Identification of Genes Involved in Familial Coronary Artery Disease
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ABSTRACT: Studying families with multiple cases of coronary artery disease (CAD) or with early onset CAD in order to identify new genes involved in CAD in an autosomal dominant manner. After identifying these genes in families that pass on CAD in Mendelian inheritance, we want to pursue their role in the pathogenesis of CAD and their contribution in the general population.
SECONDARY ACCESSION(S): PRJNA170897PRJNA170898
REPOSITORIES: dbGaP
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Project description:<p>Studying families with multiple cases of coronary artery disease (CAD) or with early onset CAD in order to identify new genes involved in CAD in an autosomal dominant manner. After identifying these genes in families that pass on CAD in Mendelian inheritance, we want to pursue their role in the pathogenesis of CAD and their contribution in the general population.</p>
| phs000514.v1.p1 | EGA
Project description:Tissue samples have been isolated during corornary artery by-pass grafting (CABG)surgery from the atheroscelrotic arterial wall (AAW, aortic root puncture for proxmal ligation of by-pass vessel), non-atherosclertoci arterial wall (NAAW, distal part of mammary artery used a graft for LAD), liver, skeletal muscle (Recturs m), pericardial mediastinal visceral fat) in CAD patients. Carotid lesions samples from 25 validation patients. We used microarrays to measure global gene expression in these tissues to cluster groups of functionally associated genes and then, second step clustering of patients within each cluster to link clusters to patient phenotypes primarily coronary stenosis (CAD) and Intima media thickness (IMT) in carotid stenosis patients. .
2012-08-21 | GSE40231 | GEO
Project description:Tissue samples have been isolated during corornary artery by-pass grafting (CABG)surgery from the atheroscelrotic arterial wall (AAW, aortic root puncture for proxmal ligation of by-pass vessel), non-atherosclertoci arterial wall (NAAW, distal part of mammary artery used a graft for LAD), liver, skeletal muscle (Recturs m), pericardial mediastinal visceral fat) in CAD patients. Carotid lesions samples from 25 validation patients. We used microarrays to measure global gene expression in these tissues to cluster groups of functionally associated genes and then, second step clustering of patients within each cluster to link clusters to patient phenotypes primarily coronary stenosis (CAD) and Intima media thickness (IMT) in carotid stenosis patients. . All samples were taken during surgery. The time of operation was less than 3 hours in most instances. Sammon plots show strong clustering of tissue-specific arrays. Even separating AAW from NAAW and carotid lesions.
2012-08-21 | E-GEOD-40231 | biostudies-arrayexpress
Project description:Coronary artery disease (CAD) is the leading cause of human morbidity and mortality worldwide, underscoring the need to improve diagnostic strategies. Platelets play a major role, not only in the process of acute thrombosis during plaque rupture, but also in the formation of atherosclerosis itself. MicroRNAs are endogenous small non-coding RNAs that control gene expression and are expressed in a tissue and disease-specific manner. Therefore they have been proposed to be useful biomarkers. It remains unknown whether differences in miRNA expression levels in platelets can be found between patients with premature CAD and healthy controls. Methodology/Principal Findings In this case-control study we measured relative expression levels of platelet miRNAs using microarrays from 12 patients with premature CAD and 12 age- and sex-matched healthy controls. Six platelet microRNAs were significantly upregulated (miR340*, miR451, miR454*, miR545:9.1. miR615-5p and miR624*) and one miRNA (miR1280) was significantly downregulated in patients with CAD as compared to healthy controls. To validate these results, we measured the expression levels of these candidate miRNAs by qRT-PCR in platelets of individuals from two independent cohorts; validation cohort I consisted of 40 patients with premature CAD and 40 healthy controls and validation cohort II consisted of 27 patients with artery disease and 40 healthy relatives. MiR340* and miR624* were confirmed to be upregulated in patients with CAD as compared to healthy controls in both validation cohorts. Conclusion/Significance Two miRNAs in platelets are significantly upregulated in patients with CAD as compared to healthy controls. miRNA array analysis of isolated platelets from subjects with premature coronary artery disease compared to healthy control subjects.
2011-09-30 | E-GEOD-28858 | biostudies-arrayexpress
Project description:Coronary artery disease (CAD) is the leading cause of human morbidity and mortality worldwide, underscoring the need to improve diagnostic strategies. Platelets play a major role, not only in the process of acute thrombosis during plaque rupture, but also in the formation of atherosclerosis itself. MicroRNAs are endogenous small non-coding RNAs that control gene expression and are expressed in a tissue and disease-specific manner. Therefore they have been proposed to be useful biomarkers. It remains unknown whether differences in miRNA expression levels in platelets can be found between patients with premature CAD and healthy controls. Methodology/Principal Findings In this case-control study we measured relative expression levels of platelet miRNAs using microarrays from 12 patients with premature CAD and 12 age- and sex-matched healthy controls. Six platelet microRNAs were significantly upregulated (miR340*, miR451, miR454*, miR545:9.1. miR615-5p and miR624*) and one miRNA (miR1280) was significantly downregulated in patients with CAD as compared to healthy controls. To validate these results, we measured the expression levels of these candidate miRNAs by qRT-PCR in platelets of individuals from two independent cohorts; validation cohort I consisted of 40 patients with premature CAD and 40 healthy controls and validation cohort II consisted of 27 patients with artery disease and 40 healthy relatives. MiR340* and miR624* were confirmed to be upregulated in patients with CAD as compared to healthy controls in both validation cohorts. Conclusion/Significance Two miRNAs in platelets are significantly upregulated in patients with CAD as compared to healthy controls.
2011-10-01 | GSE28858 | GEO
Project description:The circRNA profiles of 24 CAD patients and 7 controls were performed by microarray. Six classifiers were used to evaluate potential circRNAs biomarkers. The expression levels of candidate circRNAs were further verified by qRT-PCR in large cohorts. Logistic regression analysis and receiver operating characteristic were conducted to assess the diagnostic value. A total of 624 circRNAs and 171 circRNAs were significantly upregulated and downregulated, respectively, in CAD patients relative to controls. A four-circRNA signature was identified using six different classifiers. Among these four circRNAs, hsa_circ_001879 and hsa_circ_004104 were found significantly upregulated in validation cohorts. We offered a transcriptome-wide overview of aberrantly expressed circRNAs in CAD patients, and Hsa_circ_001879 and hsa_circ_004104 were replicated and identified to be significantly upregulated in CAD patients. Our results suggested that hsa_circ_001879 and hsa_circ_004104 might serve as diagnostic biomarkers for CAD.
2021-06-07 | GSE115733 | GEO
Project description:To date there is no clear explanation as to how Chlamydia pneumoniae heat shock protein 60 (cHSP60) gets activated either through TLR-2/4, MAPKinase (p38/JNK/ERK), apoptotic/antiapoptotic, chemokines and inflammatory cytokines pathways leading to coronary artery disease (CAD). Hence to better understanding towards cHSP60 signaling in CAD patients, we performed experiments at RNA levels in cHSP60 positive and negative groups of CAD patients. For the determination of positivity for C. pneumoniae, Helicobacter pylori, Cytomegalovirus and Herpes Simplex Virus in atheromatous plaque multiplex Real Time PCR was performed. Monoplex Real Time PCR was also performed with 16S rRNA and HSP60 gene Chlamydia pneumoniae. Further study was performed only on cHSP60 positive (negative for H. pylori, CMV & HSV-1) and cHSP60 negative (also negative for H. pylori, CMV & HSV-1) CAD patients. 1. Patients Forty patients (28 males, 12 females) in age group (51±13 year) attending Department of Cardio Thoracic & Vascular Surgery, Safdarjung Hospital, New Delhi from September 2007 to April 2008 were enrolled in the study. These patients had manifestations of CAD and were undergoing open by-pass heart surgery. Prior written consent was obtained from each patient. The study received clearance from Ethical committee, Safdarjung hospital. Patients who had a recent acute coronary syndrome or transient ischemic attack were not included in our study. 2. Atheroma collection and handling Atheromatous tissue were collected in aseptic conditions and placed in 30 ml transport medium immediately upon resection. Three types of transport medium were used for tissue: viz. Dulbecco?s phosphate-buffered saline (PBS; Gibco Life Technologies, Paisley, Scotland) for DNA, RNA later (Ambion Inc., Woodward st. Austin, Texas, USA) for RNA and optimum cutting temperature compound (Sigma, St. Louis, MO, USA) for protein. 3. Atheroma DNA & RNA isolation and testing Total DNA was isolated for checking the positivity for C. pneumoniae from atheromatous plaques as described earlier [1]. Total RNA from the atheroma samples were isolated using RNeasy fibrous tissue mini kit (Qiagen Sciences, Maryland, USA) and the concentration was determined by a RNA dye-binding assay (Pico-Green, Molecular Probes, Eugene, OR). For cDNA synthesis, RETRO script (Ambion Inc., Woodward st. Austin, Texas, USA) was used as per manufacturer instructions. For detecting positivity for C. pneumoniae, Helicobacter pylori, Cytomegalovirus and Herpes Simplex Virus in atheromatous plaques, multiplex RT-PCR was performed [as describe in reference 1]. Monoplex RT PCR amplification primers and probes were custom designed by Applied Biosystems (Foster City, CA, USA). Briefly, sequences for the 16S rRNA and HSP60 gene of the organisms of interest were aligned and inspected for regions of conserved and variable sequences. 4. Microarray experiment Further study was performed only on cHSP60 positive (negative for H. pylori, CMV & HSV-1) and cHSP60 negative (also negative for H. pylori, CMV & HSV-1) CAD patients. cHSP60 positive samples represented the test samples and cHSP60 negative samples represented the control samples. 3 samples were analysed: samples 17 and 23 were biological replicates of test samples and also performed in duplicate as technical replicates, and sample 26 was a control sample and was also performed in duplicate as a technical replicate. Reference 1. Hem C Jha, Pragya Srivastava, Aabha Divya , Jagdish Prasad, Aruna Mittal. Prevalence of Chlamydophila pneumoniae is higher in aorta and coronary artery than in carotid artery of coronary artery disease patients. APMIS, 2009: 117 (12): 905-911.
2010-05-16 | E-GEOD-19590 | biostudies-arrayexpress
Project description:Dysregulation of long non-coding RNAs (lncRNAs) has been proven to be involved in the pathogenesis of coronary artery disease (CAD). However, it remains to be extensively explored.Using microarray, we performed the transcriptome-wide lncRNA and mRNAs expression profile in peripheral blood mononuclear cells (PBMCs) of 93 CAD patients and 48 healthy controls. Gene Ontology (GO) and pathway analysis for differentially expressed mRNAs was used to investigate underlying biological associations of differentially expressed lncRNAs and create path-net to depict interactions of significant pathways. We identified 1,210 lncRNAs and 890 mRNAs differentially expressed from the expression profile and validated selected 7 lncRNAs. Two novel lncRNA biomarkers, ENST00000444488.1 and uc010yfd.1, together with CAD risk factors had the better predictive performance for discriminating CAD patients from healthy controls, and ENST00000444488.1 could diagnose acute myocardial infarction (AMI) patients from non-AMI patients.
2019-08-17 | GSE113079 | GEO
Project description:We used linkage data from CAD family to search for the responsible variant in disease. we used illumina array for linkage analysis of CAD affected family.
2014-03-28 | E-GEOD-42137 | biostudies-arrayexpress
Project description:Elevated plasma cholesterol and Type 2 Diabetes (T2D) are associated with Coronary Artery Disease (CAD). Individuals treated with cholesterol-lowering statins have increased T2D risk, while individuals with hypercholesterolemia have reduced T2D risk. We explored the relationship between lipid and glucose control by constructing network models from the STARNET study with sequencing data from seven cardiometabolic tissues obtained from CAD patients during coronary artery by-pass grafting surgery. By integrating gene expression, genotype, metabolomic and clinical data, we identified a Glucose and Lipid Determining (GLD) regulatory network showing inverse relationships with lipid and glucose traits. Master regulators of the GLD network also impacted lipid and glucose levels in inverse directions. Experimental knockdown of one of the GLD network master regulators, Lanosterol Synthase (LSS), in mouse confirmed the inverse relationships to glucose and lipid levels as predicted by our model and provided mechanistic insights.
2020-09-01 | GSE157223 | GEO