RNA-sequencing analysis of umbilical cord plasma microRNAs from healthy newborns

Abstract

MicroRNAs are a class of small non-coding RNA that regulate gene expression at a posttranscriptional level. MicroRNAs have been identified in various body fluids under normal conditions and their stability as well as their dysregulation in disease has led to ongoing interest in their diagnostic and prognostic potential. Circulating microRNAs may be valuable predictors of early-life complications such as birth asphyxia or neonatal seizures but there are relatively few data on microRNA content in plasma from healthy babies. Here we performed small RNA-sequencing analysis of plasma processed from umbilical cord blood in a set of healthy newborns. MicroRNA levels in umbilical cord plasma of four male and four female healthy babies, from two different centres were profiled. A total of 1,004 individual microRNAs were identified, which ranged from 426 to 659 per sample, of which 269 microRNAs were common to all eight samples. Many of these microRNAs are highly expressed and consistent with previous studies using other high throughput platforms. While overall microRNA expression did not differ between male and female cord blood plasma, we did detect differentially edited microRNAs in female plasma compared to male. Of note, and consistent with other studies of this type, adenylation and uridylation were the two most prominent forms of editing. Six microRNAs, miR-128-3p, miR-29a-3p, miR-9-5p, miR-218-5p, 204-5p and miR-132-3p were consistently both uridylated and adenylated in female cord blood plasma. These results provide a benchmark for micro-RNA profiling and biomarker discovery using umbilical cord plasma and can be used as comparative data for future biomarker profiles from complicated births or those with earlylife developmental disorders.

Large-scale transcriptome-wide profiling of microRNAs in human placenta and maternal plasma at early to mid gestation

“…This common difficulty with plasma data, led us to assess the detection of miRNAs of interest revealing that the 10 most abundant placental miRNAs were reflected by high abundance levels in matched plasma. Furthermore, these plasma miRNAs in our study show strong concordance with previous miRNA plasma studies [ 77 , 80 ].…”

Large-scale transcriptome-wide profiling of microRNAs in human placenta and maternal plasma at early to mid gestation

“…This common difficulty with plasma data, led us to assess the detection of miRNAs of interest revealing that the 10 most abundant placental miRNAs were reflected by high abundance levels in matched plasma. Furthermore, these plasma miRNAs in our study show strong concordance with previous miRNA plasma studies [65,68]. Differential expression and clear gestational age gradient clustering pattern in placenta miRNAs between 6-10 and 11-23 weeks' gestation were not particularly reflected by maternal plasma, indicating that plasma does not reflect the changes in the miRNA profile in placenta across early to mid gestation.…”

MicroRNA Profiles of Maternal and Neonatal Endothelial Progenitor Cells in Preeclampsia

“…Our sample was limited to six cases per group, which is due to the well-described low isolation efficiency of ECFC. However, other publications on circulating [ 37 ] and ECFC-derived miRNAs [ 38 ] in pregnant populations provided new and interesting results, even with lower sample numbers. In addition, the comparison of mother–child pairs in both study populations would be desirable, as this would provide more stable conditions and avoid possible bias.…”

“…Thirdly, we examined whether cell culture passage affects miRNA patterns overall. P3 corresponded to the earliest time when sufficient cell numbers were available after primary cell isolation, while P5 was selected to fall within a common window where ECFC are used for functional studies [ 37 , 41 , 42 ]. Separate analyses were performed in ECFC derived from cord blood (offspring group) and ECFC derived from maternal blood (maternal group).…”