Identification of microRNA biomarker candidates in urine and plasma from rats with kidney or liver damage

MicroRNAs (miRNA) are short single‐stranded RNA sequences that have a role in the post‐transcriptional regulation of genes. The identification of tissue specific or enriched miRNAs has great potential as novel safety biomarkers. One longstanding goal is to associate the increase of miRNA in biofluids (e.g., plasma and urine) with tissue‐specific damage. Next‐generation sequencing (miR‐seq) was used to analyze changes in miRNA profiles of tissue, plasma and urine samples of rats treated with either a nephrotoxicant (cisplatin) or one of two hepatotoxicants (acetaminophen [APAP] or carbon tetrachloride [CCL4]). Analyses with traditional serum chemistry and histopathology confirmed that toxicant‐induced organ damage was specific. In animals treated with cisplatin, levels of five miRNAs were significantly altered in the kidney, 14 in plasma and six in urine. In APAP‐treated animals, five miRNAs were altered in the liver, 74 in plasma and six in urine; for CCL4 the changes were five, 20 and 6, respectively. Cisplatin treatment caused an elevation of miR‐378a in the urine, confirming the findings of other similar studies. There were 17 in common miRNAs elevated in the plasma after treatment with either APAP or CCL4. Four of these (miR‐122, −802, −31a and −365) are known to be enriched in the livers of rats. Interestingly, the increase of serum miR‐802 in both hepatotoxicant treatments was comparable to that of the well‐known liver damage marker miR‐122. Taken together, comparative analysis of urine and plasma miRNAs demonstrated their utility as biomarkers of organ injury. Copyright © 2016 The Authors. Journal of Applied Toxicology published by John Wiley & Sons Ltd.

[1]  J. Bonventre,et al.  Kidney Injury Molecule-1 (KIM-1): a novel biomarker for human renal proximal tubule injury. , 2002, Kidney international.

[2]  J. She,et al.  MicroRNA-34a Is Induced via p53 during Cisplatin Nephrotoxicity and Contributes to Cell Survival , 2010, Molecular medicine.

[3]  P. Watkins,et al.  Beyond miR-122: Identification of MicroRNA Alterations in Blood During a Time Course of Hepatobiliary Injury and Biliary Hyperplasia in Rats. , 2016, Toxicological sciences : an official journal of the Society of Toxicology.

[4]  Pierre R. Bushel,et al.  The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog , 2016, BMC Genomics.

[5]  J. Ozer,et al.  The current state of serum biomarkers of hepatotoxicity. , 2008, Toxicology.

[6]  Jonathan Moggs,et al.  Circulating microRNAs as potential markers of human drug‐induced liver injury , 2011, Hepatology.

[7]  A. Poprach,et al.  Circulating miR-378 and miR-451 in serum are potential biomarkers for renal cell carcinoma , 2012, Journal of Translational Medicine.

[8]  T. Blondal,et al.  Assessing sample and miRNA profile quality in serum and plasma or other biofluids. , 2013, Methods.

[9]  Jessica A. Weber,et al.  The microRNA spectrum in 12 body fluids. , 2010, Clinical chemistry.

[10]  X. Yi,et al.  Deep sequencing analysis of microRNA expression in porcine serum-induced hepatic fibrosis rats. , 2014, Annals of hepatology.

[11]  L. Hood,et al.  Circulating microRNAs, potential biomarkers for drug-induced liver injury , 2009, Proceedings of the National Academy of Sciences.

[12]  Yong Liu,et al.  MicroRNAs contribute to the maintenance of cell-type-specific physiological characteristics: miR-192 targets Na+/K+-ATPase β1 , 2012, Nucleic acids research.

[13]  F. Wang,et al.  The Regulatory Roles of MicroRNA-146b-5p and Its Target Platelet-derived Growth Factor Receptor α (PDGFRA) in Erythropoiesis and Megakaryocytopoiesis* , 2014, The Journal of Biological Chemistry.

[14]  Inyoul Lee,et al.  Extracellular microRNA: a new source of biomarkers. , 2011, Mutation research.

[15]  H. Cathro,et al.  The urine microRNA profile may help monitor post-transplant renal graft function , 2013, Kidney international.

[16]  K. Tsuneyama,et al.  Plasma MicroRNA Profiles in Rat Models of Hepatocellular Injury, Cholestasis, and Steatosis , 2012, PloS one.

[17]  S. Tirrell,et al.  The beagle dog MicroRNA tissue atlas: identifying translatable biomarkers of organ toxicity , 2016, BMC Genomics.

[18]  F. Speleman,et al.  Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes , 2002, Genome Biology.

[19]  V. Jung,et al.  Analysis of serum microRNAs (miR-26a-2*, miR-191, miR-337-3p and miR-378) as potential biomarkers in renal cell carcinoma. , 2012, Cancer epidemiology.

[20]  O. Ichii,et al.  MicroRNA expression profiling of cat and dog kidneys. , 2014, Research in veterinary science.

[21]  J. Ward,et al.  Proliferative and Nonproliferative Lesions of the Rat and Mouse Hepatobiliary System , 2010, Toxicologic pathology.

[22]  A. Unami,et al.  Identification of urinary miRNA biomarkers for detecting cisplatin-induced proximal tubular injury in rats. , 2014, Toxicology.

[23]  Lin He,et al.  MicroRNAs: small RNAs with a big role in gene regulation , 2004, Nature Reviews Genetics.

[24]  M. Pavkovic,et al.  Urinary microRNA profiling for identification of biomarkers after cisplatin-induced kidney injury. , 2014, Toxicology.

[25]  Christopher J. Nelson,et al.  Advantages of next-generation sequencing versus the microarray in epigenetic research. , 2009, Briefings in functional genomics & proteomics.

[26]  X. Chen,et al.  A panel of five serum miRNAs as a potential diagnostic tool for early-stage renal cell carcinoma , 2015, Scientific Reports.

[27]  P. Tassone,et al.  Mir-34: A New Weapon Against Cancer? , 2014, Molecular therapy. Nucleic acids.

[28]  Toby C. Cornish,et al.  A Critical Evaluation of microRNA Biomarkers in Non-Neoplastic Disease , 2014, PloS one.

[29]  Katherine E. Hill,et al.  Next-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: preliminary assessment of cross-platform concordance. , 2013, Genomics.

[30]  Ana Kozomara,et al.  miRBase: annotating high confidence microRNAs using deep sequencing data , 2013, Nucleic Acids Res..

[31]  H. Yamada,et al.  miRNA expression atlas in male rat , 2014, Scientific Data.

[32]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[33]  Steven A. Bailey,et al.  Identification of Promising Urinary MicroRNA Biomarkers in Two Rat Models of Glomerular Injury. , 2015, Toxicological sciences : an official journal of the Society of Toxicology.

[34]  I. Kubota,et al.  A microarray analysis of urinary microRNAs in renal diseases , 2014, Clinical and Experimental Nephrology.

[35]  Paul Bertone,et al.  Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. , 2010, RNA.

[36]  A. Nishikawa,et al.  Proliferative and Nonproliferative Lesions of the Rat and Mouse Urinary System , 2012, Toxicologic pathology.

[37]  K. Tsuneyama,et al.  Changes in the expression of miRNAs at the pericentral and periportal regions of the rat liver in response to hepatocellular injury: comparison with the changes in the expression of plasma miRNAs. , 2014, Toxicology.

[38]  F. Qian,et al.  Identification of urinary microRNA profiles in rats that may diagnose hepatotoxicity. , 2012, Toxicological sciences : an official journal of the Society of Toxicology.

[39]  X. Chen,et al.  A Panel of Serum MicroRNAs as Specific Biomarkers for Diagnosis of Compound- and Herb-Induced Liver Injury in Rats , 2012, PloS one.

[40]  P. Watkins,et al.  Liver biomarker and in vitro assessment confirm the hepatic origin of aminotransferase elevations lacking histopathological correlate in beagle dogs treated with GABAA receptor antagonist NP260. , 2014, Toxicology and applied pharmacology.

[41]  Rounak Nassirpour,et al.  Identification of tubular injury microRNA biomarkers in urine: comparison of next-generation sequencing and qPCR-based profiling platforms , 2014, BMC Genomics.