Large Differences in Small RNA Composition Between Human Biofluids

Paula M Godoy; Nirav R Bhakta; Andrea J Barczak; Hakan Cakmak; Susan Fisher; Tippi C MacKenzie; Tushar Patel; Richard W Price; James F Smith; Prescott G Woodruff; David J Erle

doi:10.1016/j.celrep.2018.10.014

Large Differences in Small RNA Composition Between Human Biofluids

Cell Rep. 2018 Oct 30;25(5):1346-1358. doi: 10.1016/j.celrep.2018.10.014.

Authors

Affiliations

¹ Lung Biology Center, University of California, San Francisco, UCSF Box 3118, San Francisco, CA 94143, USA.
² Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California, San Francisco, UCSF Box 0130, San Francisco, CA 94143, USA.
³ Department of Obstetrics, Gynecology & Reproductive Sciences, University of California, San Francisco, UCSF Box 0916, San Francisco, CA 94143, USA.
⁴ Department of Surgery, University of California, San Francisco, UCSF Box 0570, San Francisco, CA 94143, USA.
⁵ Department of Transplantation, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA.
⁶ Department of Neurology, University of California, San Francisco, UCSF Box 0870, San Francisco, CA 94143, USA.
⁷ Department of Urology, University of California, San Francisco, UCSF Box 1695, San Francisco, CA 94143, USA.
⁸ Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California, San Francisco, UCSF Box 0130, San Francisco, CA 94143, USA; Cardiovascular Research Institute, University of California, San Francisco, UCSF Box 0130, San Francisco, CA 94143, USA.
⁹ Lung Biology Center, University of California, San Francisco, UCSF Box 3118, San Francisco, CA 94143, USA; Cardiovascular Research Institute, University of California, San Francisco, UCSF Box 0130, San Francisco, CA 94143, USA. Electronic address: [email protected].

Abstract

Extracellular microRNAs (miRNAs) and other small RNAs are implicated in cellular communication and may be useful as disease biomarkers. We systematically compared small RNAs in 12 human biofluid types using RNA sequencing (RNA-seq). miRNAs and tRNA-derived RNAs (tDRs) accounted for the majority of mapped reads in all biofluids, but the ratio of miRNA to tDR reads varied from 72 in plasma to 0.004 in bile. miRNA levels were highly correlated across all biofluids, but levels of some miRNAs differed markedly between biofluids. tDR populations differed extensively between biofluids. Y RNA fragments were seen in all biofluids and accounted for >10% of reads in blood plasma, serum, and cerebrospinal fluid (CSF). Reads mapping exclusively to Piwi-interacting RNAs (piRNAs) were very rare, except in seminal plasma. These results demonstrate extensive differences in small RNAs between human biofluids and provide a useful resource for investigating extracellular RNA biology and developing biomarkers.

Keywords: Y RNA; biofluids; extracellular RNA; miRNA; tRNA.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Adult
Amino Acids / genetics
Anticodon / genetics
Body Fluids / metabolism*
Female
Humans
Male
MicroRNAs / genetics*
MicroRNAs / metabolism
Middle Aged
RNA, Small Interfering / genetics
RNA, Transfer / genetics*
RNA, Transfer / metabolism
Sequence Analysis, RNA

Substances

Amino Acids
Anticodon
MicroRNAs
RNA, Small Interfering
RNA, Transfer

Abstract

Publication types

MeSH terms

Substances

Grants and funding