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Series GSE10419 Query DataSets for GSE10419
Status Public on Feb 08, 2008
Title Global expression profiles in one hour biopsy of human kidney transplantation from donors after cardiac death
Organism Homo sapiens
Experiment type Expression profiling by array
Summary Because of world-wide shortage of renal grafts, kidney transplantation (KTx) from donors after cardiac death (DCD) is an alternative way to KTx from brain-dead donors. Although the prognosis of DCD KTx is gradually improving, the graft often undergoes delayed graft function (DGF) rendering the control of DGF essential for post-KTx patient care. To know the etiology of the DGF, we performed genome-wide gene expression profiling using renal biopsy samples performed at 1 hour after KTx from DCD and compared the data with those of KTx from living donors (LD). A total of 526 genes were differentially expressed between them. Genes involved in acute inflammation were activated, while metabolic pathways were consistently down-regulated in DCD. All of these findings imply inferior performance of the DCD grafts relative to LD grafts. We identified several genes of which expression levels were correlated well with parameters indicating short- and long-term prognosis of the DCD patients. In addition, we identified several genes encoding secretory proteins that might reflect the performance of the graft and be potent non-invasive biomarkers. Our data provide good source for candidates of biomarker that are potentially useful for control of DGF.
Keywords: disease state analysis
 
Overall design This investigation was approved by the Institutional Review Boards of our centers. Written informed consent was obtained from each patient or legal guardian before enrollment. Consecutive patients undergoing either a living (n =15) or DCD KTx (n = 14) at this center were prospectively enrolled. The immunosuppressive regimen was similar in all patients, consisting of basiliximab, tacrolimus or cyclosporine with prednisone and mycophenolate mofetil. All kidney grafts were procured at this canter using in situ regional cooling technique from DCD. All donors after cardiac death from this hospital were classified as type IV in this study. The cause of donor death was cerebrovascular disease in all cases. Although most of those cases required HD (0-22 days) after KTx because of DGF, the function of all of transplanted kidneys eventually recovered. All kidney grafts from LD were procured by open nephrectomy in this study. All graft biopsies were performed one hour after reperfusion during kidney transplant operation using biopsy needles. All biopsy samples were stored immediately in RNA later (Applied Biosytems). Total cellular RNA was extracted from frozen samples using RNeasy (Qiagen, Valencia, CA, USA). For DNA microarray experiments, 200 ng aliquots of total RNA were labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, CA) according to the manufacturer'€™s instructions. RNA purified from each kidney graft was used for microarray analysis (Cy5-labeled), with pooled RNA derived from normal kidneys (Homan Kidney Total RNA #636529 BD, Franklin Lakes, NJ, USA) as a template control (Cy3-labeled). After checking the labeling efficiency, 1 ug aliquots of Cy3-labeled normal control RNA and Cy5-labeled RNA from individual grafts were mixed, and then hybridized to Agilent Human 1A (Ver. 2) Microarrays (Product No.G4110B) according to the manufacturer’s hybridization protocol. 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 2007 (Microsoft).
 
Citation(s) 20525436
Submission date Feb 07, 2008
Last update date Apr 06, 2015
Contact name Mamoru Kusaka
E-mail(s) mkusaka@fujita-hu.ac.jp
Phone 81-562-93-2181
Fax 81-562-93-7863
Organization name Fujita-Health University
Department Department of Urology
Street address 1-98 Kutsukake
City Toyoake
State/province Aichi
ZIP/Postal code 470-1192
Country Japan
 
Platforms (1)
GPL887 Agilent-012097 Human 1A Microarray (V2) G4110B (Feature Number version)
Samples (30)
GSM263590 1 hour biopsy sample of transplanted kidney from DCD 1 donor
GSM263591 1 hour biopsy sample of transplanted kidney from DCD 2 donor
GSM263592 1 hour biopsy sample of transplanted kidney from DCD 3 donor
Relations
BioProject PRJNA108067

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE10419_RAW.tar 3.3 Mb (http)(custom) TAR
Processed data included within Sample table
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