Proteomic characteristics of vessels in patients with chronic kidney disease
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Homo Sapiens (human)
TISSUE(S): Blood Vessel
DISEASE(S): Chronic Kidney Disease
SUBMITTER: 
Chunyu Zhou
LAB HEAD: Chunyu Zhou
PROVIDER: PXD010883 | Pride | 2019-06-24
REPOSITORIES: Pride
Similar Datasets
Project description:Abnormal epigenetic gene regulation may play a pivotal role in atherogenesis. In particular, global DNA hypomethylation potentially leading to proatherogenic gene expression, occurs in atherosclerotic lesions in humans and animal models. In order to identify genomic sequences targeted for DNA hypomethylation in atherosclerosis, we analysed the methylation status of CpG islands (CGIs) in 45 human arteries with advanced atherosclerotic lesions and 16 normal counterparts by a microarray approach. Methylation data for 10,367 CGIs revealed that a subset (1.5%) of such sequences was hypermethylated in normal arteries, in accordance with data previously obtained in peripheral blood cells. Ninety-four per cent of this CGI subset was demethylated in atherosclerotic tissue, while only 17 of normally hypomethylated CGIs was hypermethylated in diseased tissue. A functional classification of genes physically associated with differentially methylated CGIs revealed a bias towards transcription factors (42%). The latter include HOX members, NOTCH1 and FOXP1, which are known to regulate angiogenesis, dedifferentiation, cell migration and macrophage function. The methylation status of selected CGIs was validated in further 10 subjects for either group. Expression patterns of these factors were compatible with the observed differential methylation. Our data suggest that one of the molecular changes associated with aberrant DNA methylation in advanced atherosclerosis is the regulation of critical transcription factor genes for the induction of a proatherogenic cellular phenotype. Two-condition experiment, i.e. normal vs. atherosclerotic arteries. 16 and 45 normal and atherosclerotic samples, respectively, were pooled and used to interrogate CpG island arrays in triplicate, for a total of six arrays. Each array was co-hybridized with untreated DNA (reference) and hypermethylated DNA obtained by biochemical filtration.
2010-06-20 | E-GEOD-15552 | biostudies-arrayexpress
Project description:Protein expression is regulated by production and degradation of mRNAs and proteins, but their specific relationships remain unknown. We combine measurements of protein production and degradation and mRNA dynamics to build a quantitative genomic model of the differential regulation of gene expression in LPS stimulated mouse dendritic cells. Changes in mRNA abundance play a dominant role in determining most dynamic fold changes in protein levels. Conversely, the preexisting proteome of proteins performing basic cellular functions is remodeled primarily through changes in protein production or degradation, accounting for over half of the absolute change in protein molecules in the cell. Thus, the proteome is regulated by transcriptional induction of novel cellular functions and remodeling of preexisting functions through the protein life cycle. Mouse primary dendritic cells were treated with LPS or mock stimulus and profiled over a 12-hour time course. Cells were grown in M-labeled SILAC media, which was replaced with H-labeled SILAC media at time 0. Aliquots were taken at 0, 0.5, 1, 2, 3, 4, 5, 6, 9, and 12 hours post-stimulation and added to equal volumes of a master mix of unlabeled (L) cells for the purpose of normalization. RNA-Seq was performed at 0, 1, 2, 4, 6, 9, and 12 hours post-stimulation.
2015-03-06 | E-GEOD-59792 | biostudies-arrayexpress
Project description:We primary cultured ectopic endometrial cells from patients with endometriosis (2 cases) and without endometriosis(2 cases) and collected cell culture supernatants（P0). We isolated exosomes from cell culture supernatants by differential centrifugation and then performed proteome analysis on the two groups of exosomes to investigate the role of ectopic endometrial cell-derived exosomes in the development of endometriosis.
2022-06-09 | PXD033124 | Pride
Project description:We have undertaken a screen of mouse limb tendon cells in order to identify molecular pathways involved in tendon development. Mouse limb tendon cells were isolated based on Scleraxis (Scx) expression at different stages of development: E11.5, E12.5 and E14.5 Microarray comparisons were carried out between tendon progenitor and differentiated stages. Forelimbs from E11.5, E12.5 and E14.5 Scx-GFP embryos were collected and dissociated with trypsin to obtain cell suspensions. Scx-positive tendon cells were isolated by FACS. RNA was extracted and Fragmented biotin-labelled cRNA samples were hybridized on Affymetrix Gene Chip Mouse Genome 430 2.0 arrays.
2014-01-18 | E-GEOD-54207 | biostudies-arrayexpress
Project description:Endothelin-1 (ET-1), an endothelium-derived vasoconstrictor peptide, plays a role in the pathophysiology of cardiovascular disease. Transgenic mice that overexpress human preproET-1 selectively in the endothelium (eET-1) exhibit endothelial dysfunction, hypertrophic remodeling and vascular inflammation of resistance-size arteries in the absence of blood pressure elevation. To understand the mechanisms whereby ET-1 induces vascular damage, vascular gene expression using DNA microarrays was employed. RNA from mesenteric arteries of female and male young (6-7 weeks) and mature (6-8 months) eET-1 and wild type (WT) mice was isolated and changes in gene expression were determined by genome-wide expression profiling using Illumina microarray. This study revealed a set of genes potentially regulated by ET-1, which might be implicated in ET-1 induced-vascular damage. Samples 1-8: Total RNA obtained from the entire mesenteric arterial tree of young (6-7 weeks) female preproendothelin-1 overexpressing mice compared to age and sex matched wild type littermate controls. Samples 9-16: Total RNA obtained from the entire mesenteric arterial tree of mature (6-8 months) female preproendothelin-1 overexpressing mice compared to age and sex matched wild type littermate controls. Samples 17-24: Total RNA obtained from the entire mesenteric arterial tree of young (6-7 weeks) male preproendothelin-1 overexpressing mice compared to age and sex matched wild type littermate controls. Samples 25-32: Total RNA obtained from the entire mesenteric arterial tree of mature (6-8 months) male preproendothelin-1 overexpressing mice compared to age and sex matched wild type littermate controls.
2010-09-01 | E-GEOD-19624 | biostudies-arrayexpress
Project description:The understanding of protein alterations in the diabetic heart is of vital importance because of increased risk of cardiovascular co-morbidities. The study aims at elucidating metabolic pathways in the diabetic rat heart during development of Type 2 diabetes mellitus using MS based proteomics.
2018-06-26 | PXD009538 | Pride
Project description:The understanding of protein alterations in the diabetic heart is of vital importance because of increased risk of cardiovascular co-morbidities. The study aims at elucidating metabolic pathways in the diabetic rat heart during development of Type 2 diabetes mellitus using MS based proteomics.
2018-06-26 | PXD009554 | Pride
Project description:We found constitutive upregulation and higher degree induction of drug metabolism and disposition-related genes in a three-dimensional HepG2 culture. The upregulated genes are those believed to be regulated by different regulatory factors. The global gene expression analysis by Affymetrix GeneChip indicated that altered expressions of microtubule-related genes may change expressed levels of drug metabolism and disposition genes. Stabilization of the microtubule molecules with docetaxel, a tubulin stabilizing agent, in the two-dimensional culture showed gene expression patterns similar to those in the three-dimensional culture, indicating that culture environment affects drug metabolism functions in HepG2 cells. Experiment Overall Design: We compared the gene expression data from HepG2 cells cultured in the radial flow bioreactor (RFB) cell culture system for six days to those from HepG2 cells cultured in tissue culture plates for five days. Both cell cultures (RFB culture and plate culture) were performed twice independently. In each culture, three samples were collected from three different portions of the bioreactor or from three different tissue culture plates. Microarray analyses were performed in duplicate for each sample using the Affymetrix human genome U133A GeneChip.
2009-03-08 | E-GEOD-12939 | biostudies-arrayexpress
Project description:Gene expression in human umbilical vein endothelial cells (HUVEC) was investigated by microarray analysis after 4 h infection with S. aureus isolated from healthy nasal carriers (n=5) and from blood (n=5) of septic patients. All bacterial isolates were spa-typed and characterized with a DNA microarray to determine the presence of virulence genes. Experiment Overall Design: Five S. aureus (designated BI-BV) from a collection of blood culture isolates (Department of Clinical Microbiology, Ryhov County Hospital, Jönköping, Sweden) from septic patients were selected. Isolates from patients with diabetes, endocarditis, drug addicts and persons with an operation within the three last years were excluded. Two S. aureus isolates were from patients with an abscess in the psoas muscle, two from patients with spondylitis and one from a wound in the neck. Another five isolates (CI-CV) were randomly selected from a collection of S. aureus obtained from healthy male nasal carriers collected in a previous study.
2009-04-12 | E-GEOD-13736 | biostudies-arrayexpress
Project description:High-flow causes the remodeling of arteries, in which smooth muscle cells play an important role. To know the profile of smooth muscle gene expression under high-flow conditions in vivo, flow of rabbit basilar artery was increased by ligation of both common carotid arteries. Microarrays were performed to profile the gene expression of smooth muscle cells isolated from rabbit basilar artery. Expression profiles indicate 43603 differentially expressed genes in smooth muscle cells exposed to high-flow insult compared with the sham control, of which 1470 genes were upregulated and 780 genes downregulated using 2 fold-changes and P<0.05 as a cut-off. Bilateral common carotid arteries of female New Zealand White rabbits were ligated to increase vascular flow.The control group was performed the same procedure to expose the CCAs without ligation. Rabbits were euthanized at day 5 after ligation or exposure of bilateral CCAs in both groups (n=3 for each group). The rabbits used and all procedures in this study were approved by the local Institutional Animal Care and Use Committee. Smooth muscle cells were isolated. After euthanization of rabbits, the whole basilar arteries were removed. The arteries were cleaned in PBS buffer,cannulated and perfused at a constant flow with a cocktail which contains PBS and 0.4 mg/ml elastase (Sigma) and 1 mg/ml collagenase (type 1A, Sigma). After an incubation time of 45 min, the tissue left was removed and stored in PBS. SMCs were released from the artery by trituration. Then Total RNA was extracted and gene chip tests were performed.
2016-06-30 | E-GEOD-61212 | biostudies-arrayexpress