Human plasma and serum extracellular small RNA reference profiles and their clinical utility

Abstract

SignificanceNucleic acids mediate storage and expression of genetic information. Extracellular DNA (exDNA) and exRNA are traces of nucleic acids released from cells into the extracellular environment. Their use as disease biomarkers has been limited by technical challenges in their isolation caused by abundant RNA- and DNA-degrading enzymes in biofluids. Using isolation protocols developed especially for biofluids, we generated plasma and serum exRNA reference profiles from 13 healthy volunteers over time and determined the effect of critical clinical parameters such as gender and fasting. Surprisingly, we encountered one participant with dramatically increased endocrine-origin exRNA contributions stable over 1 year and detectable in all of his samples, thereby demonstrating the robustness of this approach and the clinical potential of circulating RNAs as biomarkers.

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

“…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.…”

“…To date, the characterization of exRNAs in biofluids has mainly focused on small RNAs in blood derived samples [1][2][3][4][7][8][9][10] . MicroRNA (miRNA) is the most studied small RNA biotype in biofluids, but other small RNAs, such as piwi-interacting RNAs (piRNAs), small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), ribosomal RNAs (rRNAs), transfer RNA fragments (tRNAs) and Y-RNAs have also been identified 5,6,8,[10][11][12] .…”

Phospho-sRNA-seq reveals extracellular mRNA/lncRNA fragments as potential biomarkers in human plasma

“…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;Max et al, 2018;Godoy et al, 2018;Yuan et al, 2016). To date, characterization of exRNAs in blood has mostly focused on miRNAs, 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 (Arroyo et al, 2011;Hunter et al, 2008).…”

“…RNA-seq has transformed transcriptome characterization in a wide range of biological contexts (Mortazavi et al, 2008;Wang et al, 2009) including its application to analyze exRNA in body fluids (Adiconis et al, 2013;Giraldez et al, 2018). These efforts have begun to elucidate the complex composition of exRNA in blood (Freedman et al, 2016;Max et al, 2018;Yeri et al, 2017;Godoy 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 (Freedman et al, 2016;Max et al, 2018;Godoy et al, 2018;Danielson et al, 2017;Koh et al, 2014;Yuan et al, 2016;Yeri et al, 2017;Huang et al, 2013).…”