Genome-wide expression profiles identify potential targets for gene-environment interactions in asthma severity.
BACKGROUND
Gene-environment interaction studies using genome-wide association study data are often underpowered after adjustment for multiple comparisons. Differential gene expression in response to the exposure of interest can capture the most biologically relevant genes at the genome-wide level.


OBJECTIVE
We used differential genome-wide expression profiles from the Epidemiology of Home Allergens and Asthma birth cohort in response to Der f 1 allergen (sensitized vs nonsensitized) to inform a gene-environment study of dust mite exposure and asthma severity.


METHODS
Polymorphisms in differentially expressed genes were identified in genome-wide association study data from the Childhood Asthma Management Program, a clinical trial in childhood asthmatic patients. Home dust mite allergen levels (<10 or ≥10 μg/g dust) were assessed at baseline, and (≥1) severe asthma exacerbation (emergency department visit or hospitalization for asthma in the first trial year) served as the disease severity outcome. The Genetics of Asthma in Costa Rica Study and a Puerto Rico/Connecticut asthma cohort were used for replication.


RESULTS
IL9, IL5, and proteoglycan 2 expression (PRG2) was upregulated in Der f 1-stimulated PBMCs from dust mite-sensitized patients (adjusted P < .04). IL9 polymorphisms (rs11741137, rs2069885, and rs1859430) showed evidence for interaction with dust mite in the Childhood Asthma Management Program (P = .02 to .03), with replication in the Genetics of Asthma in Costa Rica Study (P = .04). Subjects with the dominant genotype for these IL9 polymorphisms were more likely to report a severe asthma exacerbation if exposed to increased dust mite levels.


CONCLUSIONS
Genome-wide differential gene expression in response to dust mite allergen identified IL9, a biologically plausible gene target that might interact with environmental dust mite to increase severe asthma exacerbations in children.
Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass. Electronic address: rejoa@channing.harvard.edu.
Joanne E
JE
Sordillo
Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass.
Roxanne
R
Kelly
Department of Pediatrics, Department of Genetics and Genomic Sciences, and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY.
Supinda
S
Bunyavanich
Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass.
Michael
M
McGeachie
Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass.
Weiliang
W
Qiu
Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass.
Damien C
DC
Croteau-Chonka
Division of Pediatric Pulmonology, Hospital Nacional de Niños, San José, Costa Rica.
Manuel
M
Soto-Quiros
Division of Pediatric Pulmonology, Hospital Nacional de Niños, San José, Costa Rica.
Lydiana
L
Avila
Division of Pediatric Pulmonology, Hospital Nacional de Niños, San José, Costa Rica.
Juan C
JC
Celedón
Division of Pediatric Pulmonary Medicine, Allergy and Immunology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pa.
John M
JM
Brehm
Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass.
Scott T
ST
Weiss
Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass.
Diane R
DR
Gold
Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass.
Augusto A
AA
Litonjua
D000818:Animals; D039741:Antigens, Dermatophagoides / Q000276:immunology*; D060829:Arthropod Proteins / Q000276:immunology*; D001249:Asthma / Q000235:genetics* / Q000276:immunology*; D002478:Cells, Cultured; D002648:Child; D002675:Child, Preschool; D015331:Cohort Studies; D003364:Costa Rica; D003546:Cysteine Endopeptidases / Q000276:immunology*; D040001:Dermatophagoides farinae / Q000276:immunology*; D018450:Disease Progression; D004632:Emergency Medical Services; D004781:Environmental Exposure / Q000009:adverse effects; D047093:Eosinophil Major Basic Protein / Q000235:genetics / Q000378:metabolism; D005260:Female; D005500:Follow-Up Studies; D059647:Gene-Environment Interaction; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans; D015848:Interleukin-5 / Q000235:genetics / Q000378:metabolism; D016906:Interleukin-9 / Q000235:genetics*; D007963:Leukocytes, Mononuclear / Q000502:physiology*; D008297:Male; D020641:Polymorphism, Single Nucleotide; D011509:Proteoglycans / Q000235:genetics / Q000378:metabolism; D011647:Puerto Rico; D059467:Transcriptome; D014481:United States; D015854:Up-Regulation
D039741:Antigens, Dermatophagoides; D060829:Arthropod Proteins; D015848:Interleukin-5; D016906:Interleukin-9; D011509:Proteoglycans; C074129:PRG2 protein, human; D047093:Eosinophil Major Basic Protein; D003546:Cysteine Endopeptidases; C451159:Dermatophagoides farinae antigen f 1
Dust mite allergen; IL-9; asthma exacerbation; asthma severity; gene expression