Saliva Cited as Reservoir of Diagnostically Valuable RNA Species

Saliva has been shown to be a source for several classes of RNA molecules that can provide genomic information, which can be used to diagnose both chronic and acute diseases.

A recent study showed that despite the presence of proteolytic enzymes and other potentially degrading substances, saliva contains several classes of diagnostically valuable RNA molecules including microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and circular RNAs (circRNAs).

MicroRNAs are snippets of about 20 nucleotides that block gene expression by attaching to molecules of messenger RNA (mRNA) in a fashion that prevents them from transmitting the protein synthesizing instructions they had received from the DNA. Circular RNA (or circRNA), unlike linear RNA, forms a covalently closed continuous loop with the 3' and 5' ends normally present in an RNA molecule joined together. This feature confers numerous properties to circular RNAs, many of which have only recently been identified. While many circular RNAs arise from otherwise protein coding genes, circular RNAs have not been shown to code for proteins and have, therefore, been categorized as noncoding RNA. Piwi-interacting RNA (piRNA) is the largest class of small non-coding RNA molecules expressed in animal cells. piRNAs form RNA-protein complexes through interactions with piwi proteins. These piRNA complexes have been linked to both epigenetic and post-transcriptional gene silencing particularly those in spermatogenesis. They are distinct from microRNA in size (26–31 nucleotides rather than 21–24 nucleotides), lack of sequence conservation, and increased complexity.

To establish the usefulness of saliva samples for obtaining diagnostically useful genetic material, investigators at the University of California, Los Angeles (USA) used high-throughput RNA sequencing (RNA-Seq) to conduct an in-depth bioinformatic analysis of noncoding RNAs (ncRNAs) in human cell-free saliva (CFS) from healthy individuals.

They reported finding robust reproducibility of miRNA and piRNA profiles across individuals. Furthermore, individual variability of these salivary RNA species was highly similar to those in other body fluids or cellular samples, despite the direct exposure of saliva to potentially destabilizing agents in the environment. By comparative analysis of more than 90 RNA-Seq datasets of different origins, they observed that piRNAs were surprisingly abundant in CFS compared with other body fluid or intracellular samples, with expression levels in CFS comparable to those found in embryonic stem cells and skin cells. Conversely, miRNA expression profiles in CFS were highly similar to those in serum and cerebrospinal fluid. Finally, using a customized bioinformatics method, they identified more than 400 circRNAs in CFS.

"Saliva carries with it non-coding RNAs, microRNAs, piRNAs, and circRNAs that are biomarkers for disease and health monitoring," said contributing author Dr. David Wong, professor of dentistry at the University of California, Los Angeles. "Now we have the capability and technology to reach deeper and study non-coding RNA, which has never been done. If we can define the boundaries of molecular targets in saliva, then we can ask what the constituents in saliva are that can mark someone who has pre-diabetes or the early stages of oral cancer or pancreatic cancer — and we can utilize this knowledge for personalized medicine."

The study was published in the November 6, 2014, online edition of the journal Clinical Chemistry.

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University of California, Los Angeles