Identification of cis- and trans-acting genetic variants explaining up to half the variation in circulating vascular endothelial growth factor levels

Abstract

Rationale: Vascular endothelial growth factor (VEGF) affects 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 to explore their functional significance with gene expression and pathway analysis.

Methods and results: We undertook a genome-wide association study of serum VEGF levels in 3527 participants of the Framingham Heart Study, with preplanned replication in 1727 participants from 2 independent samples, the STANISLAS Family Study and the Prospective Investigation of the Vasculature in Uppsala Seniors study. One hundred forty single nucleotide polymorphism (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 genome-wide association study, 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 4 SNPs explained 48% of the heritability of serum VEGF levels. Six of the SNPs that reached genome-wide significance in the genome-wide association study were significantly associated with VEGF messenger RNA levels in peripheral blood mononuclear cells. 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.

Figure 1

Regional plot for associations in region centered on rs6921438 (1a), rs6993770 (1b) and rs10738760 (1c). All SNPs (triangles) are plotted with their meta-analysis p-values against their genomic position. The color of the triangles represents the linkage disequilibrium between each of the SNPs in the region with rs6921438: purple: r2 ≤0.05, light blue: 0.05<r2 ≤0.10, green: 0.10<r2≤0.30, yellow: 0.30<r2≤0.60, orange: 0.60<r2≤0.80, red: r2>0.80. Light blue line represents estimated recombination rates. Genes are shown as dark green arrows. LD and recombination rates were drawn from Hapmap (release #22).

Figure 2

Putative Gene Network based on Ingenuity Path Analysis. Edges are displayed with labels describing the nature of the relationship between the nodes. The lines between genes represent known interactions and the nodes are displayed using various shapes which represent the functional class of the gene product (legend).