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Next-Generation Sequencing to Investigate Urinary microRNAs from Macaca fascicularis (Cynomolgus Monkey)

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Drug Safety Evaluation

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1641))

Abstract

Advanced sequencing technologies like next-generation sequencing (NGS) not only detect microRNAs (miRNAs) in biological samples but also facilitate de novo identification of miRNAs. Using an Ion Torrent’s Ion Proton System, here we described miRNAs sequencing of urine samples collected from Macaca fascicularis (Cynomolgus monkey) to investigate miRNAs as potential novel biomarkers of nephrotoxicity in this species. Urinary miRNA sequencing methodologies described here include (a) urinary exosomal RNA isolation, (b) sequencing library preparation, (c) sequencing template preparation, and (d) template library sequencing using Ion Proton System. The sequencing method presented in this study serves as a valuable resource in the identification of novel urinary miRNAs in M. fascicularis.

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References

  1. Mardis ER (2013) Next-generation sequencing platforms. Annu Rev Anal Chem (Palo Alto, Calif) 6:287–303. doi:10.1146/annurev-anchem-062012-092628

    Article  CAS  Google Scholar 

  2. Ansorge WJ (2009) Next-generation DNA sequencing techniques. New Biotechnol 25:195–203. doi:10.1016/j.nbt.2008.12.009

    Article  CAS  Google Scholar 

  3. Rothberg JM, Hinz W, Rearick TM et al (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475:348–352. doi:10.1038/nature10242

    Article  CAS  PubMed  Google Scholar 

  4. Merriman B, Torrent I, Rothberg JM (2012) Progress in ion torrent semiconductor chip based sequencing. Electrophoresis 33:3397–3417. doi:10.1002/elps.201200424

    Article  CAS  PubMed  Google Scholar 

  5. Ha M, Kim VN (2014) Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol 15:509–524. doi:10.1038/nrm3838

    Article  CAS  PubMed  Google Scholar 

  6. He L, Hannon GJ (2004) MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet 5:522–531. doi:10.1038/nrg1415

    Article  CAS  PubMed  Google Scholar 

  7. Iorio MV, Croce CM (2012) MicroRNA dysregulation in cancer: diagnostics, monitoring and therapeutics. A comprehensive review. EMBO Mol Med 4:143–159. doi:10.1002/emmm.201100209

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Sun Y, Koo S, White N et al (2004) Development of a micro-array to detect human and mouse microRNAs and characterization of expression in human organs. Nucleic Acids Res 32:e188. doi:10.1093/nar/gnh186

    Article  PubMed  PubMed Central  Google Scholar 

  9. Weber JA, Baxter DH, Zhang S et al (2010) The microRNA spectrum in 12 body fluids. Clin Chem 56:1733–1741. doi:10.1373/clinchem.2010.147405

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Hayes J, Peruzzi PP, Lawler S (2014) MicroRNAs in cancer: biomarkers, functions and therapy. Trends Mol Med 20:460–469. doi:10.1016/j.molmed.2014.06.005

    Article  CAS  PubMed  Google Scholar 

  11. D’Alessandra Y, Devanna P, Limana F et al (2010) Circulating microRNAs are new and sensitive biomarkers of myocardial infarction. Eur Heart J 31:2765–2773. doi:10.1093/eurheartj/ehq167

    Article  PubMed  PubMed Central  Google Scholar 

  12. Zeng L, Cui J, Wu H, Lu Q (2014) The emerging role of circulating microRNAs as biomarkers in autoimmune diseases. Autoimmunity 47:419–429. doi:10.3109/08916934.2014.929667

    Article  CAS  PubMed  Google Scholar 

  13. Kanki M, Moriguchi A, Sasaki D et al (2014) Identification of urinary miRNA biomarkers for detecting cisplatin-induced proximal tubular injury in rats. Toxicology 324:158–168. doi:10.1016/j.tox.2014.05.004

    Article  CAS  PubMed  Google Scholar 

  14. Nassirpour R, Mathur S, Gosink MM et al (2014) Identification of tubular injury microRNA biomarkers in urine: comparison of next-generation sequencing and qPCR-based profiling platforms. BMC Genomics 15:485. doi:10.1186/1471-2164-15-485

    Article  PubMed  PubMed Central  Google Scholar 

  15. Pritchard CC, Cheng HH, Tewari M (2012) MicroRNA profiling: approaches and considerations. Nat Rev Genet 13:358–369. doi:10.1038/nrg3198

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Li N, You X, Chen T et al (2013) Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery. Nucleic Acids Res 41:3619–3634. doi:10.1093/nar/gkt072

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Veeranagouda Y, Rival P, Prades C et al (2015) Identification of microRNAs in Macaca fascicularis (Cynomolgus monkey) by homology search and experimental validation by small RNA-Seq and RT-qPCR using kidney cortex tissues. PLoS One 10:e0142708. doi:10.1371/journal.pone.0142708

    Article  PubMed  PubMed Central  Google Scholar 

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Correspondence to Yaligara Veeranagouda .

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Veeranagouda, Y., Léonard, JF., Gautier, JC., Boitier, E. (2017). Next-Generation Sequencing to Investigate Urinary microRNAs from Macaca fascicularis (Cynomolgus Monkey). In: Gautier, JC. (eds) Drug Safety Evaluation. Methods in Molecular Biology, vol 1641. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7172-5_20

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  • DOI: https://doi.org/10.1007/978-1-4939-7172-5_20

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7170-1

  • Online ISBN: 978-1-4939-7172-5

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