Circulating miRNAs, isomiRs and small RNA clusters in human plasma and breast milk

Abstract

Circulating small RNAs, including miRNAs but also isomiRs and other RNA species, have the potential to be used as non-invasive biomarkers for communicable and non-communicable diseases. This study aims to characterize and compare small RNA profiles in human biofluids. For this purpose, RNA was extracted from plasma and breast milk samples from 15 healthy postpartum mothers. Small RNA libraries were prepared with the NEBNext® small RNA library preparation kit and sequenced in an Illumina HiSeq2000 platform. miRNAs, isomiRs and clusters of small RNAs were annotated using seqBuster/seqCluster framework in 5 plasma and 10 milk samples that passed the initial quality control. The RNA yield was 81 ng/mL [standard deviation (SD): 41] and 3985 ng/mL (SD: 3767) for plasma and breast milk, respectively. Mean number of good quality reads was 4.04 million (M) (40.01% of the reads) in plasma and 12.5M (89.6%) in breast milk. One thousand one hundred eighty two miRNAs, 12,084 isomiRs and 1,053 small RNA clusters that included piwi-interfering RNAs (piRNAs), tRNAs, small nucleolar RNAs (snoRNA) and small nuclear RNAs (snRNAs) were detected. Samples grouped by biofluid, with 308 miRNAs, 1,790 isomiRs and 778 small RNA clusters differentially detected. In summary, plasma and milk showed a different small RNA profile. In both, miRNAs, piRNAs, tRNAs, snRNAs, and snoRNAs were identified, confirming the presence of non-miRNA species in plasma, and describing them for the first time in milk.

Postprandial transfer of colostral extracellular vesicles and their protein and miRNA cargo in neonatal calves

“…In general, miRNA expression profiles in colostrum-derived samples were in concordance with previous reports with a substantial overlap in the most abundant miRNAs [21,56,57]. Although miRNA expression in blood and colostrum was completely dissimilar, duplicating results obtained from milk and peripheral blood cells [58] as well as circulating miRNAs [59], differences between unfractionated colostrum and colostrum EVs were minuscule compared to colostrum cells, suggesting that the majority of miRNAs in colostrum is present in the extracellular compartment.…”

Milk MicroRNAs in Health and Disease

“…Among those, the same microRNAs are recurrently found in the top 10 most enriched sequences in milk (Table ). Most interestingly, in all the studies, these 10 microRNAs represent 40% to 80% of all sequences suggesting that, depending on the sample, a limited number of microRNA is specifically secreted in milk (Golan‐Gerstl et al., ; Kahn et al., ; Liao et al., ; Munch et al., ; Rubio et al., ; Simpson et al., ; van Herwijnen et al., ; Zhou et al., ).…”

“…Data from in silico analysis of small RNA‐sequencing databases in humans are still conflicting (Cui et al., ; Kang et al., ; Zempleni, ; Zhang, Vieira Resende, & Cui, ), mostly because microRNAs are conserved between the species. It is also because microRNAs isomeric sequences (isomiRs) are often not taken into account, which offers a supplementary challenge for milk microRNA investigations in various species (Guo & Chen, ; Rubio et al., ; Yu et al., ). Another limitation of in silico screening is about eliminating confounders, especially about dairy products intake as those are not controlled.…”

Injured pancreatic β cells enhance the release of miR‑375‑3p into the extracellular space

“…MicroRNAs (miRNAs) are small (18-25 nucleotides) non-coding RNA harboring a post-transcriptional gene regulatory function (1). Currently, miRNAs have been detected in various body fluids, including serum (2), plasma (3), urine (4), cerebrospinal fluid (5), breast milk (6), saliva (7), bronchoalveolar lavage fluid (8), ascites (9), and pleural effusion (10). Noteworthy, miRNAs are stable under non-physiological conditions, whether in body fluids or culture media.…”