Identification of cis - and trans -Acting Genetic Variants Explaining Up to Half the Variation in Circulating Vascular Endothelial Growth Factor Levels

Abstract

Rationale VEGF impacts angiogenesis, atherosclerosis and cancer. Although the heritability of circulating VEGF levels is high, little is known about its genetic underpinnings. Objective Our aim was to identify genetic variants associated with circulating VEGF levels using an unbiased genome-wide approach and explore their functional significance with gene expression and pathway analysis. Methods and results We undertook a genome-wide association study (GWAS) of serum VEGF levels in 3,527 participants of the Framingham Heart Study (FHS), with pre-planned replication in 1,727 participants from two independent samples, the STANISLAS Family Study (SFS) and the Prospective Investigation of the Vasculature in Uppsala Seniors study (PIVUS). One hundred and forty SNPs reached genome-wide significance (p<5×10−8). We found evidence of replication for the most significant associations in both replication datasets. In a conditional GWAS 4 SNPs mapping to 3 chromosomal regions were independently associated with circulating VEGF levels: rs6921438 and rs4416670 (6p21.1, p=6.11×10−506 and p=1.47×10−12), rs6993770 (8q23.1, p=2.50×10−16) and rs10738760 (9p24.2, p=1.96×10−34). A genetic score including these four SNPs explained 48% of the heritability of serum VEGF levels. Six of the SNPs that reached genome-wide significance in the GWAS were significantly associated with VEGF mRNA levels in PBMCs. Ingenuity pathway analyses showed found plausible biological links between VEGF and 2 novel genes in these loci (ZFPM2 and VLDLR). Conclusions Genetic variants explaining up to half the heritability of serum VEGF levels were identified. These new insights provide important clues to the pathways regulating circulating VEGF levels.

A common variant highly associated with plasma VEGFA levels also contributes to the variation of both LDL-C and HDL-C

“…Therefore, it could regulate the expression of surrounding genes, including VEGFA . In a recent GWAS, we showed that the minor allele of rs6921438 strongly contributed to decreased VEGFA circulating levels (with an explained variance of VEGFA levels of 41%) ( 25 ). Subsequently, it appears that rs6921438 could have a negative effect in the cardiovascular system through a decrease in HDL-C levels, an increase in LDL-C levels, and a decrease in VEGFA levels.…”

“…Also, rs6921438 has not been identifi ed in any previous GWAS concerning HDL-C and LDL-C levels (34)(35)(36)(37)(38)(39)(40)(41)(42)(43). The existing GWASs have managed to explain a small percentage of the blood lipid trait variance (e.g., for HDL-C, it ranges from 0.6% to 10%); thus, Supplemental Material can be found at: ( 23,25 ). Finally, Sandhofer et al ( 24 ) have shown that plasma VEGFA levels were negatively associated with TC and LDL-C in a healthy female sample.…”

“…Via a recent genome-wide association study (GWAS), we identifi ed four single-nucleotide polymorphisms (SNPs) that explained up to 50% of the heritability of VEGFA circulating levels ( 25 ). The investigation of the effect of these new genetic variants, as well as the interactions between them and with environmental factors, on blood lipids levels might give some insight into the relation between VEGFA and blood lipids.…”

“…LDL-C levels were calculated using the Friedewald formula ( 29 ). VEGFA plasma levels were measured in a subsample of 403 individuals from the discovery population by Randox, Ltd. (Crumlin, UK) using a biochip array analyzer (Evidence ®) ( 25 ). Blood collection was performed after overnight fasting.…”

Recent Developments in Cardiovascular Genetics

“…The challenge is further compounded by the presence of large linkage disequilibrium across large segments on the chromosomes, as well as the trans effects of other variants or chromosomal regions. 65,66 Furthermore, as stated earlier, the ENCODE findings suggest the presence of a large number of regulatory and putatively functional genomic regions, 21 which poses additional challenge in the selection of candidate genes and single nucleotide polymorphisms for functional characterizations. An additional layer of complexity is the inadequateness of in vitro models and model organisms in accurately reflecting the functional significance of the variants in humans.…”