Large Differences in Small RNA Composition Between Human Biofluids

Abstract

SUMMARY 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.

Phospho‐RNA‐seq: a modified small RNA‐seq method that reveals circulating mRNA and lncRNA fragments as potential biomarkers in human plasma

“…RNA‐seq has transformed transcriptome characterization in a wide range of biological contexts (Mortazavi et al , ; Wang et al , ) including its application to analyze exRNA in body fluids (Adiconis et al , ; Giraldez et al , ). These efforts have begun to elucidate the complex composition of exRNA in blood (Freedman et al , ; Yeri et al , ; Godoy et al , ; Max et al , ). There have been indications of extracellular mRNA and lncRNA in some studies of plasma, but results have been inconsistent, with some profiling studies reporting a variable percentage of them and others not even reporting their presence (Huang et al , ; Koh et al , ; Freedman et al , ; Yuan et al , ; Danielson et al , ; Yeri et al , ; Godoy et al , ; Max et al , ).…”

“…In recent years, the discovery of a variety of extracellular RNA (exRNA) molecules present in the human bloodstream and other biofluids has been of great interest given their potential value as minimally invasive biomarkers for a wide range of diseases (Freedman et al, 2016;Yuan et al, 2016;Godoy et al, 2018;Max et al, 2018). To date, characterization of exRNAs in blood has mostly focused on microRNAs, which have been shown to be exceptionally stable in plasma (i.e., the acellular portion of blood) by virtue of being protected in complexes with Argonaute proteins and extracellular vesicles (Hunter et al, 2008;Arroyo et al, 2011).…”

“…These efforts have begun to elucidate the complex composition of exRNA in blood (Freedman et al, 2016;Yeri et al, 2017;Godoy et al, 2018;Max et al, 2018). There have been indications of extracellular mRNA and lncRNA in some studies of plasma, but results have been inconsistent, with some profiling studies reporting a variable percentage of them and others not even reporting their presence (Huang et al, 2013;Koh et al, 2014;Freedman et al, 2016;Yuan et al, 2016;Danielson et al, 2017;Yeri et al, 2017;Godoy et al, 2018;Max et al, 2018). Moreover, these profiling studies have used a variety of methods to evaluate exRNA (e.g., microarrays and different methodologies for RNA-seq) which, not surprisingly, contributes to the variation in findings.…”

Charting extracellular transcriptomes in The Human Biofluid RNA Atlas

“…Extracellular RNAs (exRNAs) in blood and other biofluids are emerging as potential biomarkers for a wide range of diseases [1][2][3][4][5][6] . These so-called liquid biopsies may offer a non-invasive alternative to tissue biopsies for both diagnosis and treatment response monitoring.…”

Depletion of erythropoietic miR-486-5p and miR-451a improves detectability of rare microRNAs in peripheral blood-derived small RNA sequencing libraries

“…suspended in a medium known as plasma (23). Besides blood-cell expressed miR-NAs, blood also contains circulating miRNAs that are detected in serum, plasma or exosomes (24). Therefore, the expectation is that the small RNA-sequenced whole blood sample should contain convolved information about the miRNA composition of all cellular and non-cellular blood components.…”