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Series GSE65163 Query DataSets for GSE65163
Status Public on Nov 01, 2015
Title The Nasal Methylome and Childhood Atopic Asthma
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Background: Nasal epithelia are emerging as a proxy measure of gene expression of the airway epithelium in asthma. We hypothesized that epigenetic marks regulate gene expression of the nasal epithelia and consequently may provide a novel target for allergic asthma. Methods: We compared genomic DNA methylation patterns and gene expression in African American children with persistent atopic asthma [N=36] versus healthy controls [N=36]. Results were validated in an independent population of asthmatics [N=30]. Results: We identified 186 genes with significant methylation changes, either as regions (differentially methylated regions [DMRs]) or single CpGs (differentially methylated probes [DMPs]) after adjustment for age, gender, race/ethnicity, batch effects, inflation, and multiple comparisons (false discovery rate-adjusted q<0.05). Genes differentially methylated include those with established roles in asthma and atopy, components of the extracellular matrix, genes related to immunity, cell adhesion, epigenetic regulation, and airway obstruction. The methylation changes are large (median 9.5%, range: 2.6-29.5% methylation change) and similar in magnitude to those observed in malignancies. Hypo- and hyper-methylated genes were associated with increased and decreased gene expression respectively (P<2.8x10-6 for DMRs and P<7.8x10-10 for DMPs). Quantitative analysis of methylation-expression relationships in 53 differentially expressed genes demonstrated that 32 (60%) have significant (q<0.05) methylation-expression relationships within 5kb of the gene. 10 loci selected based on the relevance to asthma, magnitude of methylation change, and asthma specific methylation-expression relationships were validated in an independent cohort of children with asthma. Conclusions: Our findings that epigenetic marks in respiratory epithelia are associated with allergic asthma in inner-city children provide new targets for biomarker development, and novel approaches to understanding disease pathogenesis.
Overall design Case control design with nasal epithelial cells from 36 atopic asthmatic and 36 nonatopic nonasthmatic children from the inner city

Note: The Sample data tables are incomplete (truncated at 65535 rows, related to row-limit in older version of Excel).
Contributor(s) Yang IV, Pedersen BS, Schwartz DA
Citation(s) 27745942
Submission date Jan 21, 2015
Last update date Mar 22, 2019
Contact name David Schwartz
Phone 303-724-1783
Organization name University of Colorado, Anschutz Medical Campus
Department Medicine
Street address Anschutz Medical Campus
City Aurora
State/province CO
ZIP/Postal code 80045
Country USA
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (72)
GSM1588341 15-02-005-0
GSM1588342 15-02-008-4
GSM1588343 15-02-010-7
This SubSeries is part of SuperSeries:
GSE65205 Childhood Atopic Asthma
BioProject PRJNA273307

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE65163_RAW.tar 757.5 Mb (http)(custom) TAR (of IDAT)
Processed data included within Sample table

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