Differential Regulation of Functional Gene Clusters in Overt Coronary Artery Disease in a Transgenic Atherosclerosis-hypertensive Rat Rodel

Omics-based approaches to understand mechanosensitive endothelial biology and atherosclerosis

Atherosclerosis is a multifactorial disease that preferentially occurs in arterial regions exposed to d-flow can be used to indicate disturbed flow or disturbed blood flow. The mechanisms by which d-flow induces atherosclerosis involve changes in the transcriptome, methylome, proteome, and metabolome of multiple vascular cells, especially endothelial cells. Initially, we begin with the pathogenesis of atherosclerosis and the changes that occur at multiple levels owing to d-flow, especially in the endothelium. Also, there are a variety of strategies used for the global profiling of the genome, transcriptome, miRNA-ome, DNA methylome, and metabolome that are important to define the biological and pathophysiological mechanisms of endothelial dysfunction and atherosclerosis. Finally, systems biology can be used to integrate these 'omics' datasets, especially those that derive data based on a single animal model, in order to better understand the pathophysiology of atherosclerosis development in a holistic manner and how this integrative approach could be used to identify novel molecular diagnostics and therapeutic targets to prevent or treat atherosclerosis. WIREs Syst Biol Med 2016, 8:378-401. doi: 10.1002/wsbm.1344 For further resources related to this article, please visit the WIREs website.

The role of endothelial mechanosensitive genes in atherosclerosis and omics approaches

Atherosclerosis is the leading cause of morbidity and mortality in the U.S., and is a multifactorial disease that preferentially occurs in regions of the arterial tree exposed to disturbed blood flow. The detailed mechanisms by which d-flow induces atherosclerosis involve changes in the expression of genes, epigenetic patterns, and metabolites of multiple vascular cells, especially endothelial cells. This review presents an overview of endothelial mechanobiology and its relation to the pathogenesis of atherosclerosis with special reference to the anatomy of the artery and the underlying fluid mechanics, followed by a discussion of a variety of experimental models to study the role of fluid mechanics and atherosclerosis. Various in vitro and in vivo models to study the role of flow in endothelial biology and pathobiology are discussed in this review. Furthermore, strategies used for the global profiling of the genome, transcriptome, miR-nome, DNA methylome, and metabolome, as they are important to define the biological and pathophysiological mechanisms of atherosclerosis. These "omics" approaches, especially those which derive data based on a single animal model, provide unprecedented opportunities to not only better understand the pathophysiology of atherosclerosis development in a holistic and integrative manner, but also to identify novel molecular and diagnostic targets.

The Use of High-Throughput Technologies to Investigate Vascular Inflammation and Atherosclerosis

The greatest challenge of scientific research is to understand the causes and consequences of disease. In recent years, great efforts have been devoted to unraveling the basic mechanisms of atherosclerosis (the underlying pathology of cardiovascular disease), which remains a major cause of morbidity and mortality worldwide. Because of the complex and multifactorial pathophysiology of cardiovascular disease, different research techniques have increasingly been combined to unravel genetic aspects, molecular pathways, and cellular functions involved in atherogenesis, vascular inflammation, and dyslipidemia to gain a multifaceted picture addressing this complexity. Thanks to the rapid evolution of high-throughput technologies, we are now able to generate large-scale data on the DNA, RNA, and protein levels. With the help of sophisticated computational tools, these data sets are integrated to enhance information extraction and are being increasingly used in a systems biology approach to model biological processes as interconnected and regulated networks. This review exemplifies the use of high-throughput technologies—such as genomics, transcriptomics, proteomics, and epigenomics—and systems biology to explore pathomechanisms of vascular inflammation and atherosclerosis.

Genome-wide scan for interacting loci affecting human cholesteryl ester transfer protein-induced hypercholesterolemia in transgenic human cholesteryl ester transfer protein F2-intercross rats

OBJECTIVE

We documented susceptibility in Dahl S rats to coronary atherosclerosis upon the transgenic expression of human cholesteryl ester transfer protein (hCETP) producing severe combined hyperlipidemia, as detected in Tg[hCETP]53 (Tg53) Dahl S rats. In other genetic backgrounds (i.e. Dahl R, spontaneously hypertensive rat strains) transgene expression does not lead to severe combined hyperlipidemia. This study aimed to identify genetic loci that modify the effect of hCETP on hypercholesterolemia observed in different genetic contexts.

METHODS

To identify quantitative trait loci (QTL) that affect hCETP-mediated hyperlipidemia in Tg53 Dahl S rats in contrast to Tg53 Dahl R rats we performed a genome-wide scan for QTL affecting plasma total cholesterol in an F2[Tg (R x S)]-intercross male population (n = 159) that are transgenic for the Tg[hCETP]53 transgene. Hybrids were genotyped with 121 informative polymorphic markers.

RESULTS

We detected three novel hCETP-dependent QTL for hypercholesterolemia: one on chromosome 3 with suggestive linkage [logarithm of odds score derived from likelihood ratio statistic using a factor of 4.6 (LOD) 2.26]; one on chromosome 9 with significant linkage (LOD 4.15), and one on chromosome 11 with significant linkage (LOD 3.48) that have not been detected in other rat intercrosses.

CONCLUSION

Three cholesteryl ester transfer protein (CETP)-interacting loci were identified in a Tg53 Dahl S rat intercross study affecting cholesterol metabolism. These results could partly explain the controversy regarding the atherogenic role of CETP in humans, suggesting the hypothesis that putative CETP interacting genes confound or play an important role in CETP-mediated pro-atherogenic susceptibility in humans. Overall, these observations reiterate the key role of epistasis in complex, multifactorial traits.

Genome-Wide Expression Studies of Atherosclerosis

During the past 6 years, gene expression profiling of atherosclerosis has been used to identify genes and pathways relevant in vascular (patho)physiology. This review discusses some critical issues in the methodology, analysis, and interpretation of the data of gene expression studies that have made use of vascular specimens from animal models and humans. Analysis of gene expression studies has evolved toward the genome-wide expression profiling of large series of individual samples of well-characterized donors. Despite the advances in statistical and bioinformatical analysis of expression data sets, studies have not yet fully exploited the potential of gene expression data sets to obtain novel insights into the molecular mechanisms underlying atherosclerosis. To assess the potential of published expression data, we compared the data of a CC chemokine gene cluster between 18 murine and human gene expression profiling articles. Our analysis revealed that an adequate comparison is mainly hindered by the incompleteness of available data sets. The challenge for future vascular genomic profiling studies will be to further improve the experimental design, statistical, and bioinformatical analysis and to make data sets freely accessible.

Microarray analysis of endothelial differentially expressed genes in liver of cirrhotic rats

BACKGROUND & AIMS

There is a long-standing interest in the identification of endothelial-specific pathways for therapeutic targeting in cirrhosis. Therefore, the aim of this study was to evaluate differences in gene expression patterns between liver endothelial cells (LECs) from control and cirrhotic rats by using microarrays.

METHODS

LECs were obtained by isopycnic centrifugation. LECs gene expression was then analyzed on high-density oligonucleotide microarrays.

RESULTS

Analysis of gene expression revealed that most of the differentially expressed mRNA in cirrhosis are associated with extracellular matrix remodeling, inflammation, antioxidant/stress response, and cell signaling.

CONCLUSIONS

The collective expression changes observed within some functional groups of genes indicate that LECs in cirrhotic livers may contribute to lymphangiogenesis, enhancement of fibrogenesis and inflammatory processes, changes in cell-cell interaction with up-regulation of adherens junction proteins, and alterations in the intrahepatic vascular tone because of the down-regulation of genes involved in vasodilatation.

Analysis of gender-specific atherosclerosis susceptibility in transgenic[hCETP]25DS rat model

Epidemiological and clinical data demonstrate differences in atherosclerotic coronary heart disease prevalence between age-matched men and premenopausal women. Mechanisms underlying relative athero-susceptibility in men and athero-resistance in premenopausal women remain to be elucidated. Lack of informative animal models hinders research. We report here a moderate-expresser line transgenic for human cholesteryl ester transfer protein (CETP) in the Dahl salt-sensitive hypertensive rat strain, Tg25, that recapitulates premenopausal female athero-resistance. Having ascertained identical genetic background, environmental factors, and equivalent CETP hepatic RNA levels, we detect worse hypercholesterolemia, hypertriglyceridemia, coronary plaques and survival outcome in Tg25 male rats compared with Tg25 females. Hepatic transcription profiles of Tg25 males and females normalized to respective gender- and age-matched non-transgenic controls exhibit significant differences. Genes implicated on hierarchical cluster analysis and quantitative real-time RT-PCR pinpoint pathways associated with coronary plaque progression such as inflammation and arachidonic acid epoxygenation, and not just cholesterol metabolism pathways. The data demonstrate gender-specific factors as key modulators of atherosclerosis phenotype and suggest a possible role for the liver in atheroma progression as a large organ source of proatherogenic systemic factors.

Genome-Wide Scan Identifies Novel QTLs for Cholesterol and LDL Levels in F2[Dahl R×S]-Intercross Rats

Hypercholesterolemia is a significant risk factor for coronary artery disease development. Genes influencing nonmonogenic hypercholesterolemia susceptibility in humans remain to be identified. Animal models are key investigative systems because major confounding variables such as diet, activity, and genetic background can be controlled. We performed a 121-marker, total genome-analysis of an F2[Dahl RxS]-intercross selected for contrasting parental strain susceptibilities for hyperlipidemia on regular rat diets at 6 months of age. Quantitative traits studied were plasma total cholesterol, triglyceride, HDL, and LDL levels adjusted for obesity. Genome-wide analysis of 200 F2-intercross male rats detects two QTLs with highly significant linkage for total cholesterol (TC) on chromosome (chr) 5-133.3 Mbp (LOD 5.8), and chr5-54.2 Mbp (LOD 4.8), and two QTLs with significant linkage for TC: on chromosome 8, chr8-60.4 Mbp (LOD 3.8), and chromosome 2, chr2-243.5 Mbp (LOD 3.4). A QTL for LDL with significant linkage is detected on chromosome 5, chr5-104 Mbp (LOD 3.7). These QTLs contribute from 7% to 12% of total trait variance, respectively, with Dahl-S allele effects resulting in increased TC and LDL levels consistent with hyperlipidemia susceptibility in the parental Dahl-S rat strain. Predicted QTL-peaks do not coincide with previous genome scans. Human homologues of two TC-QTLs span genes listed in a LocusLink profile for cholesterol. Only suggestive loci were detected for HDL and total triglyceride levels. Altogether, the data demonstrates the contribution of multiple QTLs to hypercholesterolemia making a multipathway pathogenic framework imperative. QTL-peak candidate genes delineated are syntenic between rat and human genomes, increasing clinical relevance and mandating further study.

Modulation of learning and memory in Dahl rats by dietary salt restriction

The Dahl rat represents a robust animal model of salt-sensitive hypertension, with Dahl S rats being salt sensitive and Dahl R rats (the Dahl S counterparts) being salt resistant for the development of hypertension. Here we evaluate the effect of reduced dietary salt intake on learning and memory in the Dahl rat model. Salt restriction produced a significant impairment in social transmission of food preference and social recognition memory in Dahl S rats without affecting spatial learning. In contrast, social transmission of food preference and social recognition memory remained unaffected in Dahl R rats, whereas navigation performance was significantly improved. This effect on learning and memory was not generalized because sodium restriction did not influence object recognition memory in either Dahl S or Dahl R rats. The significant decrement in select cognitive functions in Dahl S rats produced by salt restriction are in sharp contrast to the well known positive effect of dietary salt restriction in alleviating high blood pressure and associated target organ complications, suggesting that caution must be exercised when weighing the benefits of salt restriction in improving cardiovascular health in salt-sensitive hypertension against the potential undesirable effects of reduced cognitive function.

Elastogenesis in human arterial disease: a role for macrophages in disordered elastin synthesis

OBJECTIVE

Elastin, an extracellular matrix protein, constitutes about 30% of the dry weight of the arteries. Elastolysis induced by inflammatory processes is active in chronic arterial diseases. However, elastogenesis in arterial diseases has received little attention. In this work we hypothesized that disordered elastogenesis is active in matrix remodeling in atheroma and abdominal aortic aneurysm (AAA).

METHODS AND RESULTS

Human AAA and atheroma have 4- to 6-fold more tropoelastin protein than nondiseased arteries. The smooth muscle cell-containing media and fibrous cap of atherosclerotic arteries contain ordered mature elastin, whereas macrophage (MPhi)-rich regions often have disorganized elastic fibers. Surprisingly, in addition to smooth muscle cells, MPhis in diseased arteries also produce the elastin precursor tropoelastin, as shown by double immunostaining, in situ hybridization, and reverse transcription-polymerase chain reaction for tropoelastin mRNA. Cultured monocyte-derived MPhis can express the elastin gene. AAA have 9-fold but atheroma only 1.6-fold lower levels of desmosine, a marker for mature cross-linked elastin, than normal arteries.

CONCLUSIONS

This study demonstrates ongoing but often ineffective elastogenesis in arterial disease and establishes human macrophages as a novel source for this important matrix protein. These results have considerable import for understanding mechanisms of extracellular matrix remodeling in arterial diseases.