Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations

Abstract

We profiled microRNAs (miRNAs) in cell-free serum and plasma samples from human volunteers using deep sequencing of barcoded small RNA cDNA libraries. By introducing calibrator synthetic oligonucleotides during library preparation, we were able to calculate the total as well as specific concentrations of circulating miRNA. Studying trios of samples from newborn babies and their parents we detected placental-specific miRNA in both maternal and newborn circulations and quantitated the relative contribution of placental miRNAs to the circulating pool of miRNAs. Furthermore, sequence variation in the placental miRNA profiles could be traced to the specific placenta of origin. These deep sequencing profiles, which may serve as a model for tumor or disease detection, allow us to define the repertoire of miRNA abundance in the circulation and potential uses as biomarkers.pregnancy | cancer

Comparative RNA-sequencing analysis of myocardial and circulating small RNAs in human heart failure and their utility as biomarkers

“…We used a small RNA-sequencing (sRNAseq) protocol developed for parallel processing of large sample collections with limited amounts of input RNA (7,34,35) to record the miRNA composition in heart tissue and in circulation in a large cohort of HF patients and normal controls. Using the same method for miRNA profiling eliminated biases (26) otherwise affecting comparison of our data with studies, which previously profiled either tissue or circulating miRNAs in HF, but never both.…”

“…Experiments with siRNAs or antagomirs (29) showed that only highly expressed miRNAs effectively repress target mRNAs. For simplicity of data presentation and discussion, we thus focused on regulatory miRNAs that contribute to ∼85% of sequencing reads per sample (7,25), corresponding to 15, 25, 21, and 28 miRNA cistrons in NFs, FETs, DCM HF, and ICM HF, respectively ( Fig. 2 A-C and Fig.…”

“…The recent detection of miRNPs in body fluids (4) pointed toward their value as biomarkers for tissue injury (5, 6), and they have also been discussed as paracrine and endocrine regulators of gene expression (4,7).…”

Potential relevance of microRNAs in inter-species epigenetic communication, and implications for disease pathogenesis

“…92 It is difficult to determine what is the minimal amount of miRNA that is sufficient for biological activity, and whether such an amount can be efficiently delivered to the host via e.g., the gastrointestinal tract. It has been suggested that miRNA copy number of about one hundred to one thousand per cell would be needed to affect gene expression.…”

“…In contrast with cancer immunosurveillance that is a rather slow process, such miRNA-mediated tumor suppressing activity could be very rapid and thus might complement the immune activity for tumor prevention. This is certainly a hypothesis and major counter arguments could be deployed against it including the very low concentration of individual miRNA in the circulation (femtomolar range), 92 the dual nature of miRNA (the same miRNA can be oncogenic in one, and tumor suppressor in another tissue), their tissue specificity etc. 105 By extending this hypothesis, it cannot be excluded that absorbed exogenous miRNA might interfere with tumor formation, as well.…”