Identification of urinary exosomal noncoding RNAs as novel biomarkers in chronic kidney disease

RNA. 2017 Feb;23(2):142-152. doi: 10.1261/rna.058834.116. Epub 2016 Nov 21.


In chronic kidney disease (CKD), the decline in the glomerular filtration rate is associated with increased morbidity and mortality and thus poses a major challenge for healthcare systems. While the contribution of tissue-derived miRNAs and mRNAs to CKD progression has been extensively studied, little is known about the role of urinary exosomes and their association with CKD. Exosomes are small, membrane-derived endocytic vesicles that contribute to cell-to-cell communication and are present in various body fluids, such as blood or urine. Next-generation sequencing approaches have revealed that exosomes are enriched in noncoding RNAs and thus exhibit great potential for sensitive nucleic acid biomarkers in various human diseases. Therefore, in this study we aimed to identify urinary exosomal ncRNAs as novel biomarkers for diagnosis of CKD. Since up to now most approaches have focused on the class of miRNAs, we extended our analysis to several other noncoding RNA classes, such as tRNAs, tRNA fragments (tRFs), mitochondrial tRNAs, or lincRNAs. For their computational identification from RNA-seq data, we developed a novel computational pipeline, designated as ncRNASeqScan. By these analyses, in CKD patients we identified 30 differentially expressed ncRNAs, derived from urinary exosomes, as suitable biomarkers for early diagnosis. Thereby, miRNA-181a appeared as the most robust and stable potential biomarker, being significantly decreased by about 200-fold in exosomes of CKD patients compared to healthy controls. Using a cell culture system for CKD indicated that urinary exosomes might indeed originate from renal proximal tubular epithelial cells.

Keywords: chronic kidney disease; lincRNAs; miRNAs; ncRNAs; sequencing; tRFs; tRNAs; urinary exosomes.

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • Biomarkers / urine
  • Case-Control Studies
  • Early Diagnosis
  • Epithelial Cells / metabolism*
  • Epithelial Cells / pathology
  • Exosomes / chemistry*
  • Exosomes / metabolism
  • Female
  • Glomerular Filtration Rate
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Kidney Tubules, Proximal / metabolism*
  • Kidney Tubules, Proximal / pathology
  • Male
  • MicroRNAs / urine*
  • Middle Aged
  • Molecular Sequence Annotation
  • RNA / urine
  • RNA, Long Noncoding / urine
  • RNA, Mitochondrial
  • RNA, Transfer / urine
  • Renal Insufficiency, Chronic / diagnosis*
  • Renal Insufficiency, Chronic / pathology
  • Renal Insufficiency, Chronic / urine
  • Sequence Analysis, RNA
  • Severity of Illness Index


  • Biomarkers
  • MIrn181 microRNA, human
  • MicroRNAs
  • RNA, Long Noncoding
  • RNA, Mitochondrial
  • RNA
  • RNA, Transfer