Investigation of Functional Genes at Homologous Loci Identified Based on Genome-wide Association Studies of Blood Lipids via High-fat Diet Intervention in Rats using an <i>in vivo</i> Approach
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<b><i>Aim</i></b>: It is challenging to identify causal (or target) genes at individual loci detected using genome-wide association studies (GWAS). In order to follow up GWAS loci, we investigated functional genes at homologous loci identified using human lipid GWAS that responded to a high-fat, high-cholesterol diet (HFD) intervention in an animal model.<br><b><i>Methods</i></b>: The HFD intervention was carried out for four weeks in male rats of the spontaneously hypertensive rat strain. The liver and adipose tissues were subsequently excised for analyses of changes in the gene expression as compared to that observed in rats fed normal rat chow (<i>n</i>=8 per group). From 98 lipid-associated loci reported in previous GWAS, 280 genes with rat orthologs were initially selected as targets for the two-staged analysis involving screening with DNA microarray and validation with quantitative PCR (qPCR). Consequently, genes showing a differential expression due to HFD were examined for changes in the expression induced by atorvastatin, which was independently administered to the rats.<br><b><i>Results</i></b>: Using the HFD intervention in the rats, seven known (<i>Abca1</i>, <i>Abcg5</i>, <i>Abcg8</i>, <i>Lpl</i>, <i>Nr1h3</i>, <i>Pcsk9</i> and <i>Pltp</i>) and three novel (<i>Madd</i>, <i>Stac3</i> and <i>Timd4</i>) genes were identified as potential significant targets, with an additional list of 23 suggestive genes. Among these 33 genes, <i>Stac3</i>, <i>Fads1</i> and six known genes exhibited nominally significant expression changes following treatment with atorvastatin. Six (of 33) genes overlapped with those previously detected in the expression QTL studies.<br><b><i>Conclusions</i></b>: Our experimental <i>in vivo</i> approach increases the ability to identify target gene(s), when combined with other functional studies, thus improving understanding of the mechanisms by which GWAS variants act.
- Journal of Atherosclerosis and Thrombosis
Journal of Atherosclerosis and Thrombosis 22(5), 455-480, 2015
Japan Atherosclerosis Society