Multi-Organ Expression Profiling Uncovers a Gene Module in Coronary Artery Disease Involving Transendothelial Migration of Leukocytes and LIM Domain Binding 2: The Stockholm Atherosclerosis Gene Expression (STAGE) Study

Abstract

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.

Identification of hypo- and hypermethylated genes related to atherosclerosis by a genome-wide analysis of DNA methylation

“…EBF1-deficient mice manifest lipodystrophy characterized by a marked decrease in the amount of white adipose tissue, as well as an increase in yellow adipose tissue in bone marrow compared with wild-type controls (20), consistent with the notion that EBF1 participates in terminal adipocyte differentiation and the initiation of adipocyte development (21). The expression of EBF1 has previously been found to be increased in visceral fat and the atherosclerotic aortic wall (10), and polymorphisms of EBF1 have been shown to be related both to the plasma concentration of low density lipoprotein-cholesterol and to coronary atherosclerosis (11). In this study, we demonstrated that EBF1 was significantly hypomethylated in atheromatous plaque and that the overexpression of EBF1 in HEK293 cells resulted in the increased expression of genes related to cell proliferation (FOXQ1, CCNE1 and PAK1), to inflammatory response (CEBPD), and to cell adhesion (CDH1).…”

“…We examined the potential relation of these 33 genes to atherosclerosis, cardiovascular disease, coronary heart disease, or vascular inflammation by searching the PubMed (NCBI) database. Three of the hypomethylated genes (HECA, EBF1 and NOD2) and three of the hypermethylated genes (MAP4K4, ZEB1 and FYN) have previously been implicated in atherosclerosis or cardiovascular disease (10)(11)(12)(13)(14)(15). Immunoblot analysis revealed that the abundance of HECA, EBF1 or NOD2 was markedly increased following the transfection of the HEK293 cells with an expression vector for the corresponding human protein (Fig.…”

“…Evidence has suggested that HECA plays an important role in human carcinogenesis (16). HECA has also previously been found to be related to coronary heart disease, with HECA expression being increased in the atherosclerotic aortic wall (10). In this study, we demonstrated that HECA was significantly hypomethylated in atheromatous plaque and that the overexpression of HECA in HEK293 cells resulted in the increased expression of genes related to cell proliferation (CDC25C, CCNC and PAK1), a process important in the development of atherosclerosis in the arterial intima.…”

NEW: Network-Enabled Wisdom in Biology, Medicine, and Health Care

“…The hallmark of NEW in biomedicine is its focus on molecular processes defined by interactions among all molecules that participate in the development of a CCD (13,14). This is in marked contrast to associations between isolated DNA sequence variations or single-target genes and CCDs.…”

Genetics paired with CT angiography in the setting of atherosclerosis

“…The transcriptional profiles of multiple tissues, including liver, skeletal muscle, visceral fat, unaffected arterial wall, and atherosclerosis gathered from CAD patients' bypass surgery. The authors conclude that functionally associated genes cluster in the transendothelial migration of the leukocytes pathways, referred to as the atherosclerosis module, essential for atherosclerosis and CAD development [65]. Taurino C et al analyzed biological pathway miRNA expression, including oxidative phosphorylation and mitochondrial function, and finally, they confirmed the value of gene expression profiling as a promising tool for discovery of CADrelated genes and biologic pathways.…”