Construction of microRNA functional families by a mixture model of position weight matrices

High-quality human preimplantation embryos stimulate endometrial stromal cell migration via secretion of microRNA hsa-miR-320a

STUDY QUESTION

How do high-quality human preimplantation embryos influence the endometrium to promote their own implantation?

SUMMARY ANSWER

High-quality human preimplantation embryos secrete a specific microRNA (miRNA), hsa-miR-320a, which promotes migration of human endometrial stromal cells (hESCs).

WHAT IS KNOWN ALREADY

We have previously shown that high-quality human preimplantation embryos excrete unknown factors that influence migration of hESCs.

STUDY DESIGN, SIZE, DURATION

Embryo excreted miRNAs, specifically those excreted by high-quality embryos, were identified and their effect on hESCs was determined by measuring the migration capacity and gene expression patterns of primary isolated hESCs.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Embryo conditioned medium (ECM) from routine ICSI procedures was used to identify embryo excreted miRNAs. miRNome analyses were performed on ECM from individually cultured embryos with high morphological quality, with low morphological quality or empty control medium. MiRNA mimics and inhibitors were then used to further study the effect of miRNAs of interest on migration and gene expression of hESCs. Migration assays were performed using hESCs that were obtained from endometrial biopsies performed on hysterectomy specimens from women that received surgery for spotting due to a niche in a cesarean section scar.

MAIN RESULTS AND THE ROLE OF CHANCE

By using miRNA mimics and inhibitors, we showed that hsa-miR-320a alone can stimulate migration of decidualized hESCs, accurately resembling the response typically triggered only by high-quality embryos. Transcriptome analysis further demonstrated that this effect is very likely mediated via altered expression of genes involved in cell adhesion and cytoskeleton organization.

LIMITATIONS, REASONS FOR CAUTION

The effect of hsa-miR-320a on hESCs was measured in vitro. Further studies on the in vivo effect of hsa-miR-320a are warranted.

WIDER IMPLICATIONS OF THE FINDINGS

Implantation failure is one of the major success limiting factors in human reproduction. By secreting hsa-miR-320a, high-quality human preimplantation embryos directly influence hESCs, most likely to prime the endometrium at the implantation site for successful implantation. Together, our results indicate that hsa-miR-320a may be a promising target to further increase success rates in assisted reproduction.

STUDY FUNDING/COMPETING INTEREST(S)

The study was funded by the Amsterdam University Medical Centers and the Amsterdam Reproduction & Development Research Institute. R.P.B., G.H. and S.M. have a patent on the use of hsa-miR-320a in assisted reproduction treatments pending.

TRIAL REGISTRATION NUMBER

N/A.

Automatic curation of large comparative animal MicroRNA datasets

MOTIVATION

MicroRNAs form an important class of RNA regulators that has been studied extensively. The miRBase and Rfam database provide rich, frequently updated information on both pre-miRNAs and their mature forms. These data sources, however, rely on individual data submission and thus are neither complete nor consistent in their coverage across different miRNA families. Quantitative studies of miRNA evolution therefore are difficult or impossible on this basis.

RESULTS

We present here a workflow and a corresponding implementation, MIRfix, that automatically curates miRNA datasets by improving alignments of their precursors, the consistency of the annotation of mature miR and miR* sequence, and the phylogenetic coverage. MIRfix produces alignments that are comparable across families and sets the stage for improved homology search as well as quantitative analyses.

AVAILABILITY AND IMPLEMENTATION

MIRfix can be downloaded from https://github.com/Bierinformatik/MIRfix.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Predicting microRNA biological functions based on genes discriminant analysis

Although thousands of microRNAs (miRNAs) have been identified in recent experimental efforts, it remains a challenge to explore their specific biological functions through molecular biological experiments. Since those members from same family share same or similar biological functions, classifying new miRNAs into their corresponding families will be helpful for their further functional analysis. In this study, we initially built a vector space by characterizing the features from miRNA sequences and structures according to their miRBase family organizations. Then we further assigned miRNAs into its specific miRNA families by developing a novel genes discriminant analysis (GDA) approach in this study. As can be seen from the results of new families from GDA, in each of these new families, there was a high degree of similarity among all members of nucleotide sequences. At the same time, we employed 10-fold cross-validation machine learning to achieve the accuracy rates of 68.68%, 80.74%, and 83.65% respectively for the original miRNA families with no less than two, three, and four members. The encouraging results suggested that the proposed GDA could not only provide a support in identifying new miRNAs' families, but also contributing to predicting their biological functions.

let-7e replacement yields potent anti-arrhythmic efficacy via targeting beta 1-adrenergic receptor in rat heart

Beta-adrenoceptor (β-AR) exerts critical regulation of cardiac function. MicroRNAs (miRNAs) are potentially involved in a variety of biological and pathological processes. This study aimed to investigate the role of miRNA let-7e in the up-regulation of β₁-AR and arrhythmogenesis in acute myocardial infarction (AMI) in rats. β₁-AR expression was significantly up-regulated and let-7a, c, d, e and i were markedly down-regulated in the infarcted heart after 6 and 24 hrs myocardial infarction. Forced expression of let-7e suppressed β₁-AR expression at the protein level, without affecting β₁-AR mRNA level, in neonatal rat ventricular cells (NRVCs). Silencing of let-7e by let-7e antisense inhibitor (AMO-let-7e) enhanced β₁-AR expression at the protein level in NRVCs. Administration of the lentivirus vector containing precursor let-7e (len-pre-let-7e) significantly inhibited β₁-AR expression in rats, whereas len-AMO-let-7e up-regulated β₁-AR relative to the baseline control level, presumably as a result of depression of tonic inhibition of β₁-AR by endogenous let-7e. Len-negative control (len-NC) did not produce significant influence on β₁-AR expression. Len-pre-let-7e also profoundly reduced the up-regulation of β₁-AR induced by AMI and this effect was abolished by len-AMO-let-7e. Importantly, len-pre-let-7e application significantly reduced arrhythmia incidence after AMI in rats and its anti-arrhythmic effect was cancelled by len-AMO-let-7e. Notably, anti-arrhythmic efficacy of len-pre-let-7e was similar to propranolol, a non-selective β-AR blocker and metoprolol, a selective β₁-AR blocker. Down-regulation of let-7e contributes to the adverse increase in β₁-AR expression in AMI and let-7e supplement may be a new therapeutic approach for preventing adverse β₁-AR up-regulation and treating AMI-induced arrhythmia.