RNA Sequencing Analysis of Salivary Extracellular RNA

Overview

Journal Methods Mol Biol

Specialty Molecular Biology

Date 2016 Dec 8

PMID 27924586

Citations 7

Authors

Blanca Majem

Feng Li

Jie Sun

David T W Wong

Affiliations

Soon will be listed here.

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.

Citing Articles

Ultrasensitive Detection of MicroRNA in Human Saliva via Rolling Circle Amplification Using a DNA-Decorated Graphene Oxide Sensor.

Pitikultham P, Putnin T, Pimalai D, Sathirapongsasuti N, Kitiyakara C, Jiang Q ACS Omega. 2023; 8(17):15266-15275.

PMID: 37151566 PMC: 10157686. DOI: 10.1021/acsomega.3c00411.

Downregulated Circulating Long Non-coding RNA GAS6-AS1 Screens and Predicts Acute Myocardial Infarction.

Wang Z, Zhang M, Fu Y Anatol J Cardiol. 2023; 27(3):167-172.

PMID: 36856591 PMC: 9995557. DOI: 10.14744/AnatolJCardiol.2022.2496.

Examining potential confounding factors in gene expression analysis of human saliva and identifying potential housekeeping genes.

Ostheim P, Alemu S, Tichy A, Sirak I, Davidkova M, Stastna M Sci Rep. 2022; 12(1):2312.

PMID: 35145126 PMC: 8831573. DOI: 10.1038/s41598-022-05670-5.

Technical and Methodological Aspects of Cell-Free Nucleic Acids Analyzes.

Pos Z, Pos O, Styk J, Mocova A, Strieskova L, Budis J Int J Mol Sci. 2020; 21(22).

PMID: 33207777 PMC: 7697251. DOI: 10.3390/ijms21228634.

exceRpt: A Comprehensive Analytic Platform for Extracellular RNA Profiling.

Rozowsky J, Kitchen R, Park J, Galeev T, Diao J, Warrell J Cell Syst. 2019; 8(4):352-357.e3.

PMID: 30956140 PMC: 7079576. DOI: 10.1016/j.cels.2019.03.004.

References

Halicka H, Bedner E, Darzynkiewicz Z . Segregation of RNA and separate packaging of DNA and RNA in apoptotic bodies during apoptosis. Exp Cell Res. 2000; 260(2):248-56. DOI: 10.1006/excr.2000.5027. View

Rosi A, Guidoni L, Luciani A, Mariutti G, Viti V . RNA-lipid complexes released from the plasma membrane of human colon carcinoma cells. Cancer Lett. 1988; 39(2):153-60. DOI: 10.1016/0304-3835(88)90100-0. View

Hu Z, Zimmermann B, Zhou H, Wang J, Henson B, Yu W . Exon-level expression profiling: a comprehensive transcriptome analysis of oral fluids. Clin Chem. 2008; 54(5):824-32. PMC: 2799536. DOI: 10.1373/clinchem.2007.096164. View

Whitelegge J, Zabrouskov V, Halgand F, Souda P, Bassilian S, Yan W . 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. 2008; 268(2-3):190-197. PMC: 2131703. DOI: 10.1016/j.ijms.2007.08.008. View

Bahn J, Zhang Q, Li F, Chan T, Lin X, Kim Y . The landscape of microRNA, Piwi-interacting RNA, and circular RNA in human saliva. Clin Chem. 2014; 61(1):221-30. PMC: 4332885. DOI: 10.1373/clinchem.2014.230433. View

Li Y, St John M, Zhou X, Kim Y, Sinha U, Jordan R . Salivary transcriptome diagnostics for oral cancer detection. Clin Cancer Res. 2004; 10(24):8442-50. DOI: 10.1158/1078-0432.CCR-04-1167. View

Juusola J, Ballantyne J . mRNA profiling for body fluid identification by multiplex quantitative RT-PCR. J Forensic Sci. 2007; 52(6):1252-62. DOI: 10.1111/j.1556-4029.2007.00550.x. View

Park N, Li Y, Yu T, Brinkman B, Wong D . Characterization of RNA in saliva. Clin Chem. 2006; 52(6):988-94. PMC: 7108156. DOI: 10.1373/clinchem.2005.063206. View

Laurent L, Abdel-Mageed A, Adelson P, Arango J, Balaj L, Breakefield X . Meeting report: discussions and preliminary findings on extracellular RNA measurement methods from laboratories in the NIH Extracellular RNA Communication Consortium. J Extracell Vesicles. 2015; 4:26533. PMC: 4553263. DOI: 10.3402/jev.v4.26533. View

10.

Navazesh M . Methods for collecting saliva. Ann N Y Acad Sci. 1993; 694:72-7. DOI: 10.1111/j.1749-6632.1993.tb18343.x. View

11.

Spielmann N, Ilsley D, Gu J, Lea K, Brockman J, Heater S . The human salivary RNA transcriptome revealed by massively parallel sequencing. Clin Chem. 2012; 58(9):1314-21. DOI: 10.1373/clinchem.2011.176941. View

12.

Majem B, Rigau M, Reventos J, Wong D . Non-coding RNAs in saliva: emerging biomarkers for molecular diagnostics. Int J Mol Sci. 2015; 16(4):8676-98. PMC: 4425103. DOI: 10.3390/ijms16048676. View

13.

Li Y, Zhou X, St John M, Wong D . RNA profiling of cell-free saliva using microarray technology. J Dent Res. 2004; 83(3):199-203. DOI: 10.1177/154405910408300303. View

14.

Park N, Zhou X, Yu T, Brinkman B, Zimmermann B, Palanisamy V . Characterization of salivary RNA by cDNA library analysis. Arch Oral Biol. 2006; 52(1):30-5. PMC: 2743855. DOI: 10.1016/j.archoralbio.2006.08.014. View

15.

Juusola J, Ballantyne J . Multiplex mRNA profiling for the identification of body fluids. Forensic Sci Int. 2005; 152(1):1-12. DOI: 10.1016/j.forsciint.2005.02.020. View