MATERIALS AND METHODS
Microscopy/Oil Red O staining
Mouse endothelial cell isolation
Macrophage/foam cell isolation
Human cell culture and treatment
Total RNA extraction
cDNA synthesis and RT-qPCR
Gene expression profiling and analysis
Genotyping and association analysis
where μ= mean, x = SNP, β= SNP effect, and u = random effects due to genetic relatedness, with Var(u) =σg2K and Var(e) =σe2, where K = IBS (identity-by-state) matrix across all genotypes in the panel. We computed a restricted maximum likelihood estimate for σg2 and σe2, and we performed association based on the estimated variance component with an F test to test that β does not equal 0. Expression values of the 18,630 probes in control and oxPAPC-treated conditions were considered as quantitative traits, and the association analysis of SNPs was carried out using the 574,391 informative SNPs that passed the filtering criteria. In the donor population, 108 males and 39 females were present; therefore, sex was considered as a covariate in the mixed model for association analysis. For cis (local) associations, we considered the SNPs within the ±1 Mb window on each side of the probe locations. We considered the remaining SNPs for trans (distal) associations. For cis and trans associations, 35,186,928 and 10,665,717,400 P-values, respectively, were calculated. FDRs were calculated using the Benjamini and Hochberg (
A majority of GWAS candidate genes are expressed in at least one of the cell types present in mouse atherosclerotic lesions
Differential expression of GWAS candidate genes in disease conditions in mice
GWAS candidate genes with differential expression from healthy to disease state in more than one cell type
Genetic regulation of human endothelial genes in GWAS loci
|GWAS P-value||Risk Allele||Reported Gene(s)||cis eQTL Gene(s)||eQTL P-value (Control, oxPAPC)||eQTLs in Other Tissues|
|rs11556924||7q32.2||9.00E-18||C||ZC3HC1||KLHDC10||6.72E-8, 1.16E-5||KLHDC10 (m)|
|rs216172||17p13.3||rs7217226 (r2= 1)||1.00E-09||C||SMG6, SRR||SRR||1.77E-7, 3.42E-8||SRR (a, l)|
|rs46522||17q21.32||2.00E-08||T||UBE2Z, GIP, ATP5G1, SNF8||SNF8||5.85E-5, 1.50E-4||ATP5G1 (m, a, l, s), UBE2Z (m, a, l, s)|
|rs3184504||12q24.12||rs653178 (r2= 0.873)||6.00E-06|
|rs3184504||12q24.12||rs653178 (r2= 0.873)||6.00E-06|
|rs7136259||12q21.33||6.00E-10||T||ATP2B1||GALNT4||8.80E-4, 4.26E-5||GALNT4 (m)|
|rs17114036||1p32.2||rs6588635 (r2= 0.831)||4.00E-19||A||PPAP2B||PPAP2B||2.94E-4, 3.36E-3|
Differential expression of predicted causal human GWAS genes in murine vascular cells in vivo
|Gene||Fold-change: Mice||Direction with Respect to Healthy Cells||Mouse Cell Type||HAEC eQTL Risk Allele Association|
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This work was supported by National Institutes of Health Grants HL-30568 and HL-28481 (A.J.L. and J.A.B.), Leducq Transatlantic Networks of Excellence in Cardiovascular Research Program Award (A.J.L.), American Heart Association predoctoral fellowship 10PRE3420032 and Ruth L. Kirschstein National Research Service Award GM-07185 (A.E.), American Heart Association postdoctoral fellowship 10POST3660048, and Ruth L. Kirschstein National Research Service Award T32 HL-69766 (M.C.).
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