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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
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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.
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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
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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 |
Citation missing |
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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
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Organization name |
Weill Cornell Medical College
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Department |
Department of Genetic Medicine
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Lab |
Crystal
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Street address |
1300 York Avenue
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City |
New York |
State/province |
NY |
ZIP/Postal code |
10021 |
Country |
USA |
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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 |
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Samples (142)
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Relations |
BioProject |
PRJNA192212 |
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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