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Geisinger eMERGE - Abdominal Aortic Aneurysm Project (AAAP)

ABSTRACT:

A large research cohort of Geisinger Abdominal Aortic Aneurysm (AAA) patients was created by enrolling and consenting patients of the Geisinger Department of Vascular Surgery. Consented patients provide blood, serum and DNA samples for research and authorize use of data in their medical record for research. They also complete a data questionnaire that asks information about family history of AAA and other vascular diseases, as well as information on known or suspected AAA risk factors, including smoking history, body mass index, hypertension, type 2 diabetes, and atherosclerotic disease. The AAA cases are 78% male, with a mean age of 74 years; 39% have undergone surgical or endovascular repair; more than 85% or current or past smokers; approximately 20% of cases report a positive family history of AAA. Geisinger AAA patients undergo regular imaging studies, typically every 6 months, to monitor the progression of aneurysm expansion. This allows the growth rates of their aneurysm to be calculated. DNA samples from a total of 910 AAA patients were used for whole genome genotyping; these results are included in the dbGaP.

PROVIDER: phs000387 | dbGaP |

SECONDARY ACCESSION(S): PRJNA75967PRJNA75965

REPOSITORIES: dbGaP

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Similar Datasets

eMERGE Geisinger eGenomic Medicine (GeM) Abdominal Aortic Aneurysm Project (AAAP)

Project description:<p>A large research cohort of Geisinger Abdominal Aortic Aneurysm (AAA) patients was created by enrolling and consenting patients of the Geisinger Department of Vascular Surgery. Consented patients provide blood, serum and DNA samples for research and authorize use of data in their medical record for research. They also complete a data questionnaire that asks information about family history of AAA and other vascular diseases, as well as information on known or suspected AAA risk factors, including smoking history, body mass index, hypertension, type 2 diabetes, and atherosclerotic disease. The AAA cases are 78% male, with a mean age of 74 years; 39% have undergone surgical or endovascular repair; more than 85% or current or past smokers; approximately 20% of cases report a positive family history of AAA. Geisinger AAA patients undergo regular imaging studies, typically every 6 months, to monitor the progression of aneurysm expansion. This allows the growth rates of their aneurysm to be calculated. DNA samples from a total of 910 AAA patients were used for whole genome genotyping; these results are included in the dbGaP.</p>

| phs000387.v1.p1 | EGA

Genetic Copy Number Variants in Myocardial Infarction Patients with Hyperlipidemia

Project description:We identified 7 CNV regions that were associated significantly with hyperlipidemia and myocardial infarction in our patients through multistage analysis (P<0.001). The inclusion criteria for enrolling patients were drawn from the Prospective Cardiovascular Munster study [http://www.ncbi.nlm.nih.gov/pubmed/3202078] and Framingham Heart Study [http://www.ncbi.nlm.nih.gov/pubmed/9737513]. In brief, patients aged between 20 and 75 years with coronary arterial disease with more than 50% stenosis, as proven by cardiac catheterization, and a history of hyperlipidemia with serum cholesterol level greater than 240 mg/dL or low-density lipoprotein greater than 155 mg/dL were enrolled. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from whole blood samples. 40 Samples.

2014-08-09 | E-GEOD-31276 | biostudies-arrayexpress

eMERGE Geisinger eGenomic Medicine (GeM) - MyCode Project Controls

Project description:<p>A research cohort of adult Geisinger Clinic patients was enrolled from community-based primary care clinics of the Geisinger Health System. Patients were eligible for enrollment if they were a primary care patient of a Geisinger Clinic physician and were scheduled for a non-emergent clinic visit. All participants provided written informed consent and HIPAA authorization. Consenting patient agreed to provide blood samples for broad biomedical research use, and permission to access data in their Geisinger electronic medical record for research. The enrollment rate was 90% of patients approached. The demographics of the cohort approximate those of the Geisinger Clinic outpatient population. Research blood samples were collected during an outpatient clinical phlebotomy encounter. Research blood samples are coded and stored in a central biorepository. Samples are linkable to clinical data in a de-identified manner for research via an IRB-approved data broker process. For genomic analysis, DNA is extracted from EDTA-anticoagulated whole blood. For the initial eMERGE Geisinger eGenomic Medicine (GeM) genotyping project, a subset of 1,232 unique samples were genotyped using Illumina HumanOmniExpress-12 v1.0 arrays, and used as population controls for other Geisinger Clinic case cohorts, including abdominal aortic aneurysm and gastric bypass surgery cases. These samples were selected from a larger subset of approximately 6,000 MyCode DNA samples using a partial matching algorithm that included age, sex, and body mass index as variables.</p>

| phs000381.v1.p1 | EGA

Genetic Copy Number Variants in Myocardial Infarction Patients with Hyperlipidemia

2014-08-09 | GSE31276 | GEO

Shotgun LC-MS analysis of aorta and liver tissues from WT and Gal-1 KO mice to study the role of Galectin-1 in vascular remodeling in atherosclerosis and abdominal aortic aneurysm

Project description:Pathological vascular remodeling is the underlying cause of main cardiovascular diseases (CVD) including atherosclerosis and abdominal aortic aneurysm (AAA). We analyzed the potential role of galectin-1 (Gal-1) in atherosclerosis and AAA. Atherosclerosis was induced in mice lacking Gal-1 (Lgals1-/-) and wild-type (WT) by pAAV/D377Y-mPCSK9 adenovirus injection (1011 vector genome copies) followed by western diet during 16 weeks. In a second model, atherosclerostic WT mice were treated with recombinant Gal-1 protein (rGal-1, 100 µg 3 days/week) or vehicle during 16 weeks. Moreover, the same therapeutic approach was performed in elastase-induced AAA in mice treated for 2 weeks. Finally, Gal-1 expression was assessed in human atherosclerotic plaques and AAA lesions. Gal-1 deletion led to higher atherosclerotic burden along the aorta and larger atherosclerotic plaques in the aortic root. This deleterious effect was associated to higher circulating and lesional lipid levels and lower alpha- smooth muscle actin (α-SMA) staining in the plaques. Proteomic analysis of aorta homogenates showed an upregulation of Fibronectin and VCAM-1 in Lgals1-/- mice as compared to WT aortic tissues. In vitro experiments in VSMCs from Lgals1-/- mice or transfected with Gal-1 siRNA showed increased Fibronectin, VCAM-1 and KLF4 mRNA expression along with a decrease in α-SMA mRNA expression. Treatment with rGal-1 decreased atherosclerotic plaques (size and burden) and elastase-induced aortic dilatation, associated to higher content of α-SMA staining, in both experimental models. Gal-1 protein and mRNA tissue levels were decreased in human atherosclerotic plaques and AAA as compared to control aortic tissues.

2022-04-04 | PXD024637 | Pride

Adenosine-to-inosine RNA editing controls cathepsin S expression in atherosclerosis by enabling HuR-mediated post-transcriptional regulation

Project description:Adenosine-to-inosine (A-to-I) RNA editing, which is catalyzed by a family of adenosine deaminase acting on RNA (ADAR) enzymes, is important in the epitranscriptomic regulation of RNA metabolism. However, the role of A-to-I RNA editing in vascular disease is unknown. Here we show that cathepsin S mRNA (CTSS), which encodes a cysteine protease associated with angiogenesis and atherosclerosis, is highly edited in human endothelial cells. The 3′ untranslated region (3′ UTR) of the CTSS transcript contains two inverted repeats, the AluJo and AluSx+ regions, which form a long stem–loop structure that is recognized by ADAR1 as a substrate for editing. RNA editing enables the recruitment of the stabilizing RNA-binding protein human antigen R (HuR; encoded by ELAVL1) to the 3′ UTR of the CTSS transcript, thereby controlling CTSS mRNA stability and expression. In endothelial cells, ADAR1 overexpression or treatment of cells with hypoxia or with the inflammatory cytokines interferon-γ and tumor-necrosis-factor-α induces CTSS RNA editing and consequently increases cathepsin S expression. ADAR1 levels and the extent of CTSS RNA editing are associated with changes in cathepsin S levels in patients with atherosclerotic vascular diseases, including subclinical atherosclerosis, coronary artery disease, aortic aneurysms and advanced carotid atherosclerotic disease. These results reveal a previously unrecognized role of RNA editing in gene expression in human atherosclerotic vascular diseases.

2016-09-05 | GSE60217 | GEO

A comparison of genome-wide DNA methylation patterns between different tissues from patients with coronary heart disease

Project description:Using the Illumina Infinium Human Methylation27 BeadChip, we performed a genome-wide analysis of DNA methylation in right coronary artery in the area of advanced atherosclerotic plaques, atherosclerotic-resistant internal mammary arteries, and great saphenous veins obtained from same patients with coronary heart disease. The resulting DNA methylation patterns were markedly different between all the vascular tissues. The genes hypomethylated in athero-prone arteries to compare with atherosclerotic-resistant arteries were predominately involved in regulation of inflammation and immune processes, as well as development. The great saphenous veins exhibited an increase of the DNA methylation age in comparison to the internal mammary arteries. Gene ontology analysis for genes harboring hypermethylated CpG-sites in veins revealed the enrichment for biological processes associated with the development. Four CpG-sites located within the MIR10B gene sequence and about 1 Kb upstream of the HOXD4 gene were also confirmed as hypomethylated in the independent dataset of right coronary arteries in the area of advanced atherosclerotic plaques in comparison with the other vascular tissues. Bisulfite converted genomic DNA from 24 samples was denatured, whole-genome amplified, fragmented and subsequently hybridized to the Illumina Infinium 27k Human Methylation Beadchip.

2014-10-31 | E-GEOD-62867 | biostudies-arrayexpress

KFAM 1 and 2

Project description:Tumour samples from patients with a family history of breast cancer.

2012-11-23 | E-MEXP-3688 | biostudies-arrayexpress

Geisinger eMERGE - MyCode Project

| phs000381 | dbGaP

Nuclear factor 90 isoform of vascular smooth muscle cells accelerates diabetic arteriosclerotic calcification by mediating FBXW7-AGER1-AGEs axis

Project description:Hyperglycemia accelerates calcification of atherosclerotic plaques in diabetic patients, and the prolonged accumulation of advanced glycation end products (AGEs) induced by hyperglycemia may be closely related to the pathogenesis of aortic calcification. However, the mechanisms underlying this association remain unclear. In the current study, we investigated the role of vascular smooth muscle cell nuclear factor 90/110 (NF90/110) in mediating AGEs accumulation and accelerating diabetic atherosclerotic calcification. Using vascular smooth muscle cells (VSMCs), human samples, and mouse models, we found that hyperglycemia-mediated AGEs markedly increased VSMC NF90/110 activation both in human and mouse atherosclerotic calcified tissues with diabetes. Silencing of NF90/110 in vitro and genetic deletion of VSMC NF90/110 in mice decreased obviously AGEs-induced arteriosclerotic calcification. Mechanistically, AGEs increased the activity of NF90, which then enhanced ubiquitination and degradation of AGE receptor 1 (AGER1) by stabilizing the mRNA of E3 ubiquitin ligase, F-box, and WD repeat domain 7 (FBXW7), thus causing the accumulation of more AGEs. Furthermore, AGEs accumulation accelerated diabetic atherosclerotic calcification by inducing VSMC phenotypic changes to osteoblast-like cells, apoptosis, and matrix vesicle release. Collectively, our study demonstrated the effects of VSMC NF90 in mediating the metabolic imbalance of AGEs to accelerate diabetic arteriosclerotic calcification. These novel findings elucidate a pivotal mechanism underlying AGE-induced diabetic atherosclerotic calcification and provide a framework for potential interventions against diabetic vascular complications.

2024-04-02 | GSE253682 | GEO

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