Gene expression signatures differ with extent of atherosclerosis in monkey iliac artery

Comparative Analysis of Transcriptome Profiles in Patients with Thromboangiitis Obliterans

BACKGROUND

Thromboangiitis obliterans (TAO) causes vascular insufficiency due to chronic inflammation and abrupt thrombosis of the medium and small arteries of the extremities. In our study, we aimed to determine biomarkers for the diagnosis of TAO by evaluating 15 male TAO patients with Shinoya diagnostic criteria and 5 healthy controls who did not have TAO-related symptoms in their family histories.

METHODS

The Clariom D Affymetrix platform was used to conduct microarray analysis on total RNA extracted from whole blood. A total of 477 genes (FC ≤ 5 or >5) common to the fifteen patient and five control samples were selected using comparative microarray analysis; among them, 79 genes were upregulated and 398 genes were downregulated.

RESULTS

According to FC ≤ 10 or >10, in the same TAO patient and control group, 13 genes out of 28 were upregulated, whereas 15 genes were downregulated. The 11 key genes identified according to their mean log2FC values were PLP2, RPL27A, CCL4, FMNL1, EGR1, EIF4A1, RPL9, LAMP2, RNF149, EIF4G2, and DGKZ. The genes were ranked according to their relative expression as follows: FMNL1 > RNF149 > RPL27A > EIF4G2 > EIF4A1 > LAMP2 > EGR1 > PLP2 > DGKZ > RPL9 > CCL4. Using protein-protein interaction network analysis, RPL9, RPL27A, and RPL32 were found to be closely related to EIF4G2 and EIF4A1. The Reactome pathway found pathways linked to 28 genes. These pathways included the immune system, cellular responses to stress, cytokine signaling in the immune system, and signaling by ROBO receptors.

CONCLUSIONS

By figuring out the protein expression levels of the genes that have been found to explain how TAO disease works at the molecular level, it will be possible to figure out how well these chosen transcripts can diagnose and predict the disease.

Identification of Disease-Related Genes That Are Common between Alzheimer's and Cardiovascular Disease Using Blood Genome-Wide Transcriptome Analysis

Accumulating evidence has suggested a shared pathophysiology between Alzheimer’s disease (AD) and cardiovascular disease (CVD). Based on genome-wide transcriptomes, specifically those of blood samples, we identify the shared disease-related signatures between AD and CVD. In addition to gene expressions in blood, the following prior knowledge were utilized to identify several candidate disease-related gene (DRG) sets: protein–protein interactions, transcription factors, disease–gene relationship databases, and single nucleotide polymorphisms. We selected the respective DRG sets for AD and CVD that show a high accuracy for disease prediction in bulk and single-cell gene expression datasets. Then, gene regulatory networks (GRNs) were constructed from each of the AD and CVD DRG sets to identify the upstream regulating genes. Using the GRNs, we identified two common upstream genes (GPBP1 and SETDB2) between the AD and CVD GRNs. In summary, this study has identified the potential AD- and CVD-related genes and common hub genes between these sets, which may help to elucidate the shared mechanisms between these two diseases.

Model-based clustering of multi-tissue gene expression data

MOTIVATION

Recently, it has become feasible to generate large-scale, multi-tissue gene expression data, where expression profiles are obtained from multiple tissues or organs sampled from dozens to hundreds of individuals. When traditional clustering methods are applied to this type of data, important information is lost, because they either require all tissues to be analyzed independently, ignoring dependencies and similarities between tissues, or to merge tissues in a single, monolithic dataset, ignoring individual characteristics of tissues.

RESULTS

We developed a Bayesian model-based multi-tissue clustering algorithm, revamp, which can incorporate prior information on physiological tissue similarity, and which results in a set of clusters, each consisting of a core set of genes conserved across tissues as well as differential sets of genes specific to one or more subsets of tissues. Using data from seven vascular and metabolic tissues from over 100 individuals in the STockholm Atherosclerosis Gene Expression (STAGE) study, we demonstrate that multi-tissue clusters inferred by revamp are more enriched for tissue-dependent protein-protein interactions compared to alternative approaches. We further demonstrate that revamp results in easily interpretable multi-tissue gene expression associations to key coronary artery disease processes and clinical phenotypes in the STAGE individuals.

AVAILABILITY AND IMPLEMENTATION

Revamp is implemented in the Lemon-Tree software, available at https://github.com/eb00/lemon-tree.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Nuclear stiffening and chromatin softening with progerin expression leads to an attenuated nuclear response to force

Progerin is a mutant form of the nucleoskeletal protein lamin A, and its expression results in the rare premature aging disorder Hutchinson-Gilford progeria syndrome (HGPS). Patients with HGPS demonstrate several characteristic signs of aging including cardiovascular and skeletal dysfunction. Cells from HGPS patients show several nuclear abnormalities including aberrant morphology, nuclear stiffening and loss of epigenetic modifications including heterochromatin territories. However, it is unclear why these changes disproportionately impact mechanically-responsive tissues. Using micropipette aspiration, we show that nuclei in progerin-expressing cells are stiffer than control cells. Conversely, our particle tracking reveals the nuclear interior becomes more compliant in cells from HGPS patients or with progerin expression, as consistent with decreased chromatin condensation as shown previously. Additionally, we find the nuclear interior is less responsive to external mechanical force from shear or compression likely resulting from damped force propagation due to nucleoskeletal stiffening. Collectively our findings suggest that force is similarly transduced into the nuclear interior in normal cells. In HGPS cells a combination of a stiffened nucleoskeleton and softened nuclear interior leads to mechanical irregularities and dysfunction of mechanoresponsive tissues in HGPS patients.

Effects of estradiol on transcriptional profiles in atherosclerotic iliac arteries in ovariectomized cynomolgus macaques

OBJECTIVE

This study aimed to assess the in vivo effects of estradiol treatment on arterial gene expression in atherosclerotic postmenopausal female monkeys.

METHODS

Eight ovariectomized cynomolgus monkeys were fed atherogenic diets for 6.5 years. The left iliac artery was biopsied before randomization to the estradiol group (human equivalent dose of 1 mg/d, n = 4) or the vehicle group (n = 4) for 8 months. The right iliac artery was obtained at necropsy. Transcriptional profiles in pretreatment versus posttreatment iliac arteries were compared to assess the responses of atherosclerotic arteries to estradiol.

RESULTS

Iliac artery plaque size did not differ between the estradiol group and the placebo group at baseline or during the treatment period. Nevertheless, estradiol treatment was associated with increased expression of 106 genes and decreased expression of 26 genes in the iliac arteries. Estradiol treatment increased the expression of extracellular matrix genes, including the α1 chain of type I collagen, the α2 chain of type VI collagen, and fibulin 2, suggestive of an increase in the proportion or phenotype of smooth muscles or fibroblasts in lesions. Also increased were components of the insulin-like growth factor pathway (insulin-like growth factor 1, insulin-like growth factor binding protein 4, and insulin-like growth factor binding protein 5) and the Wnt signaling pathway (secreted frizzled-related protein 2, secreted frizzled-related protein 4, low-density lipoprotein receptor-related protein 6, and Wnt1-inducible signaling pathway protein 2).

CONCLUSIONS

Estradiol treatment of monkeys with established atherosclerosis affected iliac artery gene expression, suggesting changes in the cellular composition of lesions. Moreover, it is probable that the presence of atherosclerotic plaque affected the gene expression responses of arteries to estrogen.

Effects of equol on gene expression in female cynomolgus monkey iliac arteries

BACKGROUND AND AIMS

To examine effects of equol, the soy phytoestrogen metabolite, on gene expression in the monkey iliac artery.

METHODS AND RESULTS

A high fat/high cholesterol diet was fed to eight ovariectomized cynomolgus monkeys for 6.5 years. After biopsy of the left iliac artery, the animals were randomized to two treatment groups for 8 months; the treatment groups were equol (23.7 mg/100 g diet, n = 4) and vehicle (n = 4). The right iliac artery was removed at necropsy. Gene expression in the iliac arteries in response to equol was determined by DNA microarray. Comparison of atherosclerotic lesions and plasma lipids at pre-versus post-equol treatment time points and in vehicle versus equol treatment groups did not identify any significant differences. Despite the lack of effect of equol on these parameters, 59 genes were down-regulated and 279 were up-regulated in response to equol. Comparison of these data to previous work identified 10 genes regulated in opposite directions by equol compared to presence of atherosclerosis plaque (Menopause 2011; 18:1087-1095) and 55 genes differentially expressed in the same direction in response to both equol and estradiol (Eyster et al., Menopause 2014;21:143-152.).

CONCLUSIONS

Similar responses of genes to both equol and estradiol may reflect the extent to which equol serves as a natural selective estrogen receptor modulator in the arteries. Opposite responses of 10 genes to equol versus the presence of atherosclerosis implicates those genes in the potential protective effects of equol in arteries.

Association between kidney function and Framingham global cardiovascular disease risk score: a Chinese longitudinal study

Background

Chronic kidney disease (CKD) is generally considered an independent risk factor for cardiovascular disease (CVD) development, but rates in individuals with estimated glomerular filtration rate (eGFR) >60 ml/min/1.73 m² are uncertain. The Framingham global CVD risk score (FRS) equation is a widely accepted tool used to predict CVD risk in the general population. The purpose of the present study was to examine whether an association exists between eGFR and FRS in a Chinese population with no CKD or CVD.

Methods

A total of 333 participants were divided into three groups based on FRS. The Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equation and CKD-EPI equation for Asians (CKD-EPI-ASIA) were used to measure eGFR.

Results

A significant inverse association between eGFR and FRS was confirmed with Pearson correlation coefficients of –0.669, –0.698 (eGFR_CKD-EPI, P<0.01) and –0.658, –0.690 (eGFR_CKD-EPI-ASIA, P<0.01). This association gradually diminished with progression from the low- to high-risk groups (eGFR_CKD-EPI, r = –0.615, –0.282, –0.197, P<0.01, P<0.01, P>0.05; similar results according to the CKD-EPI-ASIA equation). In the low- or moderate-risk new-groups, this association became stronger with increased FRS (eGFR_CKD-EPI-ASIA, r = –0557, –0.622 or –0.326, –0.329, P<0.01). In contrast to the results from 2008, eGFR was independently associated with FRS following adjustment for traditional cardiovascular risk factors (P<0.05).

Conclusion

Renal function has multiple influences on predicting CVD risk in various populations. With increasing FRS and decreasing eGFR, it is also independently associated with CVD, even in individuals with eGFR >60 ml/min/1.73 m².

Growth differentiation factor-15 deficiency inhibits atherosclerosis progression by regulating interleukin-6-dependent inflammatory response to vascular injury

BACKGROUND

Growth differentiation factor (GDF)-15 is a distant and divergent member of the transforming growth factor-β superfamily (TGF-β) . There is growing evidence indicating the involvement of GDF-15 in various pathologies. Expression of GDF-15 is induced under conditions of inflammation and increased GDF-15 serum levels are suggested as a risk factor for cardiovascular diseases.

METHODS AND RESULTS

We show here that GDF-15 and proinflammatory cytokine interleukin (IL)-6 levels are highly increased (5-fold) in cultured oxidized low-density lipoproteins-stimulated peritoneal macrophages derived from GDF-15(+/+)/apolipoprotein (apo) E(-/-), mice. Notably, IL-6 induction on oxidized low-density lipoproteins stimulation is completely abolished in the absence of GDF-15. Consistent with our in vitro data GDF-15 mRNA expression and protein levels are upregulated (2.5- to 6-fold) in the atherosclerotic vessel wall of GDF-15(+/+)/apoE(-/-) mice after a cholesterol-enriched diet. GDF-15 deficiency inhibits lumen stenosis (52%) and (18)FDG uptake (34%) in the aortic arch despite increased serum triglyceride/cholesterol levels and elevated body weight. Immunohistomorphometric investigations of atherosclerotic lesions reveal a decreased percentage of inflammatory CD11b(+) (57%) or IL-6(+), leukocytes, and apoptotic cells (74%) after 20 weeks. However, the total number of macrophages and cell density in atherosclerotic lesions of the innominate artery are increased in GDF-15(-/-)/apoE(-/-) mice.

CONCLUSIONS

Our data suggest that GDF-15 is involved in orchestrating atherosclerotic lesion progression by regulating apoptotic cell death and IL-6-dependent inflammatory responses to vascular injury.

Modulation of oxidative stress, inflammation, and atherosclerosis by lipoprotein-associated phospholipase A2

Lipoprotein-associated phospholipase A(2) (Lp-PLA(2)), also known as platelet-activating factor acetylhydrolase (PAF-AH), is a unique member of the phospholipase A(2) superfamily. This enzyme is characterized by its ability to specifically hydrolyze PAF as well as glycerophospholipids containing short, truncated, and/or oxidized fatty acyl groups at the sn-2 position of the glycerol backbone. In humans, Lp-PLA(2) circulates in active form as a complex with low- and high-density lipoproteins. Clinical studies have reported that plasma Lp-PLA(2) activity and mass are strongly associated with atherogenic lipids and vascular risk. These observations led to the hypothesis that Lp-PLA(2) activity and/or mass levels could be used as biomarkers of cardiovascular disease and that inhibition of the activity could offer an attractive therapeutic strategy. Darapladib, a compound that inhibits Lp-PLA(2) activity, is anti-atherogenic in mice and other animals, and it decreases atherosclerotic plaque expansion in humans. However, disagreement continues to exist regarding the validity of Lp-PLA(2) as an independent marker of atherosclerosis and a scientifically justified target for intervention. Circulating Lp-PLA(2) mass and activity are associated with vascular risk, but the strength of the association is reduced after adjustment for basal concentrations of the lipoprotein carriers with which the enzyme associates. Genetic studies in humans harboring an inactivating mutation at this locus indicate that loss of Lp-PLA(2) function is a risk factor for inflammatory and vascular conditions in Japanese cohorts. Consistently, overexpression of Lp-PLA(2) has anti-inflammatory and anti-atherogenic properties in animal models. This thematic review critically discusses results from laboratory and animal studies, analyzes genetic evidence, reviews clinical work demonstrating associations between Lp-PLA(2) and vascular disease, and summarizes results from animal and human clinical trials in which administration of darapladib was tested as a strategy for the management of atherosclerosis.