Genome-wide association studies (GWAS) have identified hundreds of cardiometabolic disease (CMD) risk loci. However, they contribute little to genetic variance, and most downstream gene-regulatory mechanisms are unknown. We genotyped and RNA-sequenced vascular and metabolic tissues from 600 coronary artery disease patients in the STARNET study. Gene expression traits associated with CMD risk SNPs identified by GWAS were more extensively found in STARNET than in tissue- and disease-unspecific gene-tissue expression studies, indicating sharing of downstream cis-/trans-gene regulation across tissues and CMDs. In contrast, the regulatory effects of other GWAS risk SNPs were tissue-specific; abdominal fat emerged as an important gene-regulatory site for blood lipids, such as for the LDL-cholesterol and coronary artery disease risk-gene PCSK9. STARNET provides insights into gene-regulatory mechanisms for CMD risk loci, facilitating their translation into opportunities for diagnosis, therapy and prevention.

Environmental exposures filtered through the genetic make-up of each individual alter the transcriptional repertoire in organs central to metabolic homeostasis, thereby affecting arterial lipid accumulation, inflammation, and the development of coronary artery disease (CAD). The primary aim of the Stockholm Atherosclerosis Gene Expression (STAGE) study was to determine whether there are functionally associated genes (rather than individual genes) important for CAD development. To this end, two-way clustering was used on 278 transcriptional profiles of liver, skeletal muscle, and visceral fat (n = 66/tissue) and atherosclerotic and unaffected arterial wall (n = 40/tissue) isolated from CAD patients during coronary artery bypass surgery. The first step, across all mRNA signals (n = 15,042/12,621 RefSeqs/genes) in each tissue, resulted in a total of 60 tissue clusters (n = 3958 genes). In the second step (performed within tissue clusters), one atherosclerotic lesion (n = 49/48) and one visceral fat (n = 59) cluster segregated the patients into two groups that differed in the extent of coronary stenosis (P = 0.008 and P = 0.00015). The associations of these clusters with coronary atherosclerosis were validated by analyzing carotid atherosclerosis expression profiles. Remarkably, in one cluster (n = 55/54) relating to carotid stenosis (P = 0.04), 27 genes in the two clusters relating to coronary stenosis were confirmed (n = 16/17, P<10−27and−30). Genes in the transendothelial migration of leukocytes (TEML) pathway were overrepresented in all three clusters, referred to as the atherosclerosis module (A-module). In a second validation step, using three independent cohorts, the A-module was found to be genetically enriched with CAD risk by 1.8-fold (P<0.004). The transcription co-factor LIM domain binding 2 (LDB2) was identified as a potential high-hierarchy regulator of the A-module, a notion supported by subnetwork analysis, by cellular and lesion expression of LDB2, and by the expression of 13 TEML genes in Ldb2–deficient arterial wall. Thus, the A-module appears to be important for atherosclerosis development and, together with LDB2, merits further attention in CAD research.

SUMMARY Inferring molecular networks can reveal how genetic perturbations interact with environmental factors to cause common complex diseases. We analyzed genetic and gene expression data from seven tissues relevant to coronary artery disease (CAD) and identified regulatory gene networks (RGNs) and their key drivers. By integrating data from genome-wide association studies, we identified 30 CAD-causal RGNs interconnected in vascular and metabolic tissues, and we validated them with corresponding data from the Hybrid Mouse Diversity Panel. As proof of concept, by targeting the key drivers AIP, DRAP1, POLR2I, and PQBP1 in a cross-species-validated, arterial-wall RGN involving RNA-processing genes, we re-identified this RGN in THP-1 foam cells and independent data from CAD macrophages and carotid lesions. This characterization of the molecular landscape in CAD will help better define the regulation of CAD candidate genes identified by genome-wide association studies and is a first step toward achieving the goals of precision medicine.

Objective-The objective of this work was to explore the role of peroxisome proliferator-activated receptor delta (PPARD) in lipid metabolism in humans. Methods and Results-PPARD is a nuclear receptor involved in lipid metabolism in primates and mice. We screened the 5Ј-region of the human gene for polymorphisms to be used as tools in association studies. Four polymorphisms were detected: Ϫ409C/T in the promoter region, ϩ73C/T in exon 1, ϩ255A/G in exon 3, and ϩ294T/C in exon 4. The frequencies of the rare alleles were 4.2%, 4.2%, 1.2% and 15.6%, respectively, in a population-based group of 543 healthy men. Only the ϩ294T/C polymorphism showed significant association with a metabolic trait. Homozygotes for the rare C allele had a higher plasma LDL-cholesterol concentration than homozygotes for the common T allele, which was verified in an independent cohort consisting of 282 healthy men. Transfection studies showed that the rare C allele had higher transcriptional activity than the common T allele. Electrophoretic mobility shift assays demonstrated that the ϩ294T/C polymorphism influenced binding of Sp-1. An interaction with the PPAR alpha L162V polymorphism was also detected for several lipid parameters. Key Words: genetics Ⅲ cholesterol Ⅲ peroxisome proliferator-activated receptor Ⅲ polymorphism P eroxisome proliferator-activated receptors (PPARs) are ligand-activated transcription factors involved in the regulation of lipid and glucose metabolism. Three distinct PPARs, termed alpha (PPARA), gamma (PPARG), and delta (PPARD), have been isolated. They are encoded by separate genes and characterized by distinct tissue and developmental distribution patterns. PPARD is, in contrast with the other two PPARs, ubiquitously expressed. 1 PPARA is involved in lipid metabolism and fatty acid oxidation whereas PPARG influences adipocyte differentiation and insulin action. 2 The function of PPARD is not yet fully understood, but it has been shown to play a role in cholesterol metabolism in animal models. Treatment with a PPARD agonist increased plasma cholesterol concentrations in mice with a dysfunctional leptin receptor (db/db mice). 3 A recent study showed that treatment with a potent selective PPARD agonist increased plasma cholesterol concentrations, decreased plasma triglyceride concentrations, increased HDL cholesterol, and decreased the fraction of small and dense LDLs in obese rhesus monkeys. 4 Furthermore, PPARD plays a central role in fatty acidcontrolled differentiation of preadipocytes, where it promotes induction of PPARG and other genes involved in adipocyte differentiation. 5,6 Taken together, these data suggest that PPARD may play a role in the development of metabolic perturbations associated with dyslipidemia and predisposing to atherosclerosis. Conclusions-TheseBecause the promoter and 5Ј-untranslated region (5Ј-UTR) of the gene contain important regulatory regions for gene expression 7 one might speculate that nucleotide changes in these regions of PPARD may result in altered mRNA and protein levels wh...