Identification of genetic variants influencing plasma lipid levels in the population isolate of Kosrae by whole genome approaches and characterization of their functional role in metabolism
Final Report Abstract
Plasma concentrations of lipoproteins, including low-density lipoprotein cholesterol (LDL-C), highdensity lipoprotein cholesterol (HDL-C) and triglycerides (TG) are well-established risk factors for atherosclerotic cardiovascular disease and show substantial heritability. Recently, the availability of high-density single nucleotide polymorphism (SNP) chips has facilitated well powered genome-wide association studies (GWAS) to identify common variations contributing to complex genetic traits. We performed a GWAS to detect genetic loci contributing to plasma lipoproteins in a cohort from the Island of Kosrae (Federated States of Micronesia), a genetic isolate with significant founder effects, where dyslipidemia and other traits related to the metabolic syndrome are highly prevalent. This study was the first publication of a GWAS using 500k high-density SNP chips in an isolate founder population. Despite very different population genetics and environmental influences, we discovered the same variants and similiar effect sizes in several known lipid loci as shown in populations of European ancestry. Subsequent functional studies focused on LDL-C associated variants in the HMG-CoA Reductase gene (HMGCR), encoding the enzyme for the rate limiting step in cholesterol biosynthesis. These studies led to the identification of a functional intronic SNP that modulates alternative splicing of exon13. We could demonstrate that carriers of the major allele at SNP rs3846662 have significantly higher levels of alternatively spliced HMGCR mRNA as compared to carriers of the minor allele. In addition, the exon 13 spliced variant could not restore enzyme activity when expressed in HMGCR- deficient cells. Our work, characterizing a genetic variant in HMGCR as a modulator of splicing efficiency of HMGCR mRNA is also of pharmacologic relevance, since independant studies have demonstrated that this variant is correlated with the response to cholesterol lowering therapy with statin drugs. In separate studies, we followed up GWAS results for a novel locus at chromosome 8q24, associated with plasma levels of TG, LDL-C and HDL-C in humans. This locus contains only one annotated gene, TRIB1, which had no prior connection to lipid metabolism. Using knockout mice, we demonstrated that Trib1 deficiency leads to elevation of plasma cholesterol and TG by 54% and 33%, respectively. Further, we showed that Trib1 deficiency significantly upregulated hepatic expression of key lipogenic genes acetyl-CoA carboxylase1 (ACC1), fatty acid synthase (FAS) and stearoyl-Coenzyme A desaturase1 (SCD1). Concomitantly, we observed a higher VLDL-triglyceride production rate in Trib1 deficient mice. In conclusion, our findings strongly suggest that Trib1 is the causal gene underlying the 8q24 locus in humans and establish Trib1 as a novel factor involved in the regulation of plasma cholesterol and TG level. Trib1-modulating agents may represent a promising approach for the treatment of dyslipidemia and prevention of atherosclerosis.
Publications
- Common SNPs in HMGCR in micronesians and whites associated with LDL-cholesterol levels affect alternative splicing of exon13. Arterioscler Thromb Vasc Biol. 2008 Nov;28(11):2078-84
Burkhardt R, Kenny EE, Lowe JK, Birkeland A, Josowitz R, Noel M, Salit J, Maller JB, Pe'er I, Daly MJ, Altshuler D, Stoffel M, Friedman JM, Breslow JL
- Genomewide association studies and lipid risk factors Current Cardiovascular Risk Reports. 2009;3(1):12-17
Burkhardt R, Kenny EE; Breslow JL
- Genomewide association studies in an isolated founder population from the Pacific Island of Kosrae. PLoS Genet. 2009 Feb;5(2):e1000365
Lowe JK, Maller JB, Pe'er I, Neale BM, Salit J, Kenny EE, Shea JL, Burkhardt R, Smith JG, Ji W, Noel M, Foo JN, Blundell ML, Skilling V, Garcia L, Sullivan ML, Lee HE, Labek A, Ferdowsian H, Auerbach SB, Lifton RP, Newton-Cheh C, Breslow JL, Stoffel M, Daly MJ, Altshuler DM, Friedman JM
