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.
Highlights
Discovery of novel biomarkers for early detection and improved prognosis in non-communicable and infectious diseases is a research priority
QCed reads were mapped to miRNAs, and miRNA complexity was estimated as the number of miRNA genes that are observed as a function of the number of miRNA reads
We identified several species of small RNAs, including miRNAs, piwi-interfering RNAs (piRNAs), tRNAs, small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNA) in both plasma and breast milk
Summary
Discovery of novel biomarkers for early detection and improved prognosis in non-communicable and infectious diseases is a research priority. Promising classes of molecular biomarkers are small RNAs, and special attention has been given to microRNAs (miRNAs) [2]. MiRNAs are short (21–23 nt), single-stranded, non-coding RNAs that regulate gene expression and play essential roles in fundamental biological processes. Recent studies have shown the involvement of miRNAs in various aspects of major chronic diseases including bronchial asthma and diabetes, as well as in regulation and induction of senescence, brain function and cancer [3,4,5,6,7,8]. Changes in miRNA expression can be triggered by environmental factors such as exposure to pesticides, heavy metals, air pollution, bisphenol A and cigarette smoking [9, 10]. The content of miRNAs is influenced by host-pathogen interactions, as has been shown for bacteria, viruses and apicomplexan parasites [11]
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