The landscape of microRNA, Piwi-interacting RNA, and circular RNA in human saliva.
BACKGROUND
Extracellular RNAs (exRNAs) in human body fluids are emerging as effective biomarkers for detection of diseases. Saliva, as the most accessible and noninvasive body fluid, has been shown to harbor exRNA biomarkers for several human diseases. However, the entire spectrum of exRNA from saliva has not been fully characterized.


METHODS
Using high-throughput RNA sequencing (RNA-Seq), we conducted an in-depth bioinformatic analysis of noncoding RNAs (ncRNAs) in human cell-free saliva (CFS) from healthy individuals, with a focus on microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), and circular RNAs (circRNAs).


RESULTS
Our data demonstrated 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 environmental impacts. By comparative analysis of >90 RNA-Seq data sets of different origins, we 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. Using a customized bioinformatics method, we identified >400 circRNAs in CFS. These data represent the first global characterization and experimental validation of circRNAs in any type of extracellular body fluid.


CONCLUSIONS
Our study provides a comprehensive landscape of ncRNA species in human saliva that will facilitate further biomarker discoveries and lay a foundation for future studies related to ncRNAs in human saliva.
Department of Integrative Biology and Physiology, Molecular Biology Institute.
Jae Hoon
JH
Bahn
Department of Integrative Biology and Physiology, Molecular Biology Institute.
Qing
Q
Zhang
School of Dentistry.
Feng
F
Li
Department of Integrative Biology and Physiology, Molecular Biology Institute.
Tak-Ming
TM
Chan
Department of Integrative Biology and Physiology, Molecular Biology Institute.
Xianzhi
X
Lin
School of Dentistry, Jonsson Comprehensive Cancer Center, Broad Stem Cell Research Center.
Yong
Y
Kim
Molecular Biology Institute, School of Dentistry, Jonsson Comprehensive Cancer Center, School of Engineering, Department of Head & Neck Surgery/Otolaryngology, UCLA, Los Angeles, CA. gxxiao@ucla.edu dtww@ucla.edu.
David T W
DT
Wong
Department of Integrative Biology and Physiology, Molecular Biology Institute, Jonsson Comprehensive Cancer Center, School of Engineering, gxxiao@ucla.edu dtww@ucla.edu.
Xinshu
X
Xiao
D001483:Base Sequence; D015415:Biomarkers / Q000032:analysis; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000032:analysis* / Q000097:blood / Q000134:cerebrospinal fluid / Q000235:genetics; D008969:Molecular Sequence Data; D012313:RNA / Q000032:analysis* / Q000097:blood / Q000134:cerebrospinal fluid / Q000235:genetics; D000079962:RNA, Circular; D034741:RNA, Small Interfering / Q000032:analysis* / Q000097:blood / Q000134:cerebrospinal fluid / Q000235:genetics; D015203:Reproducibility of Results; D012463:Saliva / Q000737:chemistry*; D012680:Sensitivity and Specificity; D017423:Sequence Analysis, RNA / Q000379:methods*
D015415:Biomarkers; D035683:MicroRNAs; D000079962:RNA, Circular; D034741:RNA, Small Interfering; D012313:RNA