Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression profiling of the early postnatal stage of Polycystic Kidney Disease in the B6C3Fe a/a-bpck mice

ABSTRACT: To understand the molecular and cellular mechanisms of pathogenesis of autosomal recessive polycystic kidney disease , we performed a microarray gene expression profiling in early stage kidneys of B6C3Fe a/a-bpck mutant and wild-type mice at postnatal day 3. Genes with over 1.5-fold expression changes in mutant kidneys compared with age matched wild-type tissues were selected for analysis. This study represents the first widespread profiling of B6C3Fe a/a-bpck mutant mouse kidney and provides a valuable platform for better understanding the molecular mechanisms of polycystic kidney disease in human. Mutational analysis was performed in accordance with the protocol of Jackson Laboratory, total RNA was extracted from kidneys of 3 days of postnatal age using a monophasic solution of phenol/guanidine isothiocyanate and TRIzol reagent (Invitrogen) according to their manual, and the samples were incubated with RNase-free DNase I (Ambion). The quality and concentration of each sample were confirmed by spectrophotometry. Affymetrix 430 2.0 arrays were used according to standard Affymetrix procedures. Data analysis was performed with dChip software (Dec.2010 version). These measurements were confirmed by Real-Time PCR.

ORGANISM(S): Mus musculus

SUBMITTER: E Du

PROVIDER: E-GEOD-34051 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Kidneys are enlarged by aberrant proliferation of tubule epithelial cells leading to the formation of numerous cysts, nephron loss, and interstitial fibrosis in polycystic kidney disease (PKD). Pioglitazone (PIO), a PPAR-M-NM-3 agonist, decreased cell proliferation, interstitial fibrosis and inflammation, and ameliorated PKD progression in PCK rats. To examine the genetic mechanisms in this efficacy, we analyzed changes in global gene expression. By Gene Set Enrichment Analysis of 30655 genes, 13 of the top 20 down-regulated gene ontology biological process gene sets, and six of the top 20 curated gene set canonical pathways identified to be down-regulated by PIO-treatment were related to cell cycle and proliferation, including EGF, PDGF and JNK pathways. Their relevant pathways were identified using the Kyoto Encyclopedia of Gene and Genomes database. Stearoyl-Coenzyme A desaturase 1 is a key enzyme in fatty acid metabolism found in the top 5 genes down-regulated by PIO treatment. Immunohistochemical analysis revealed that the gene product of this enzyme was highly expressed in PCK kidneys, and decreased by PIO. These data show that PIO alters the expression of genes involved in cell cycle progression, cell proliferation, and fatty acid metabolism. RNA was extracted from kidneys of rats with or without PIO treatment using a monophasic solution of phenol/guanidine isothiocyanate and TRIzol reagent (Invitrogen Co., Carlsbad, CA, USA) in accordance with their manual, and the samples were incubated with RNase-free DNase I (Ambion, TX, USA). The quality and concentration of each sample was confirmed by spectrophotometry (NanoDropTM ND-1000; Asahi glass Co. Ltd., Tokyo, Japan). Total RNA obtained from five females were pooled in each PIO-treated or control vehicle-treated (CONT) group. Briefly, 500 ng aliquots of total RNA obtained from kidneys of three rats were labeled using an Quick Amp Labeling Kit, one-color (Agilent Technologies, Inc., Santa Clara, CA, USA) according to the manufacturerM-bM-^@M-^Ys instructions. The pooled renal RNA of PIO- or vehicle-treated rats were labeled with the Cy3-fluorescence dye. After determination of labeling efficiency, 1.65 M-NM-<g aliquots of Cy3-labeled RNA were hybridized using the Gene Expression hybridization kit (Agilent Technologies) onto Rat Oligo Microarrays (Agilent Technologies, product no. G4130A) according to the manufacturerM-bM-^@M-^Ys hybridization protocol. The microarray slides were examined with an Agilent microarray scanner and software. Data analysis was performed with Agilent Feature Extraction software (version 10.7.3.1).

Project description:Background: Autosomal dominant polycystic kidney disease (ADPKD) affects more than 12 million people worldwide. Mutations in PKD1 and PKD2 cause cyst formation through unknown mechanisms. To unravel the pathogenic mechanisms in ADPKD, multiple studies have investigated transcriptional mis-regulation in cystic kidneys from patients and mouse models, and numerous dysregulated genes and pathways have been described. Yet, the concordance between studies has been rather limited. Furthermore, the cellular and genetic diversity in cystic kidneys has hampered the identification of mis-expressed genes in kidney epithelial cells with homozygous PKD mutations, which are critical to identify polycystin-dependent pathways. Methods: Autosomal dominant polycystic kidney disease (ADPKD) affects more than 12 million people worldwide. Mutations in PKD1 and PKD2 cause cyst formation through unknown mechanisms. To unravel the pathogenic mechanisms in ADPKD, multiple studies have investigated transcriptional mis-regulation in cystic kidneys from patients and mouse models, and numerous dysregulated genes and pathways have been described. Yet, the concordance between studies has been rather limited. Furthermore, the cellular and genetic diversity in cystic kidneys has hampered the identification of mis-expressed genes in kidney epithelial cells with homozygous PKD mutations, which are critical to identify polycystin-dependent pathways. Results: Autosomal dominant polycystic kidney disease (ADPKD) affects more than 12 million people worldwide. Mutations in PKD1 and PKD2 cause cyst formation through unknown mechanisms. To unravel the pathogenic mechanisms in ADPKD, multiple studies have investigated transcriptional mis-regulation in cystic kidneys from patients and mouse models, and numerous dysregulated genes and pathways have been described. Yet, the concordance between studies has been rather limited. Furthermore, the cellular and genetic diversity in cystic kidneys has hampered the identification of mis-expressed genes in kidney epithelial cells with homozygous PKD mutations, which are critical to identify polycystin-dependent pathways. Conclusions: Autosomal dominant polycystic kidney disease (ADPKD) affects more than 12 million people worldwide. Mutations in PKD1 and PKD2 cause cyst formation through unknown mechanisms. To unravel the pathogenic mechanisms in ADPKD, multiple studies have investigated transcriptional mis-regulation in cystic kidneys from patients and mouse models, and numerous dysregulated genes and pathways have been described. Yet, the concordance between studies has been rather limited. Furthermore, the cellular and genetic diversity in cystic kidneys has hampered the identification of mis-expressed genes in kidney epithelial cells with homozygous PKD mutations, which are critical to identify polycystin-dependent pathways.

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Expression profiling of the early postnatal stage of Polycystic Kidney Disease in the B6C3Fe a/a-bpck mice

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