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Glomerular Transcriptome from Experimental Nephrotic Syndrome Model and Treatment with PPARgamma Agonists

ABSTRACT: Nephropathy was induced with puromycin amino-nucleoside (PAN) in Wistar rats and treated with daily treatments of Pioglitazone (Pio) and GQ-16. Total glomerular RNA was isolated, and mRNA libraries were generated and subjected to sequencing using NovaSeq6000 SP. Injury with PAN resulted in 1089 DEGs compared to controls, and 26 of these DEGs were restored by both Pio and GQ-16 treatments, whereas 106 unique GQ-16 regulated DEGs and 17 unique Pio-regulated DEGs were identified (Fig. 4A). Overall, Pio and GQ-16 treatment resulted in 75 and 173 DEGs compared to PAN injury, which included 29 common and 190 distinct genes (Fig. 4A). Of the 29 common DEGs, 28 DEGs were down-regulated by both Pio and GQ-16 and only 1 DEG upregulated by both treatments, when compared to PAN (Fig. 4B). Of the 190 distinct DEGs identified between Pio and GQ-16 treatments, 41 were down-regulated and 5 up-regulated by Pio and 124 down-regulated and 20 up-regulated by GQ-16 treatment.

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE179945 | GEO | 2022/03/09

REPOSITORIES: GEO

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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).

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Glomerular Transcriptome from Experimental Nephrotic Syndrome Model and Treatment with PPARgamma Agonists

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