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Liu Y, Brossard M, Sarnowski C, Vaysse A, Moffatt M, Margaritte-Jeannin P, Llinares-López F, Dizier MH, Lathrop M, Cookson W, Bouzigon E, Demenais F. Network-assisted analysis of GWAS data identifies a functionally-relevant gene module for childhood-onset asthma. Sci Rep 2017; 7:938. [PMID: 28428554 PMCID: PMC5430538 DOI: 10.1038/s41598-017-01058-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 03/21/2017] [Indexed: 11/10/2022] Open
Abstract
The number of genetic factors associated with asthma remains limited. To identify new genes with an undetected individual effect but collectively influencing asthma risk, we conducted a network-assisted analysis that integrates outcomes of genome-wide association studies (GWAS) and protein-protein interaction networks. We used two GWAS datasets, each consisting of the results of a meta-analysis of nine childhood-onset asthma GWASs (5,924 and 6,043 subjects, respectively). We developed a novel method to compute gene-level P-values (fastCGP), and proposed a parallel dense-module search and cross-selection strategy to identify an asthma-associated gene module. We identified a module of 91 genes with a significant joint effect on childhood-onset asthma (P < 10−5). This module contained a core subnetwork including genes at known asthma loci and five peripheral subnetworks including relevant candidates. Notably, the core genes were connected to APP (encoding amyloid beta precursor protein), a major player in Alzheimer’s disease that is known to have immune and inflammatory components. Functional analysis of the module genes revealed four gene clusters involved in innate and adaptive immunity, chemotaxis, cell-adhesion and transcription regulation, which are biologically meaningful processes that may underlie asthma risk. Our findings provide important clues for future research into asthma aetiology.
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Affiliation(s)
- Y Liu
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France. .,Université Paris Diderot, Université Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France.
| | - M Brossard
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France.,Université Paris Diderot, Université Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - C Sarnowski
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France.,Université Paris Diderot, Université Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - A Vaysse
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France.,Université Paris Diderot, Université Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - M Moffatt
- Genomic Medicine Section, National Heart Lung Institute, Imperial College London, London, UK
| | - P Margaritte-Jeannin
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France.,Université Paris Diderot, Université Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - F Llinares-López
- Machine Learning and Computational Biology Lab, Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - M H Dizier
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France.,Université Paris Diderot, Université Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - M Lathrop
- McGill University and Genome Québec Innovation Centre, Montréal, Québec, Canada
| | - W Cookson
- Genomic Medicine Section, National Heart Lung Institute, Imperial College London, London, UK
| | - E Bouzigon
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France.,Université Paris Diderot, Université Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - F Demenais
- INSERM, Genetic Variation and Human Diseases Unit, UMR-946, Paris, France. .,Université Paris Diderot, Université Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France.
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Bouzigon E, Nadif R, Thompson EE, Concas MP, Kuldanek S, Du G, Brossard M, Lavielle N, Sarnowski C, Vaysse A, Dessen P, van der Valk RJP, Duijts L, Henderson AJ, Jaddoe VWV, de Jongste JC, Casula S, Biino G, Dizier MH, Pin I, Matran R, Lathrop M, Pirastu M, Demenais F, Ober C. A common variant in RAB27A gene is associated with fractional exhaled nitric oxide levels in adults. Clin Exp Allergy 2015; 45:797-806. [PMID: 25431337 DOI: 10.1111/cea.12461] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 10/06/2014] [Accepted: 11/19/2014] [Indexed: 12/28/2022]
Abstract
BACKGROUND Exhaled nitric oxide (FeNO) is a biomarker for eosinophilic inflammation in the airways and for responsiveness to corticosteroids in asthmatics. OBJECTIVE We sought to identify in adults the genetic determinants of fractional exhaled nitric oxide (FeNO) levels and to assess whether environmental and disease-related factors influence these associations. METHODS We performed a genome-wide association study of FeNO through meta-analysis of two independent discovery samples of European ancestry: the outbred EGEA study (French Epidemiological study on the Genetics and Environment of Asthma, N = 610 adults) and the Hutterites (N = 601 adults), a founder population living on communal farms. Replication of main findings was assessed in adults from an isolated village in Sardinia (Talana study, N = 450). We then investigated the influence of asthma, atopy and tobacco smoke exposure on these genetic associations, and whether they were also associated with FeNO values in children of the EAGLE (EArly Genetics & Lifecourse Epidemiology, N = 8858) consortium. RESULTS We detected a common variant in RAB27A (rs2444043) associated with FeNO that reached the genome-wide significant level (P = 1.6 × 10(-7) ) in the combined discovery and replication adult data sets. This SNP belongs to member of RAS oncogene family (RAB27A) and was associated with an expression quantitative trait locus for RAB27A in lymphoblastoid cell lines from asthmatics. A second suggestive locus (rs2194437, P = 8.9 × 10(-7) ) located nearby the sodium/calcium exchanger 1 (SLC8A1) was mainly detected in atopic subjects and influenced by inhaled corticosteroid use. These two loci were not associated with childhood FeNO values. CONCLUSIONS AND CLINICAL RELEVANCE This study identified a common variant located in RAB27A gene influencing FeNO levels specifically in adults and with a biological relevance to the regulation of FeNO levels. This study provides new insight into the biological mechanisms underlying FeNO levels in adults.
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Affiliation(s)
- E Bouzigon
- Inserm, UMR-946, Paris, France; Univ Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
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