RNA Sequencing Analysis of Salivary Extracellular RNA

Blanca Majem; Feng Li; Jie Sun; David T W Wong

doi:10.1007/978-1-4939-6685-1_2

RNA Sequencing Analysis of Salivary Extracellular RNA

Methods Mol Biol. 2017:1537:17-36. doi: 10.1007/978-1-4939-6685-1_2.

Authors

Blanca Majem¹, Feng Li², Jie Sun³, David T W Wong^{4

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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.
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.
³ Medical School of Shenzhen University, Shenzhen, Guangdong, China.
⁴ 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. [email protected].
⁵ Johnson Comprehensive Cancer Center, University of California Los Angeles (UCLA), Los Angeles, CA, USA. [email protected].
⁶ Molecular Biology Institute, University of California Los Angeles (UCLA), Los Angeles, CA, USA. [email protected].
⁷ Head & Neck Surgery/Otolaryngology, Henry Samuel School of Engineering and Applied Science, University of California Los Angeles (UCLA), Los Angeles, CA, 90095-1668, USA. [email protected].

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.

Keywords: Biomarkers; RNA sequencing; Saliva; Small and long ncRNA profiling; exRNAs.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Biomarkers
DNA Barcoding, Taxonomic
Gene Library
High-Throughput Nucleotide Sequencing
Humans
Liquid Biopsy
RNA / genetics*
RNA / isolation & purification
RNA, Long Noncoding
RNA, Small Untranslated
Saliva / metabolism*
Sequence Analysis, RNA*

Substances

Biomarkers
RNA, Long Noncoding
RNA, Small Untranslated
RNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding