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

BMC Genomics

Laurence O Whiteley⁵  Bruce L Homer⁴  Shawn P O’Neil⁴  Joanna Wood¹  Ahmed M Shoieb³  Yizheng Li²  Mark M Gosink³  Sachin Mathur²  Rounak Nassirpour⁴ 

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

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

[5]200 Cambridge Park, Cambridge, MA 01810, USA

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

Others  :  1216577
DOI  :  10.1186/1471-2164-15-485

 received in 2013-12-01, accepted in 2014-06-09,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Nassirpour et al.; licensee BioMed Central Ltd.

【 图 表 】

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