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Series GSE89652 Query DataSets for GSE89652
Status Public on Sep 01, 2017
Title Specific normalization of urinary mRNAs reveals genome-wide patterns associated with renal allograft subclinical injury
Organism Homo sapiens
Experiment type Expression profiling by array
Summary urinary mRNA quantification using an Agilent 60k microarray in 26 stable kidney transplant patients with or without renal partial Epithelial to Mesenchymal Transition
Subclinical pathological features on the 3-month biopsy of renal allografts predict a poor prognosis, but it is unclear whether surveillance biopsies are beneficial. Non-invasive biomarkers are wanted, and urinary pellet RNA quantification of selected candidate genes has been used with some success do detect overt rejection. We performed a mRNA microarray study using different normalization methods on the urinary cell pellet to evaluate the feasibility of using urine to detect renal partial epithelial mesenchymal transition of the renal allograft (renal pEMT) non-invasively in a group of 26 stable transplanted patients. We found that, when using a novel method of normalization by Upk1a mRNA, renal pEMT of the renal allograft was associated in urine with differential expression of genes belonging to predefined gene sets of kidney-expressed genes and epithelial mesenchymal transition genes. An unbiased pathway analysis revealed that the immune response was the main urinary biological process associated with pEMT in the kidney. In urine from patients with pristine biopsies, pEMT was not associated with inflammation, but with reduced metabolic functions. Thus, we show that pEMT translates into specific UPK1a-normalized mRNA patterns in urine and use genome-wide analyses to characterize underlying molecular patterns, i.e. increased inflammation and decreased metabolic functions.
Overall design 12 pateins without renal partial Epithelial to Mesenchymal Transition and 14 patients with renal partial Epithelial to Mesenchymal Transition
Contributor(s) Galichon P
Citation(s) 29697267
Submission date Nov 08, 2016
Last update date Nov 27, 2018
Contact name Pierre Galichon
Phone +33685717580
Organization name Assistance Publique - Hopitaux de Paris
Department Hopital Tenon - Urgences Nephrologiques et Transplantation Renale
Street address 4 rue de la Chine
City Paris
ZIP/Postal code 75020
Country France
Platforms (1)
GPL13607 Agilent-028004 SurePrint G3 Human GE 8x60K Microarray (Feature Number version)
Samples (26)
GSM2386106 urine_pEMTneg_1
GSM2386107 urine_pEMTneg_2
GSM2386108 urine_pEMTneg_3
BioProject PRJNA352832

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE89652_RAW.tar 321.2 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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