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Series GSE44865 Query DataSets for GSE44865
Status Public on Jun 05, 2024
Title Vitamin-D Responsive SGPP2 Variants Associated with Lung Cell Expression and Lung Function
Organism Homo sapiens
Experiment type Expression profiling by array
SNP genotyping by SNP array
Genome variation profiling by SNP array
Summary Background: Vitamin D is associated with lung health in epidemiologi studies, but mechanisms mediating observed associations are poorly understood. This study explores mechanisms for an effect of vitamin D in lung through an in vivo gene expression study, an expression quantitative trait loci (eQTL) analysis in lung tissue, and a population-based cohort study of sequence variants.
Methods: Microarray analysis investigated the association of gene expression in small airway epithelial cell with serum 25[OH]D in adult nonsmokers. Sequence variants in candidate genes identified by the microarray were investigated in a lung tissue eQTL database, and also in relation to cross-sectional pulmonary function in Health, Aging, and Body Composition [Health ABC] study, stratified by race, with replication in the Framingham Heart Study [FHS].
Results: 13 candidate genes had significant differences in expression by serum 25[OH]D (nominal p<0.05), and a genome-wide significant eQTL association was detected for SGPP2. In Health ABC, SGPP2 SNPs were associated with FEV1 in both European and African-Americans, and the gene-level association was replicated in European-American FHS participants. SNPs in 5 additional candidate genes (DAPK1, FSTL1, KAL1, KCNS3 and RSAD2) were associated with FEV1 in Health ABC participants.
Conclusions: SGPP2, a sphingosine-1-phosphate, is a novel vitamin D-responsive gene associated with lunh function. The identified associations will need to be followed up in further studies.
 
Overall design Bronchial brushing used to collect airway epithelial cells from 26 healthy nonsmokers. Microarray analysis investigated the association of gene expression in small-airway epithelial cells and genotypes from blood DNA from 116 individuals with serum 25(OH)D for 156 genes regulated by vitamin D
 
Contributor(s) Reardon B, Hansen JG, Crystal RG, Houston DK, Kritchevsky SB, Harris T, Lohman K, Liu Y, O’Connor GT, Wilk JB, Mezey J, Gao C, Cassano PA
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Submission date Mar 05, 2013
Last update date Jun 05, 2024
Contact name Yael Strulovici-Barel
E-mail(s) yas2003@med.cornell.edu
Organization name Weill Cornell Medical College
Department Department of Genetic Medicine
Lab Crystal
Street address 1300 York Avenue
City New York
State/province NY
ZIP/Postal code 10021
Country USA
 
Platforms (2)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
GPL6804 [GenomeWideSNP_5] Affymetrix Genome-Wide Human SNP 5.0 Array
Samples (142)
GSM549682 DGM-00030
GSM549695 DGM-00244
GSM549696 DGM-00249
Relations
BioProject PRJNA192212

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
GSE44865_RAW.tar 3.6 Gb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file

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