title: New miRNA profiles accurately distinguish renal cell carcinomas and upper tract urothelial carcinomas from the normal kidney.
abstract: BACKGROUND
  Upper tract urothelial carcinomas (UT-UC) can invade the pelvicalyceal system making differential diagnosis of the various histologically distinct renal cell carcinoma (RCC) subtypes and UT-UC, difficult. Correct diagnosis is critical for determining appropriate surgery and post-surgical treatments. We aimed to identify microRNA (miRNA) signatures that can accurately distinguish the most prevalent RCC subtypes and UT-UC form the normal kidney.
  
  
  RESULTS
  miRNA profiling was performed on FFPE tissue sections from RCC and UT-UC and normal kidney and 434 miRNAs were significantly deregulated in cancerous vs. the normal tissue. Hierarchical clustering distinguished UT-UCs from RCCs and classified the various RCC subtypes among them. qRT-PCR validated the deregulated expression profile for the majority of the miRNAs and ROC analysis revealed their capability to discriminate between tumour and normal kidney. An independent cohort of freshly frozen RCC and UT-UC samples was used to validate the deregulated miRNAs with the best discriminatory ability (AUC>0.8, p<0.001). Many of them were located within cytogenetic regions that were previously reported to be significantly aberrated. miRNA targets were predicted using the miRWalk algorithm and ingenuity pathway analysis identified the canonical pathways and curated networks of the deregulated miRNAs. Using the miRWalk algorithm, we further identified the top anti-correlated mRNA/miRNA pairs, between the deregulated miRNAs from our study and the top co-deregulated mRNAs among 5 independent ccRCC GEO datasets. The AB8/13 undifferentiated podocyte cells were used for functional assays using luciferase reporter constructs and the developmental transcription factor TFCP2L1 was proved to be a true target of miR-489, which was the second most upregulated miRNA in ccRCC.
  
  
  CONCLUSIONS
  We identified novel miRNAs specific for each RCC subtype and UT-UC, we investigated their putative targets, the networks and pathways in which they participate and we functionally verified the true targets of the top deregulated miRNAs.
authors.affiliation: Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus. zaravinos.apostolos@ucy.ac.cy
authors.forename: Apostolos
authors.initials: A
authors.lastname: Zaravinos
authors.affiliation: Choremeio Research Laboratory, First Department of Pediatrics, University of Athens, Athens, Greece.
authors.forename: George I
authors.initials: GI
authors.lastname: Lambrou
authors.affiliation: Department of Urology, Asklipieio General Hospital, Athens, Greece.
authors.forename: Nikos
authors.initials: N
authors.lastname: Mourmouras
authors.affiliation: Department of Urology, Asklipieio General Hospital, Athens, Greece.
authors.forename: Patroklos
authors.initials: P
authors.lastname: Katafygiotis
authors.affiliation: Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus.
authors.forename: Gregory
authors.initials: G
authors.lastname: Papagregoriou
authors.affiliation: Department of Medical Genetics, Medical School, University of Athens, Athens, Greece.
authors.forename: Krinio
authors.initials: K
authors.lastname: Giannikou
authors.affiliation: Department of Urology, Asklipieio General Hospital, Athens, Greece.
authors.forename: Dimitris
authors.initials: D
authors.lastname: Delakas
authors.affiliation: Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus.
authors.forename: Constantinos
authors.initials: C
authors.lastname: Deltas
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002292:Carcinoma, Renal Cell / Q000235:genetics* / Q000473:pathology; D002869:Chromosome Aberrations; D015331:Cohort Studies; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D007668:Kidney / Q000166:cytology* / Q000378:metabolism / Q000473:pathology*; D007680:Kidney Neoplasms / Q000235:genetics* / Q000473:pathology; D008297:Male; D035683:MicroRNAs / Q000235:genetics*; D008875:Middle Aged; D019459:Urothelium / Q000378:metabolism*
chemical_list: D035683:MicroRNAs