title: MicroRNA sequence profiles of human kidney allografts with or without tubulointerstitial fibrosis.
abstract: BACKGROUND
  MicroRNA (miRNA) alterations accompanying interstitial fibrosis and tubular atrophy (IFTA) in kidney allografts may point toward pathologic mechanisms. Small-RNA sequencing provides information on total miRNA abundance and specific miRNA expression and allows analysis of differential expression based on read counts.
  
  
  METHODS
  MiRNA expression profiles of 8 human kidney allograft biopsies (4 IFTA and 4 normal biopsies, discovery set) were characterized using barcoded deep-sequencing of a cDNA library prepared from multiplexed RNA. Statistical analysis of the sequence data guided selection of miRNAs for validation and the levels of selected miRNAs were quantified in 18 biopsies (10 IFTA and 8 normal) using real-time quantitative PCR assays (RT-QPCR).
  
  
  RESULTS
  Total miRNA content was 50% lower in RNA from IFTA compared with normal biopsies. Global miRNA profiles clustered in partial agreement with diagnosis. Several miRNAs, including miR-21, 142-3p, and 5p and the cluster comprising miR-506 on chromosome X had twofold to sevenfold higher expression in IFTA compared with normal biopsies, whereas miRNA miR-30b and 30c were lower in IFTA biopsies (miR-30a, -30d, -30e, and all respective star sequences showed similar trends). IFTA and normal biopsy distinction was also noted in the pattern of miRNA nucleotide sequence variations. Differentially expressed miRNAs were confirmed on the larger set of allograft biopsies using RT-QPCR, and the levels of miRNAs were found to be associated with allograft function and survival.
  
  
  CONCLUSIONS
  Differentially expressed miRNAs and their predicted targets identified by deep sequencing are candidates for further investigation to decipher the mechanism and management of kidney allograft fibrosis.
authors.affiliation: Howard Hughes Medical Institute, Laboratory for RNA Molecular Biology, The Rockefeller University, New York, NY, USA.
authors.forename: Iddo Z
authors.initials: IZ
authors.lastname: Ben-Dov
authors.forename: Thangamani
authors.initials: T
authors.lastname: Muthukumar
authors.forename: Pavel
authors.initials: P
authors.lastname: Morozov
authors.forename: Franco B
authors.initials: FB
authors.lastname: Mueller
authors.forename: Thomas
authors.initials: T
authors.lastname: Tuschl
authors.forename: Manikkam
authors.initials: M
authors.lastname: Suthanthiran
mesh_terms: D000328:Adult; D001284:Atrophy; D001706:Biopsy; D016022:Case-Control Studies; D016000:Cluster Analysis; D005260:Female; D005355:Fibrosis; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation; D005819:Genetic Markers; D006801:Humans; D007668:Kidney / Q000737:chemistry* / Q000473:pathology / Q000601:surgery*; D016030:Kidney Transplantation / Q000009:adverse effects*; D008297:Male; D035683:MicroRNAs / Q000032:analysis*; D008875:Middle Aged; D011183:Postoperative Complications / Q000235:genetics* / Q000473:pathology; D011379:Prognosis; D060888:Real-Time Polymerase Chain Reaction; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers; D035683:MicroRNAs