Advertisement

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

  • Yaligara VeeranagoudaEmail author
  • Jean-François Léonard
  • Jean-Charles Gautier
  • Eric Boitier
Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

Next-Generation Sequencing microRNAs Ion Torrent Cynomolgus monkey Urine Biomarkers Kidney 

References

  1. 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 CrossRefGoogle Scholar
  2. 2.
    Ansorge WJ (2009) Next-generation DNA sequencing techniques. New Biotechnol 25:195–203. doi: 10.1016/j.nbt.2008.12.009 CrossRefGoogle Scholar
  3. 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 CrossRefPubMedGoogle Scholar
  4. 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 CrossRefPubMedGoogle Scholar
  5. 5.
    Ha M, Kim VN (2014) Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol 15:509–524. doi: 10.1038/nrm3838 CrossRefPubMedGoogle Scholar
  6. 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 CrossRefPubMedGoogle Scholar
  7. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  8. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  9. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  10. 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 CrossRefPubMedGoogle Scholar
  11. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  12. 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 CrossRefPubMedGoogle Scholar
  13. 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 CrossRefPubMedGoogle Scholar
  14. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Pritchard CC, Cheng HH, Tewari M (2012) MicroRNA profiling: approaches and considerations. Nat Rev Genet 13:358–369. doi: 10.1038/nrg3198 CrossRefPubMedPubMedCentralGoogle Scholar
  16. 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 CrossRefPubMedPubMedCentralGoogle Scholar
  17. 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 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Yaligara Veeranagouda
    • 1
    Email author
  • Jean-François Léonard
    • 2
  • Jean-Charles Gautier
    • 3
  • Eric Boitier
    • 2
  1. 1.Molecular Biology & Genomics, Translational ScienceSanofi R&DChilly-MazarinFrance
  2. 2.Translational Medicine and Early Development, Biomarkers and Clinical Bioanalyses—GenomicsSanofi R&DVitry-sur-SeineFrance
  3. 3.Preclinical SafetySanofi, R&DVitry-sur-SeineFrance

Personalised recommendations