Skip to main content
SpringerLink
Log in

RNA Sequencing Analysis of Salivary Extracellular RNA

  • Protocol
  • First Online:
Oral Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1537))

Abstract

Salivary biomarkers for disease detection, diagnostic and prognostic assessments have become increasingly well established in recent years. In this chapter we explain the current leading technology that has been used to characterize salivary non-coding RNAs (ncRNAs) from the extracellular RNA (exRNA) fraction: HiSeq from Illumina® platform for RNA sequencing. Therefore, the chapter is divided into two main sections regarding the type of the library constructed (small and long ncRNA libraries), from saliva collection, RNA extraction and quantification to cDNA library generation and corresponding QCs. Using these invaluable technical tools, one can identify thousands of ncRNA species in saliva. These methods indicate that salivary exRNA provides an efficient medium for biomarker discovery of oral and systemic diseases.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Hu Z, Zimmermann BG, Zhou H, Wang J, Henson BS, Yu W, Elashoff D, Krupp G, Wong DTW (2008) Exon-level expression profiling: a comprehensive transcriptome analysis of oral fluids. Clin Chem 54:824–832

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Li Y, Zhou X, St John MAR, Wong DTW (2004) RNA profiling of cell-free saliva using microarray technology. J Dent Res 83:199–203

    Article  CAS  PubMed  Google Scholar 

  3. Li Y, St John MA, Zhou X, Kim Y, Sinha U, Jordan RC, Eisele D, Abemayor E, Elashoff D, Park NH, Wong DTW (2004) Salivary transcriptome diagnostics for oral cancer detection. Clin Cancer Res 10:8442–8450

    Article  CAS  PubMed  Google Scholar 

  4. Juusola J, Ballantyne J (2005) Multiplex mRNA profiling for the identification of body fluids. Forensic Sci Int 152:1–12

    Article  CAS  PubMed  Google Scholar 

  5. Juusola J, Ballantyne J (2007) mRNA profiling for body fluid identification by multiplex quantitative RT-PCR. J Forensic Sci 52:1252–1262

    CAS  PubMed  Google Scholar 

  6. Park NJ, Li Y, Yu T, Brinkman BMN, Wong DTW (2006) Characterization of RNA in saliva. Clin Chem 52:988–994

    Article  CAS  PubMed  Google Scholar 

  7. Rosi A, Guidoni L, Luciani AM, Mariutti G, Viti V (1988) RNA-lipid complexes released from the plasma membrane of human colon carcinoma cells. Cancer Lett 39:153–160

    Article  CAS  PubMed  Google Scholar 

  8. Whitelegge JP, Zabrouskov V, Halgand F, Souda P, Bassilian S, Yan W, Wolinsky L, Loo JA, Wong DTW, Faull KF (2007) Protein-sequence polymorphisms and post-translational modifications in proteins from human saliva using top-down Fourier-transform ion cyclotron resonance mass spectrometry. Int J Mass Spectrom 268:190–197

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Halicka HD, Bedner E, Darzynkiewicz Z (2000) Segregation of RNA and separate packaging of DNA and RNA in apoptotic bodies during apoptosis. Exp Cell Res 260:248–256

    Article  CAS  PubMed  Google Scholar 

  10. Park NJ, Zhou X, Yu T, Brinkman BM, Zimmermann BG, Palanisamy V, Wong DTW (2007) Characterization of salivary RNA by cDNA library analysis. Arch Oral Biol 52:30–35

    Article  CAS  PubMed  Google Scholar 

  11. Spielmann N, Ilsley D, Gu J, Lea K, Brockman J, Heater S, Setterquist R, Wong DTW (2012) The human salivary RNA transcriptome revealed by massively parallel sequencing. Clin Chem 58:1314–1321

    Article  CAS  PubMed  Google Scholar 

  12. Bahn JH, Zhang Q, Li F, Chan TM, Lin X, Kim Y, Wong DTW, Xiao X (2014) The landscape of microRNA, Piwi-interacting RNA, and circular RNA in human saliva. Clin Chem 61:221–230

    Article  PubMed  PubMed Central  Google Scholar 

  13. Majem B, Rigau M, Reventós J, Wong DTW (2015) Non-coding RNAs in saliva: emerging biomarkers for molecular diagnostics. Int J Mol Sci 16:8676–8698

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Navazesh M (1993) Methods for collecting saliva. Ann NY Acad Sci 694:72–77

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by National Institutes of Health grant (UH2/UH3 TR000923). We thank Kai Kao, Leo lee, and Hui Zhou for technical suggestions.

Conflict of Interests

 David Wong is cofounder of RNAmeTRIX Inc., a molecular diagnostic company. He holds equity in RNAmeTRIX, and serves as Scientific Advisor. The University of California also holds equity in RNAmeTRIX. Intellectual property that David Wong invented and which was patented by the University of California has been licensed to RNAmeTRIX.

Author information

Authors and Affiliations

  1. Biomedical Research Unit in Gynecology, Laboratory 209, Collserola Building, Vall Hebron Research Institute (VHIR) and University Hospital, University Autonoma of Barcelona (UAB), Pg. Vall Hebron 119-129, 08035, Barcelona, Spain

    Blanca Majem

  2. Division of Oral Biology and Oral Medicine, School of Dentistry, University of California Los Angeles (UCLA), 10833 Le Conte Avenue, Los Angeles, CA, 90095, USA

    Feng Li & David T. W. Wong

  3. Medical School of Shenzhen University, Shenzhen, Guangdong, China

    Jie Sun

  4. Johnson Comprehensive Cancer Center, University of California Los Angeles (UCLA), Los Angeles, CA, USA

    David T. W. Wong

  5. Molecular Biology Institute, University of California Los Angeles (UCLA), Los Angeles, CA, USA

    David T. W. Wong

  6. Head & Neck Surgery/Otolaryngology, Henry Samuel School of Engineering and Applied Science, University of California Los Angeles (UCLA), Los Angeles, CA, 90095-1668, USA

    David T. W. Wong

Authors
  1. Blanca Majem
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Feng Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jie Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. David T. W. Wong
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to David T. W. Wong .

Editor information

Editors and Affiliations

  1. University of Otago Fac. Dentistry, Dunedin, New Zealand

    Gregory J. Seymour

  2. Department of Oral Sciences, University of Otago Faculty of Dentistry, Dunedin, New Zealand

    Mary P. Cullinan

  3. Sir John Walsh Research Institute, University of Otago Faculty of Dentistry, Dunedin, New Zealand

    Nicholas C.K. Heng

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Majem, B., Li, F., Sun, J., Wong, D.T.W. (2017). RNA Sequencing Analysis of Salivary Extracellular RNA. In: Seymour, G., Cullinan, M., Heng, N. (eds) Oral Biology. Methods in Molecular Biology, vol 1537. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6685-1_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-6685-1_2

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6683-7

  • Online ISBN: 978-1-4939-6685-1

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation