Abstract 367: Identification of the VNN1 Gene as a Novel CVD Risk Factor
In this study we utilized a novel integrative genomic approach to rapidly identify genes and their regulatory variants that mediate CVD risk. We focused on cis-regulated genes whose quantitative mRNA expression correlates with CVD risk factors. Using a unique dataset of whole-genome lymphocyte transcriptional profiles from 1,240 individuals in large extended Mexican American families of the San Antonio Family Heart Study (SAFHS), we identified over 400 cis-regulated transcripts that were significantly associated with HDL-C or triglyceride levels. A gene of particular interest was VNN1 (vanin1) as its transcript levels exhibited very strong support for both cis-regulation (p=1.2x10–11) and correlation with HDL-C levels (p=4.0x10 –9). We re-sequenced 2 kb of the proximal promoter in 96 founders and identified 22 SNPs, some of which showed strong association with VNN1 transcript abundance. We then typed the best six SNPs in the rest of the subjects and found that a variant at position −587 was highly correlated with VNN1 expression levels (p=6.9x10 – 85), as were SNPs at positions −137 (p=5.7x10 – 83), −612 (p=2.0x10 –36), −708 (p=3.0x10 –34), and −667 (p=8.3x10 –7). Multivariant analysis suggested at least two independent functional sites and the promoter variants at positions −667 (p=2.7x10 –5) and −137 (p=4.0x10 – 4) also exhibited strong associations with HDL-C levels. Molecular evidence from electrophoretic mobility shift assays supports the contention that the −137 T/G change has functional consequences with respect to binding transcription factors, leading to differences in expression of VNN1 mRNA. Both the T and the G alleles preferentially form distinct DNA:transcription factor complexes using nuclear extracts derived from a human T cell line (Jurkat) indicating that more than one factor is involved in binding to the sequence in an allele-specific way. To further examine the potential role of this regulatory variant, we examined its effect on the in vivo quantitative expression of other genes to identify a causal pathway involving known components of lipoprotein metabolism. These results indicate an important role for the VNN1 gene as a novel determinant of HDL-C levels, a major risk factor for CVD.