Diversity and signature of small RNA in different bodily fluids using next generation sequencing

Abstract

BackgroundSmall RNAs are critical components in regulating various cellular pathways. These molecules may be tissue-associated or circulating in bodily fluids and have been shown to associate with different tumors. Next generation sequencing (NGS) on small RNAs is a powerful tool for profiling and discovery of microRNAs (miRNAs).ResultsIn this study, we isolated total RNA from various bodily fluids: blood, leukocytes, serum, plasma, saliva, cell-free saliva, urine and cell-free urine. Next, we used Illumina’s NGS platform and intensive bioinformatics analysis to investigate the distribution and signature of small RNAs in the various fluids. Successful NGS was accomplished despite the variations in RNA concentrations among the different fluids. Among the fluids studied, blood and plasma were found to be the most promising fluids for small RNA profiling as well as novel miRNA prediction. Saliva and urine yielded lower numbers of identifiable molecules and therefore were less reliable in small RNA profiling and less useful in predicting novel molecules. In addition, all fluids shared many molecules, including 139 miRNAs, the most abundant tRNAs, and the most abundant piwi-interacting RNAs (piRNAs). Fluids of similar origin (blood, urine or saliva) displayed closer clustering, while each fluid still retains its own characteristic signature based on its unique molecules and its levels of the common molecules. Donor urine samples showed sex-dependent differential clustering, which may prove useful for future studies.ConclusionsThis study shows the successful clustering and unique signatures of bodily fluids based on their miRNA, tRNA and piRNA content. With this information, cohorts may be differentiated based on multiple molecules from each small RNA class by a multidimensional assessment of the overall molecular signature.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4785-8) contains supplementary material, which is available to authorized users.

Charting extracellular transcriptomes in The Human Biofluid RNA Atlas

“…observed in blood-derived fluids is in line with a previous study 11 and with the Y-RNA function in platelets. The fraction of reads mapping to miRNAs is lower than 15% in all samples but platelet-free plasma and one synovial fluid sample.…”

“…Our small RNA results confirm previous studies observing high miRNA concentration in tears 12 , low mapping rates in CSF 5,41 and low miRNA concentration in cell-free urine 11 .…”

“…In the discovery cohort, 20 different biofluids were collected in two donors or in a pool of [4][5] donors. In the case/control cohorts, selected biofluids (sputum, CSF, urine and saliva) were collected in [8][9][10][11][12] patients and an equal number of healthy controls. Both small RNA sequencing and mRNA capture sequencing were performed in the discovery cohort.…”

“…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] . While most studies have focused on plasma and serum, some groups have investigated the small RNA content of other human biofluids.…”

“…Weber et al 12 was the first to compare the miRNA content in 12 different human biofluids 5,8,10,10,11 . The distribution of small RNA biotypes clearly varies across these biofluids, with a high abundance of piRNAs and tRNAs reported in urine and a high abundance of Y-RNAs in plasma 6,8,11 . Also non-human RNA sequences, mapping to bacterial genomes, were reported in plasma, urine and saliva 6 .…”