Open Access Research article

Identification of tubular injury microRNA biomarkers in urine: comparison of next-generation sequencing and qPCR-based profiling platforms

Rounak Nassirpour1, Sachin Mathur2, Mark M Gosink3, Yizheng Li2, Ahmed M Shoieb3, Joanna Wood4, Shawn P O’Neil1, Bruce L Homer1 and Laurence O Whiteley15*

Author Affiliations

1 Drug Safety, Pfizer Worldwide Research and Development, 1 Burtt Rd, Andover, MA 01810, USA

2 Business Technology, Pfizer Research and Development, Burtt Rd, Andover, MA 01810, USA

3 Drug Safety, Pfizer Research and Development, MS 8274 E. Point Road, Groton, CT 06340, USA

4 Quintiles Drug Research Unit at Guy’s Hospital, 6 Newcomen St, London SE1 1YR, UK

5 200 Cambridge Park, Cambridge, MA 01810, USA

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BMC Genomics 2014, 15:485  doi:10.1186/1471-2164-15-485

Published: 18 June 2014

Abstract

Background

MicroRNAs (miRNAs) are small, non-coding RNAs that regulate protein levels post-transcriptionally. miRNAs play important regulatory roles in many cellular processes and have been implicated in several diseases. Recent studies have reported significant levels of miRNAs in a variety of body fluids, raising the possibility that miRNAs could serve as useful biomarkers. Next-generation sequencing (NGS) is increasingly employed in biomedical investigations. Although concordance between this platform and qRT-PCR based assays has been reported in high quality specimens, information is lacking on comparisons in biofluids especially urine. Here we describe the changes in miRNA expression patterns in a rodent model of renal tubular injury (gentamicin). Our aim is to compare RNA sequencing and qPCR based miRNA profiling in urine specimen from control and rats with confirmed tubular injury.

Results

Our preliminary examination of the concordance between miRNA-seq and qRT-PCR in urine specimen suggests minimal agreement between platforms probably due to the differences in sensitivity. Our results suggest that although miRNA-seq has superior specificity, it may not detect low abundant miRNAs in urine samples. Specifically, miRNA-seq did not detect some sequences which were identified by qRT-PCR. On the other hand, the qRT-PCR analysis was not able to detect the miRNA isoforms, which made up the majority of miRNA changes detected by NGS.

Conclusions

To our knowledge, this is the first time that miRNA profiling platforms including NGS have been compared in urine specimen. miRNAs identified by both platforms, let-7d, miR-203, and miR-320, may potentially serve as promising novel urinary biomarkers for drug induced renal tubular epithelial injury.

Keywords:
Next-generation sequencing; NGS; Small RNA; TruSeq; qRT-PCR; Urine; miRNA; Gentamicin; Kidney injury