Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA92805 | ENA |
REPOSITORIES: ENA
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Project description:We compared gene expression profiles from six donor kidneys prior to surgical manipulation to six kidneys removed after laparoscopic donor nephrectomy (LDN) and several hours of CO2 pneumoperitoneum. Biopsies were obtained from renal cortex and hybridized to Affymetrix HG-U133A GeneChips. For control kidneys we identified 1380 genes present on all 6 samples that had a signal intensity greater than 1000. Functional classification of these revealed genes for cellular signaling (201; 15%), regulation of transcription (156; 11%), cellular transport (144; 10%) and cellular metabolism (111; 8%). A class comparison between the controls and LDN kidneys yielded 865 differentially expressed genes. Functional classification of the 502 genes differentially up-regulated in LDN kidneys identified associations with apoptosis, cell adhesion, cell signaling, regulation of cell growth/proliferation, immune/inflammation, ischemia/stress response and proteolysis/peptidolysis. These data demonstrate an altered renal transcriptome induced by several hours of CO2 pneumoperitoneum and laparoscopic surgery characterized by up-regulation of ischemia and injury associated genes. Keywords: Comparative Expression
2005-09-14 | GSE3297 | GEO
Project description:We compared gene expression profiles from six donor kidneys prior to surgical manipulation to six kidneys removed after laparoscopic donor nephrectomy (LDN) and several hours of CO2 pneumoperitoneum. Biopsies were obtained from renal cortex and hybridized to Affymetrix HG-U133A GeneChips. For control kidneys we identified 1380 genes present on all 6 samples that had a signal intensity greater than 1000. Functional classification of these revealed genes for cellular signaling (201; 15%), regulation of transcription (156; 11%), cellular transport (144; 10%) and cellular metabolism (111; 8%). A class comparison between the controls and LDN kidneys yielded 865 differentially expressed genes. Functional classification of the 502 genes differentially up-regulated in LDN kidneys identified associations with apoptosis, cell adhesion, cell signaling, regulation of cell growth/proliferation, immune/inflammation, ischemia/stress response and proteolysis/peptidolysis. These data demonstrate an altered renal transcriptome induced by several hours of CO2 pneumoperitoneum and laparoscopic surgery characterized by up-regulation of ischemia and injury associated genes. Keywords: Comparative Expression Twelve healthy adult kidney donors signed a consent form, and were approved for donation according to the usual evaluation and practice of the Cleveland Clinic Renal Transplant Program. To avoid potentially significant differences in gene expression based on race and/or ethnicity, only white recipients were selected. The patients were divided into two groups; six controls from open donor nephrectomy and six from LDN. Demographic information included age, gender, race, HLA type, and renal function data including serum creatinine (mg/dL), GFR measured by iothalamate clearance (cc/min.), and urine protein excretion (mg/24 hr). Each patient was given general anesthesia and had a diuresis induced with saline, mannitol, and furosemide. The controls had an extraperitoneal flank incision made, and with only minimal manipulation of the kidney two subcapsular core renal biopsies were obtained using a 15-gauge spring-loaded needle. For the LDN cases two core renal biopsies were obtained using the same needles after the kidneys underwent 2 to 3 hours of C02 pneumoperitoneum. Study biopsies went immediately into 1.5 mL of RNALater (Ambion, Austin, TX), and were stored at –80 0C until they were processed. Biopsy specimens were homogenized in 1 mL of Trizol (Invitrogen, Carlsbad, CA); total RNA was purified using an RNeasy column (Qiagen, Valencia, CA); and quality confirmed with an Agilent 2100 BioAnalyzer (Palo Alto, CA). Standard Affymetrix GeneChip (Santa Clara, CA) protocols were used, and labelled samples were hybridized to HG-U133A GeneChip arrays containing 22,283 probe sets representing over 14,500 human genes. Data was analyzed using Signal intensities generated using GeneChip Operating System version 1.0 and were subsequently analysed by Robust Multichip Average Express (RMA Express) using all Affymetrix .CEL files as a training set. BRB ArrayTools (http://linus.nci.nih.gov/BRB-ArrayTools.html) was used to perform class comparisons (significance level of p < 0.005), and create dendrograms. We used NetAffyx (www.affymetrix.com) to annotate the differentially expressed genes according to biological function based on the Gene Ontology database. A Heatmap was created using Cluster and TreeView software. This dataset is part of the TransQST collection.
2005-09-14 | E-GEOD-3297 | biostudies-arrayexpress
Project description:Males are 50% more likely to develop end stage kidney failure compared to women. In this study we wanted to find out the molecular mechanism responsible for this increased risk. We collected kidney samples from patients with and without kidney disease and performed a comprehensive gene expression analysis in healthy and diseased male and female kidneys. Interestingly, the set of gender biased genes in healthy kidneys were different from those in diseased kidneys indicating not only baseline gene expression differences but also that the male and female kidney respond differently to disease condition. Our studies indicate that men and women with kidney problems might need to be treated differently. Keywords: Gender difference We collected 42 kidney samples from healthy living transplant donors, nephrectomies and from diagnostic kidney biopsies. Preliminary studies did not show significant gene expression differences in control kidneys based on the collection method (i.e. living kidney biopsy vs. unaffected portion of tumor nephrectomy). We grouped the tissue samples based on the histological readings of the kidney biopsies. Samples with evidence of glomerular and tubulointerstitial fibrosis were assigned into the diseased group. Characteristics of the research participants indicate diverse ethnic and disease groups and mild (StageIII) CKD. The tissue was microdissected into glomerular and tubulointerstitial fractions and expression arrays were performed separately.
2010-04-13 | E-GEOD-12682 | biostudies-arrayexpress
Project description:CpG island methylation profiling of anaplastic gliomas compared to healthy control
| PRJNA314887 | ENA
Project description:This study was designed to investigate gene expression in kidneys of adult Sabra rats (SBH/y and SBN/y rat strains) with two indwelling kidneys or after uni-ninephrectomy, seeking those genes that are differentially expressed between the two strains, and between animals with one or two kidneys. SBH/y after uninephrectomy develop proteinuria to a much greater extent than SBN/y. The study was performed as part of an overall effort to detect the genes that are associated with the pathophysiology of proteinuria. Keywords: Analysis of genes that are differentially expressed in the kidneys, contrasting between an animal strain that tends to develop proteinuria which is amplified by uninephrectomy and another strain that is relatively resistant to the development of proteinuria The experiment was performed in male animals after weaning. Four groups were studied: SBN/y with 2 kidneys (ham uni-nephrectomy), SBN/y after uni-nephrectomy, SBH/y with 2 kidneys (sham uninephrectomy) and SBH/y after uni-nephrectomy. Animals were provided rat chow ad libitum. At age 4 months, 3 months after uninephrectomy or sham operation, animals were sacrificed under ether anesthesia, killed by exsanguination and the kidneys were rapidly removed and snap frozen with liquid nitrogen. The kidneys were stored at -800C until RNA was extracted for the differentiale xpression experiment.
2009-02-03 | E-GEOD-14676 | biostudies-arrayexpress
Project description:This study was designed to investigate gene expression in kidneys of adult female Sabra rats (SBH/y and SBN/y rat strains) with two indwelling kidneys or after uni-ninephrectomy, seeking those genes that are differentially expressed between the two strains, and between animals with one or two kidneys. SBH/y after uninephrectomy develop proteinuria to a much greater extent than SBN/y. The study was performed as part of an overall effort to detect the genes that are associated with the pathophysiology of proteinuria. Keywords: Analysis of genes that are differentially expressed in the kidneys, contrasting between an animal strain that tends to develop proteinuria which is amplified by uninephrectomy and another strain that is relatively resistant to the development of proteinuria The experiment was performed in female animals after weaning. Four groups were studied: SBN/y with 2 kidneys (sham uni-nephrectomy), SBN/y after uni-nephrectomy, SBH/y with 2 kidneys (sham uninephrectomy) and SBH/y after uni-nephrectomy. Animals were provided rat chow ad libitum. At age 5 months, 4 months after uninephrectomy or sham operation, animals were sacrificed under ether anesthesia, killed by exsanguination and the kidneys were rapidly removed and snap frozen with liquid nitrogen. The kidneys were stored at -800C until RNA was extracted for the differential expression experiment.
2009-01-31 | E-GEOD-14666 | biostudies-arrayexpress
Project description:In this study, we compared the transcriptomes of the kidney subjected to unilateral IRI with contralateral nephrectomy (IRI/CL-NX) and the normal healthy control kidney at the single cell level to identify major cell types in the kidney and the differential transcriptional response during kidney repair following IRI.
2022-03-23 | GSE188966 | GEO
Project description:Proteomic dataset of 15 murine kidneys of 14-week-old male C57Bl6 mice. Mice were divided into 3 treatment groups four weeks prior to nephrectomy and 5 mice had ad libitum access to food and water, while another 10 mice received 30% food restriction. Calorically restricted mice either received intraperitoneal supplementation of 20-HETE or vehicle (EtOH in sodiumchloride 0.9%) for 8 days on a daily basis prior to nephrectomy. Ad libitum fed mice received vehicle injections for 8 days on a daily basis prior to nephrectomy.
2022-06-17 | PXD031604 | Pride
Project description:Deceased kidney donation after brain death (DBD) is the main source of transplants, yet these grafts yield inferior transplant outcomes when compared to living donation. In brain death, cerebral injury contributes to systemic biological dysregulation, causing significant cellular stress in donor kidneys that adversely impacts the quality of grafts. Here, we hypothesized that proteolytic processes in DBD kidneys might lead to podocyte damage with subsequent development of post-transplant dysfunction. Using protein topography and migration analysis platform (PROTOMAP), we mapped degradation profiles of cytoskeletal proteins in DBD kidneys. Cytoskeletal proteolytic degradation was further studied by Immunoblotting on a separate cohort of deceased and living donor kidney biopsies. To investigate potential mechanism of kidney cytoskeletal protein degradation, in-vitro human podocytes and ex-vivo precision-cut human kidney slices were employed. We found novel proteolytic profiles of key podocyte cytoskeletal proteins in donor kidneys associated with suboptimal posttransplant function. These were unique to brain-death and were not observed in circulatory-death or living-donor kidneys. Talin-specific protein degradation in DBD kidneys indicated Calpain-1 activation may have a key role in proteolytic processes observed in the dysfunctional kidneys. Investigation of the underlying mechanism suggests that Transforming-Growth Factor-β (TGFβ) induces Calpain-1 activation, leading to brain-death specific podocyte degradation patterns and dysregulation of actin cytoskeleton; events that were prevented, in-vitro, by Calpain inhibition. Conclusion Our data demonstrate that podocyte protein degradation impacts the quality of DBD kidneys, propose a role of TGFβ mediated Calpain-1 proteolytic processing of cytoskeletal Talin-1, suggesting therapeutic opportunities to prevent kidney dysfunction.
2022-08-12 | PXD022074 | Pride