Kidney Data

Research Title	Genome-wide expression profile in rat model of renal isografts from brain dead donors.	Global gene expression profiling on renal scarring in rat model of pyelonephritis.
Investigator	Mamoru Kusaka (Fujita Health University, Department of Urology)	Manabu Ichino (Fujita Health University, Department of Urology)
Summary	Brain death (BD) and the subsequent ischemia/reperfusion (I/R) injury have cardinal implications for the pathogenesis of kidney transplantation (Tx). However, the precise mechanistic pathway of BD and the subsequent I/R injury are unknown. In this study, we performed genome-wide analysis for differential gene expression in kidney isografts from BD donors. Their gene expressions were compared with those from living sources. Kidneys from BD rats were engrafted and their gene expressions were compared with those from living controls. Donors were intubated, and mechanically ventilated for 6 hours. Grafts were harvested 6 hours after BD, and 1 hour after engraftment. The expression profile of approximately 20,500 genes was analyzed.	Renal scarring is a serious complication of chronic pyelonephritis due to vesicoureteral reflux. Elucidation of particular mechanism is required for innovation of specific therapy or identification of novel biomarker for indication of early intervention. We investigated global expression profile of kidney during renal scarring formation using rat pyelonephritis model. An inoculum of the DS-17 strain Escherchia coli was injected directly into renal cortex of Wister rat. Histologically, renal scarring developed during 3 and 4 weeks after injection. The time course expression profile of approximately 20,500 genes was analyzed using high density oligonucleotide microarray followed by validation using real time RT-PCR. Most of up-regulated genes during this experimental renal scarring were associated with immune and defense response, including cytokines, chemokines, their receptors, complements, and adhesion molecules as well as proteins related to extra cellular matrix. These genes were up-regulated as early as 1 week after injection when histological examination did not show fibrotic change yet, peaked at 2 weeks and gradually decreased thereafter. However, a subset of cytokine genes is persistently activated even in 6 weeks after the injection, which includes IL-1beta and TGF-beta. Indeed, pathway analysis indicates that both IL-1beta related inflammation pathway and TGF-beta related tissue regeneration pathway are activated in later stage of renal scarring. The products of these genes may potentially be the source of novel non-invasive diagnostic or prognostic biomarkers for renal scarring.
Organism	Rat	Rat
Data Description	B21: kidney graft 1 hr after transplantation from brain dead donor （6hr after induction of BD) B23: kidney graft 1 hr after transplantation from brain dead donor （6hr after induction of BD) B27: kidney graft 1 hr after transplantation from brain dead donor （6hr after induction of BD) BD1: kidney sample from brain dead donor （6hr after induction of BD) BD2: kidney sample from brain dead donor （6hr after induction of BD) BD3: kidney sample from brain dead donor （6hr after induction of BD) C22: kidney graft 1 hr after transplantation from normal donor C24: kidney graft 1 hr after transplantation from normal donor C25: kidney graft 1 hr after transplantation from normal donor NK1: normal kidney sample NK2: normal kidney sample NK3: normal kidney sample
Data (Downloadable) Help	B21 B23 B27 BD1 BD2 BD3 C22 C24 C25 NK1 NK2 NK3	S17 1week_SLOT03_S01_A01 DS17 2weeks_SLOT01_S01_A01 DS17 3weeks_SLOT01_S01_A01 DS17 4weeks_SLOT08_S01_A01 DS17 6weeks_SLOT07_S01_A01 normal_SLOT06_S01_A01 saline 1week_SLOT05_S01_A01 saline 2weeks_SLOT09_S01_A01 saline 3weeks_SLOT09_S01_A01 saline 4weeks_SLOT04_S01_A01
Experimental Design	Inbred male Lewis rats were used for these experiments as recipients and donors. The left kidney was transplanted orthotopically by end-to-end anastomosis. The contralateral right kidney was removed at the time of transplantation. The time of operative ischemia for transplantation was 30 min, which did not vary between animals. Donor animals were divided into two groups. The experimental group received kidneys from BD rats, while kidneys from living donors were used in the control group. Brain death was produced by gradually increasing the intracranial pressure that led to brain stem herniation. The rats were mechanically ventilated for a period of 6 hours. We compared the gene expression profiles of renal isografts from BD donors and grafts from living donors using a high-density oligonucleotide microarray that contained approximately 20,500 genes. For DNA microarray experiments, 200 ng aliquots of total RNA were labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies Product) according to the manufacturer's instructions. RNA purified from each kidney graft was used for microarray analysis (Cy3-labeled), with pooled RNA derived from normal kidneys as a template control (Cy5-labeled). After checking the labeling efficiency, 1ug aliquots of Cy5-labeled normal control RNA and Cy3-labeled RNA from individual grafts (control 0 hour, 1 hour, BD 0 hour, BD 1 hour, n=3/group) were mixed, and then hybridized to Agilent Rat Oligo Microarrays (Product No. G4130A). After washing, the microarray slides were analyzed with an Agilent Microarray scanner and software (scanner model G2565BA). Data analysis was performed using Agilent Feature Extraction software (Ver. A.7.1.1), and Excel 2003 (Microsoft). The data were imported into GeneSpring 7.0 (Silicon Genetics, Redwood City, CA), with per spot, per chip, and intensity dependent (lowess) normalization being applied for each array. The ratio of the normalized channels (Cy3/Cy5) was used to assess the level of expression.
GEO Series Accession No.	GSE5104	GSE7087