, Saint-Pierre P, Paluel-Marmont C, Fontaine C, Lambert N, Couderc R, Gonzalez JR, Just J. The IL-4 rs2070874 polymorphism may be associated with the severity of recurrent viral-induced wheeze. Pediatr Pulmonol 2017; 52:1435-1442. [PMID: 28950434 DOI: 10.1002/ppul.23834] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 08/10/2017] [Accepted: 09/01/2017] [Indexed: 11/07/2022]
Abstract
BACKGROUND Childhood recurrent wheezing and consequently asthma corresponds to various phenotypes. Our aim was to link genetic variants of asthma candidate genes to the phenotypes of early onset wheezing. STUDY DESIGN We included very young consecutive children presenting with recurrent wheezing who had been evaluated for the severity of wheezing, associated atopic comorbidities, and tested for biomarkers of atopy and inflammation. All were genotyped for 16 single nucleotide polymorphisms (SNPs) linked with asthma or atopy. An unsupervised hierarchical bottom-up method was used for clustering the phenotypes and a multinomial logistic regression was performed for each individual SNP. RESULTS We replicated the three phenotypes previously described Trousseau Asthma Program in 317 children aged 21.5 ± 7.9 months: cluster 1 (nonatopic uncontrolled severe wheeze), n = 207, a severe viral-induced wheeze, cluster 2 (atopic multiple trigger wheeze), n = 61, with multiple allergic comorbidities, and cluster 3 (episodic viral wheeze), n = 49, a mild viral-induced wheeze. The TT-genotype of the IL-4 rs2070874 polymorphism was significantly associated with the nonatopic uncontrolled severe wheeze compared to the episodic viral wheeze (OR 7.9; CI95% [2.5-25.3]; P = 0.001). CONCLUSION Association between the TT-genotype of IL-4 rs2070874 polymorphism and a severe phenotype of viral-induced wheeze further underlines the role IL-4 plays in the inflammation pathway leading to viral respiratory infections.
Collapse
Affiliation(s)
- Flore Amat
- Department of Allergology-Centre de l'Asthme et des Allergies, Hôpital d'Enfants Armand Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France.,UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,Equipe EPAR, Institut Pierre Louis d'Epidémiologie et de Santé Publique, UMR_S1136, INSERM, Faculté de Médecine Saint-Antoine, rue de Chaligny, Paris, France.,ISGlobal, Barcelona Institute for Global Health-Campus MAR, Barcelona Biomedical Research Park (PRBB) Doctor Aiguader, 88, 08003, Barcelona, Spain
| | - Malek Louha
- Laboratory of Biochemistry and Molecular Biology-Laboratoire de Biochimie et Biologie Moléculaire, Hôpital d'Enfants Armand Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Marta Benet
- ISGlobal, Barcelona Institute for Global Health-Campus MAR, Barcelona Biomedical Research Park (PRBB) Doctor Aiguader, 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Tamazoust Guiddir
- Department of Allergology-Centre de l'Asthme et des Allergies, Hôpital d'Enfants Armand Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Mélisande Bourgoin-Heck
- Department of Allergology-Centre de l'Asthme et des Allergies, Hôpital d'Enfants Armand Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France.,UPMC Univ Paris 06, Sorbonne Universités, Paris, France
| | - Philippe Saint-Pierre
- Institut de Mathématiques de Toulouse, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Colombe Paluel-Marmont
- Department of Allergology-Centre de l'Asthme et des Allergies, Hôpital d'Enfants Armand Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France.,UPMC Univ Paris 06, Sorbonne Universités, Paris, France
| | - Cécile Fontaine
- Department of Allergology-Centre de l'Asthme et des Allergies, Hôpital d'Enfants Armand Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Nathalie Lambert
- Department of Allergology-Centre de l'Asthme et des Allergies, Hôpital d'Enfants Armand Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Rémy Couderc
- Laboratory of Biochemistry and Molecular Biology-Laboratoire de Biochimie et Biologie Moléculaire, Hôpital d'Enfants Armand Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Juan-Ramon Gonzalez
- ISGlobal, Barcelona Institute for Global Health-Campus MAR, Barcelona Biomedical Research Park (PRBB) Doctor Aiguader, 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Jocelyne Just
- Department of Allergology-Centre de l'Asthme et des Allergies, Hôpital d'Enfants Armand Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France.,UPMC Univ Paris 06, Sorbonne Universités, Paris, France.,Equipe EPAR, Institut Pierre Louis d'Epidémiologie et de Santé Publique, UMR_S1136, INSERM, Faculté de Médecine Saint-Antoine, rue de Chaligny, Paris, France
| |
Collapse
|
57
|
Koopmans T, Gosens R. Revisiting asthma therapeutics: focus on WNT signal transduction. Drug Discov Today 2017; 23:49-62. [PMID: 28890197 DOI: 10.1016/j.drudis.2017.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 07/20/2017] [Accepted: 09/01/2017] [Indexed: 12/16/2022]
Abstract
Asthma is a complex disease of the airways that develops as a consequence of both genetic and environmental factors. This interaction has highlighted genes important in early life, particularly those that control lung development, such as the Wingless/Integrase-1 (WNT) signalling pathway. Although aberrant WNT signalling is involved with an array of human conditions, it has received little attention within the context of asthma. Yet it is highly relevant, driving events involved with inflammation, airway remodelling, and airway hyper-responsiveness (AHR). In this review, we revisit asthma therapeutics by examining whether WNT signalling is a valid therapeutic target for asthma.
Collapse
Affiliation(s)
- Tim Koopmans
- Department of Molecular Pharmacology, University of Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, The Netherlands
| | - Reinoud Gosens
- Department of Molecular Pharmacology, University of Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, The Netherlands.
| |
Collapse
|
58
|
Schleimer RP, Berdnikovs S. Etiology of epithelial barrier dysfunction in patients with type 2 inflammatory diseases. J Allergy Clin Immunol 2017; 139:1752-1761. [PMID: 28583447 DOI: 10.1016/j.jaci.2017.04.010] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/21/2017] [Accepted: 04/21/2017] [Indexed: 12/11/2022]
Abstract
Epithelial barriers of the skin, gastrointestinal tract, and airway serve common critical functions, such as maintaining a physical barrier against environmental insults and allergens and providing a tissue interface balancing the communication between the internal and external environments. We now understand that in patients with allergic disease, regardless of tissue location, the homeostatic balance of the epithelial barrier is skewed toward loss of differentiation, reduced junctional integrity, and impaired innate defense. Importantly, epithelial dysfunction characterized by these traits appears to pre-date atopy and development of allergic disease. Despite our growing appreciation of the centrality of barrier dysfunction in initiation of allergic disease, many important questions remain to be answered regarding mechanisms disrupting normal barrier function. Although our external environment (proteases, allergens, and injury) is classically thought of as a principal contributor to barrier disruption associated with allergic sensitization, there is a need to better understand contributions of the internal environment (hormones, diet, and circadian clock). Systemic drivers of disease, such as alterations of the endocrine system, metabolism, and aberrant control of developmental signaling, are emerging as new players in driving epithelial dysfunction and allergic predisposition at various barrier sites. Identifying such central mediators of epithelial dysfunction using both systems biology tools and causality-driven laboratory experimentation will be essential in building new strategic interventions to prevent or reverse the process of barrier loss in allergic patients.
Collapse
Affiliation(s)
- Robert P Schleimer
- Division of Allergy and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Ill
| | - Sergejs Berdnikovs
- Division of Allergy and Immunology, Northwestern University Feinberg School of Medicine, Chicago, Ill.
| |
Collapse
|
59
|
Loxham M, Davies DE. Phenotypic and genetic aspects of epithelial barrier function in asthmatic patients. J Allergy Clin Immunol 2017; 139:1736-1751. [PMID: 28583446 PMCID: PMC5457128 DOI: 10.1016/j.jaci.2017.04.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/13/2017] [Accepted: 04/14/2017] [Indexed: 12/22/2022]
Abstract
The bronchial epithelium is continuously exposed to a multitude of noxious challenges in inhaled air. Cellular contact with most damaging agents is reduced by the action of the mucociliary apparatus and by formation of a physical barrier that controls passage of ions and macromolecules. In conjunction with these defensive barrier functions, immunomodulatory cross-talk between the bronchial epithelium and tissue-resident immune cells controls the tissue microenvironment and barrier homeostasis. This is achieved by expression of an array of sensors that detect a wide variety of viral, bacterial, and nonmicrobial (toxins and irritants) agents, resulting in production of many different soluble and cell-surface molecules that signal to cells of the immune system. The ability of the bronchial epithelium to control the balance of inhibitory and activating signals is essential for orchestrating appropriate inflammatory and immune responses and for temporally modulating these responses to limit tissue injury and control the resolution of inflammation during tissue repair. In asthmatic patients abnormalities in many aspects of epithelial barrier function have been identified. We postulate that such abnormalities play a causal role in immune dysregulation in the airways by translating gene-environment interactions that underpin disease pathogenesis and exacerbation.
Collapse
Affiliation(s)
- Matthew Loxham
- Clinical and Experimental Sciences and the Southampton NIHR Respiratory Biomedical Research Unit, University of Southampton Faculty of Medicine, Sir Henry Wellcome Laboratories, University Hospital Southampton, Southampton, United Kingdom
| | - Donna E Davies
- Clinical and Experimental Sciences and the Southampton NIHR Respiratory Biomedical Research Unit, University of Southampton Faculty of Medicine, Sir Henry Wellcome Laboratories, University Hospital Southampton, Southampton, United Kingdom.
| |
Collapse
|
60
|
DeVries A, Vercelli D. The neonatal methylome as a gatekeeper in the trajectory to childhood asthma. Epigenomics 2017; 9:585-593. [PMID: 28322586 DOI: 10.2217/epi-2016-0149] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Asthma is a heterogeneous group of conditions that typically begin in early life and result in recurrent, reversible bronchial obstruction. The role played by epigenetic mechanisms in the pathogenesis of childhood asthma is understood only in part. Here we discuss asthma epigenetics within a developmental perspective based on our recent demonstration that the epigenetic trajectory to childhood asthma begins at birth. We next discuss how this trajectory may be affected by prenatal environmental exposures. Finally, we examine in vitro studies that model the impact of asthma-associated exposures on the epigenome. All of these studies specifically surveyed human DNA methylation and involved a genome-wide component. In combination, their results broaden our understanding of asthma pathogenesis and the role the methylome plays in this process.
Collapse
Affiliation(s)
- Avery DeVries
- Graduate Program in Cellular & Molecular Medicine, University of Arizona, Tucson, AZ, USA.,Asthma & Airway Disease Research Center, University of Arizona, Tucson, AZ, USA
| | - Donata Vercelli
- Asthma & Airway Disease Research Center, University of Arizona, Tucson, AZ, USA.,Arizona Center for the Biology of Complex Diseases, University of Arizona, Tucson, AZ, USA.,Department of Cellular & Molecular Medicine, University of Arizona, Tucson, AZ, USA.,The Bio5 Institute, University of Arizona, Tucson, AZ, USA
| |
Collapse
|
61
|
Guan Y, Jin X, Liu X, Huang Y, Wang M, Li X. Uncovering potential key genes associated with the pathogenesis of asthma: A microarray analysis of asthma-relevant tissues. Allergol Immunopathol (Madr) 2017; 45:152-159. [PMID: 27842724 DOI: 10.1016/j.aller.2016.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 08/03/2016] [Accepted: 08/19/2016] [Indexed: 01/18/2023]
Abstract
BACKGROUND The present study aimed to discover more potential genes associated with the pathogenesis of asthma. METHODS The microarray data of GSE67940 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified in bronchial alveolar lavage cells from patients with mild-moderate asthma (notSA) and severe asthma (SA) compared with normal controls (NC), respectively. Functional and pathway enrichment analysis, protein-protein interaction (PPI) network analysis were performed upon the identified up- and down-regulated DEGs. Besides, the gene association network based on the common up-regulated and down-regulated genes was generated and transcriptional regulatory pairs of overlapping DEGs in the PPI network were identified. RESULTS A total of 104 DEGs (30 up- and 74 down-regulated genes) were identified in notSA vs. NC. Additionally, 2796 DEGs were screened out in SA vs. NC group, including 320 up-regulated DEGs, and 135 down-regulated DEGs. Specially, 41 overlapping DEGs were screened out in notSA vs. NC and SA vs. NC, including 16 common up-regulated genes and 25 common down-regulated genes. No pathways were enriched by the DEGs in notSA vs. NC. DEGs in SA vs. NC were associated with cytokine-cytokine receptor interaction. VEGFA was a hub protein in both the PPI networks of DEGs in notSA vs. NC and SA vs. NC. Gene association network showed that signalling pathways and cytokine-cytokine receptor interaction were involved in. The overlapping VEGFA, and IFRD1, and ZNF331 were regulated by more TFs. CONCLUSION Genes such as VEGFA, and IFRD1, and ZNF331 may be associated with pathogenesis of asthma.
Collapse
|
62
|
Park HW, Tantisira KG. Genetic Signatures of Asthma Exacerbation. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2017; 9:191-199. [PMID: 28293925 PMCID: PMC5352570 DOI: 10.4168/aair.2017.9.3.191] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 10/14/2016] [Accepted: 10/18/2016] [Indexed: 01/15/2023]
Abstract
Asthma exacerbation (AE) usually denotes worsening of asthma symptoms that requires intense management to prevent further deterioration. AE has been reported to correlate with clinical and demographic factors, such as race, gender, and treatment compliance as well as environmental factors, such as viral infection, smoking, and air pollution. In addition, recent observations suggest that there are likely to be genetic factors specific to AE. Understanding genetic factors specific to AE is essential to develop therapy tailored for exacerbation-prone asthma. Here, we summarize the results of studies involving genetic risk factors for AE. To simplify and enhance understanding, we reviewed the studies according to the following categories: hypothesis-driven approaches, hypothesis-free approaches, gene-environment interactions, and pharmacogenetics.
Collapse
Affiliation(s)
- Heung Woo Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea.,The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kelan G Tantisira
- The Channing Division of Network Medicine, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
63
|
Hoffjan S. Dissecting the genetic background of multifactorial diseases and traits - A major challenge for genetic research. Mol Cell Probes 2016; 30:345. [PMID: 27888871 DOI: 10.1016/j.mcp.2016.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sabine Hoffjan
- Department of Human Genetics, Ruhr-University, Bochum, Germany.
| |
Collapse
|