Background: Extracellular RNAs (exRNAs) are found in numerous extracellular fluids, including milk. Until recently, microRNAs were the focus of research in this area, leaving aside other exRNAs.Recently, a modified small RNA-sequencing (sRNA-seq) approach led to the discovery of very short, 12 and 13 nucleotides (nt) ribosomal RNA (rRNA) fragments (rRFs), designated as dodecaRNAs (doRNAs), in reference to the number of core nucleotides (12 nt) they contain. Since milk is highly enriched in extracellular vesicles (EVs) and exRNAs, we inquired about the existence of doRNAs and other very short exRNAs in milk and milk EV (mEV)-enriched ultracentrifugation fractions.
Methods:We used sRNA-seq to explore exRNAs shorter than 16 nt in cow's milk and milk fractions obtained by ultracentrifugation. Results were validated with high-specificity splint-ligated reverse transcription quantitative polymerase chain reaction (RT-qPCR) using high sensitivity locked nucleic acid (LNA) oligonucleotides.Results: Cow's milk was abundant in doRNAs and c-doRNAs, a doRNA derivative harboring an additional cytosine (C) at its 5' end. Together, these two sequences represented 66.5% of all 8-to 15-nt RNA species.The abundance of doRNAs in milk was 11 to 49 times higher than the most abundant microRNAs. These RNAs were differentially distributed in milk ultracentrifugation fractions; their concentration was highest in the lower speed fractions (12,000 and 35,000 g). We also observed an increased c-doRNA/doRNA ratio with centrifugation speed, suggesting a possible selective release of c-doRNA over doRNA in denser mEVs. RT-qPCR quantification confirmed the presence of doRNAs in milk and supported the differential enrichment of doRNAs in different mEV subsets compared to that of the most enriched milk bta-let-7b, bta-miR-30a-5p and bta-miR-148a, yet not without discrepancies with the sequencing data.Conclusions: These findings suggest that exRNAs might be more diverse in cow's milk than previously thought. As doRNAs were found to be downregulated and to modulate cell proliferation/migration of prostate cancer cells, this could have health implications in adult and infant consumers which warrant further investigations.