Peroxisomes are dispensable for normal renal function.
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ABSTRACT:
PROVIDER: PRJNA742694 | ENA |
REPOSITORIES: ENA
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Project description:Peroxisomes are highly abundant in proximal tubules where peroxisomal enzymes have been proposed to play an important role in a variety of metabolic and antioxidant functions. This hypothesis was supported by human genetic studies that identified mutations leading to peroxisomal biogenesis deficiency, resulting in severe multi-organ damage (Zellweger’s spectrum disorders (ZSD)), including renal impairment. However, the role of proximal tubule peroxisomes in renal (patho)physiology remains uninvestigated. We addressed this question in mice with conditional ablation of peroxisomal biogenesis in the renal tubule. Our results demonstrate that renal tubular peroxisomes are dispensable for normal renal function and suggest that renal damage in ZSD patients is of extrarenal origin.
2022-03-02 | GSE179202 | GEO
Project description:Histologic findings on 1-year biopsies such as inflammation with fibrosis and transplant glomerulopathy predict renal allograft loss by 5 years. However, almost half of the patients with graft loss have a 1-year biopsy that is either normal or has only interstitial fibrosis. The goal of this study was to determine if there was a gene expression profile in these relatively normal 1-year biopsies that predicted subsequent decline in renal function. Using transcriptome microarrays we measured intragraft mRNA levels in a retrospective Discovery cohort (170 patients with a normal/minimal fibrosis 1-year biopsy, 54 with progressive decline in function/graft loss and 116 with stable function) and developed a nested 10-fold cross-validated gene classifier that predicted progressive decline in renal function (positive predictive value=38±34%%; negative predictive value=73±30%, c-statistic=0.59). In a prospective, multicenter Validation cohort (270 patients with Normal/Interstitial Fibrosis [IF]), the classifier had a 20% positive predictive value, 85% negative predictive value and 0.58 c-statistic. Importantly, the majority of patients with graft loss in the prospective study had 1-year biopsies scored as Normal or IF. We conclude predicting graft loss in many renal allograft recipients (i.e. those with a relatively normal 1-year biopsy and eGFR >40) remains difficult.
2021-08-31 | GSE181757 | GEO
Project description:Progressive Decline of Function in Renal Allografts with Normal One Year Biopsies
| PRJNA753311 | ENA
Project description:Each total RNA sample is hybridized to two different arrays: Affymetrix U133A (GPL96) and U133B (GPL97). For most of the normal tissue samples there is a renal clear cell carcinoma sample from the same patient. There is no matching tumor sample for normal sample N1. For most of the renal clear cell carcinoma samples there is a corresponding adjacent normal tissue sample from the same patient. There are no matching normal tissue samples for C011 or C032. Keywords = kidney Keywords = renal Keywords = RCC Keywords = carcinoma Keywords = cancer Keywords: parallel sample
2003-11-25 | GSE781 | GEO
Project description:Each total RNA sample is hybridized to two different arrays: Affymetrix U133A (GPL96) and U133B (GPL97). For most of the normal tissue samples there is a renal clear cell carcinoma sample from the same patient. There is no matching tumor sample for normal sample N1. For most of the renal clear cell carcinoma samples there is a corresponding adjacent normal tissue sample from the same patient. There are no matching normal tissue samples for C011 or C032. Keywords = kidney Keywords = renal Keywords = RCC Keywords = carcinoma Keywords = cancer Keywords: parallel sample
2003-11-25 | E-GEOD-781 | biostudies-arrayexpress
Project description:The kidney is a major organ in which fluid balance and waste excretion is regulated. To obtain mature functions of the kidney, normal renal developmental processes need to be preceded. Comprehensive genetic programs underlying renal development during prenatal life have been widely studied. However, postnatal renal development, from infancy to juvenile period, have not been studied yet. Here, we investigated if structural and functional kidney development was still undergoing in early life by analyzing renal transcriptional networks of infant (4 weeks old) and juvenile (7 weeks old) mice. We further examined the effects of dehydration on kidney development. Kidneys at 4 weeks and 7 weeks old showed significantly distinctive functional network of genes. Gene sets related to cell cycle regulators and immature glomerular barrier integrity (COL4A1, COL4A2) were enriched in infantile kidneys while genes associated with ion transport and drug metabolism (CYP450 family) were shown in juvenile kidneys. Dehydration during infancy suppressed renal growth by interrupting SHH signaling pathway which targets cell cycle regulators. Importantly, disruption of developmental program ultimately led to long-term alterations in renal filtration function, by causing a decline in glomerular filtration barrier integrity. Taken together, we provide meaningful perspectives of renal development in infancy which suggests molecular and physiological background why infants are more vulnerable to dehydration than adults. These results provide new insights into the systemic effects of dehydration on renal development and may propose possible markers for clinical application in pediatric dehydration.
2016-07-01 | GSE75604 | GEO
Project description:RNA editing is the essential function of ADAR1 and, in the absence of MDA5, is dispensable for normal adult homeostasis
| PRJNA369541 | ENA
Project description:Uncovering a protein abundance-based gene panel specific to clear cell Renal Cell Carcinoma (ccRCC) could provide support for the everyday clinical decision-making process. We used proteomic data to differentiate between normal kidney and ccRCC tissues. By using datasets of patients with paired normal tissue samples from gene array cohorts, we uncovered the top genes over-expressed in ccRCC. We collected surgically resected ccRCC specimens at Semmelweis University to validate the strongest genes. Differential expression was evaluated at the protein level using targeted mass spectrometry (MS).
2023-05-10 | PXD033709 | Pride
Project description:The kidney is a major organ in which fluid balance and waste excretion is regulated. To obtain mature functions of the kidney, normal renal developmental processes need to be preceded. Comprehensive genetic programs underlying renal development during prenatal life have been widely studied. However, postnatal renal development, from infancy to juvenile period, have not been studied yet. Here, we investigated if structural and functional kidney development was still undergoing in early life by analyzing renal transcriptional networks of infant (4 weeks old) and juvenile (7 weeks old) mice. We further examined the effects of dehydration on kidney development. Kidneys at 4 weeks and 7 weeks old showed significantly distinctive functional network of genes. Gene sets related to cell cycle regulators and immature glomerular barrier integrity (COL4A1, COL4A2) were enriched in infantile kidneys while genes associated with ion transport and drug metabolism (CYP450 family) were shown in juvenile kidneys. Dehydration during infancy suppressed renal growth by interrupting SHH signaling pathway which targets cell cycle regulators. Importantly, disruption of developmental program ultimately led to long-term alterations in renal filtration function, by causing a decline in glomerular filtration barrier integrity. Taken together, we provide meaningful perspectives of renal development in infancy which suggests molecular and physiological background why infants are more vulnerable to dehydration than adults. These results provide new insights into the systemic effects of dehydration on renal development and may propose possible markers for clinical application in pediatric dehydration. Total RNA obtained from isolated kidneys subjected to water restriction for 1 week (RES 1W, 4-week-old) and 4 weeks (RES 4W, 7-week-old), and each group was compared to control group; CON 1W (4-week-old), CON 4W (7-week-old) respectively.
2016-07-01 | E-GEOD-75604 | biostudies-arrayexpress
Project description:These are supporting RAW files for 'Detergent-free simultaneous sample preparation method for proteomics and metabolomics' SiTrap method manuscript.
Frozen renal tissue from three matched clear cell renal carcinoma (G2 pT3a, G2 pT1b, G1 pT2) /adjacent normal sample pairs were obtained from The Leeds Multidisciplinary Research Tissue Bank. Approximately 1 cm2 sections with a thickness of 10 um were lysed and processed according to SiTrap protocol using SiTrap cellulose tips. The SiTrap load was normalized by protein concentration. 50 ug of protein was loaded. The collected flow-through fraction, devoid of proteins, was dried down for targeted metabolomics analysis. The captured protein fraction was reduced and alkylated in situ and digested with trypsin according to SiTrap protocol. The resulting peptides were concentrated for proteomics analysis.
2019-10-02 | MSV000084405 | MassIVE