Reversing the miRNA -5p/-3p stoichiometry reveals physiological roles and targets of miR-140 miRNAs

Looking for a needle in a haystack: de novo phenotypic target identification reveals Hippo pathway-mediated miR-202 regulation of egg production

Understanding microRNA (miRNA) functions has been hampered by major difficulties in identifying their biological target(s). Currently, the main limitation is the lack of a suitable strategy to identify biologically relevant targets among a high number of putative targets. Here we provide a proof of concept of successful de novo (i.e. without prior knowledge of its identity) miRNA phenotypic target (i.e. target whose de-repression contributes to the phenotypic outcomes) identification from RNA-seq data. Using the medaka mir-202 knock-out (KO) model in which inactivation leads to a major organism-level reproductive phenotype, including reduced egg production, we introduced novel criteria including limited fold-change in KO and low interindividual variability in gene expression to reduce the list of 2853 putative targets to a short list of 5. We selected tead3b, a member of the evolutionarily-conserved Hippo pathway, known to regulate ovarian functions, due to its remarkably strong and evolutionarily conserved binding affinity for miR-202-5p. Deleting the miR-202-5p binding site in the 3' UTR of tead3b, but not of other Hippo pathway members sav1 and vgll4b, triggered a reduced egg production phenotype. This is one of the few successful examples of de novo functional assignment of a miRNA phenotypic target in vivo in vertebrates.

Reduced glycolysis links resting zone chondrocyte proliferation in the growth plate

A gain-of-function mutation of the chondrocyte-specific microRNA, miR-140-5p, encoded by the MIR140 gene, causes spondyloepiphyseal dysplasia, Nishimura type (SEDN, also known as SED, MIR140 type; MIM, 611894). We reported that a mouse model for SEDN showed a unique growth plate phenotype that is characterized by an expansion of the resting zone of the growth plate and an increase in resting chondrocytes, of which the mechanism of regulation is poorly understood. We found that the miR-140 mutant chondrocytes showed a significant reduction of Hif1a, the master transcription factor that regulates energy metabolism in response to hypoxia. Based on this finding, we hypothesized that energy metabolism plays a regulatory role in resting chondrocyte proliferation and growth plate development. In this study, we show that suppression of glycolysis via LDH ablation causes an expansion of the resting zone and skeletal developmental defects. We have also found that reduced glycolysis results in reduced histone acetylation in the miR-140 mutant as well as LDH-deficient chondrocytes likely due to the reduction in acetyl-CoA generated from mitochondria-derived citrate. Reduction in acetyl-CoA conversion from citrate by deleting Acly caused an expansion of the resting zone and a similar gross phenotype to LDH-deficient bones without inducing energy deficiency, suggesting that the reduced acetyl-CoA, but not the ATP synthesis deficit, is responsible for the increase in resting zone chondrocytes. Comparison of the transcriptome between LDH-deficient and Acly-deficient chondrocytes also showed overlapping changes including upregulation in Fgfr3. We also confirmed that overexpression of an activation mutation of Ffgr3 causes an expansion of resting zone chondrocytes. These data demonstrate the association between reduced glycolysis and an expansion of the resting zone and suggest that it is caused by acetyl-CoA deficiency, but not energy deficiency, possibly through epigenetic upregulation of FGFR3 signaling.

Oral Delivery of miR-320-3p with Lipidic Aminoglycoside Derivatives at Mid-Lactation Alters miR-320-3p Endogenous Levels in the Gut and Brain of Adult Rats According to Early or Regular Weaning

To investigate if the artificial delivery of microRNAs naturally present in the breastmilk can impact the gut and brain of young rats according to weaning. Animals from a new transgenic rat line expressing the green-fluorescent protein in the endocrine lineage (cholecystokinin expressing cells) received a single oral bolus of miR-320-3p or miR-375-3p embedded in DiOleyl-Succinyl-Paromomycin (DOSP) on D-12. The pups were weaned early (D-15), or regularly (D-30). The expression of relevant miRNA, mRNAs, chromatin complexes, and duodenal cell density were assessed at 8 h post-inoculation and on D-45. The miR-320-3p/DOSP induced immediate effects on H3K4me3 chromatin complexes with polr3d promoter (p < 0.05). On regular weaning, on D-45, miR-320-3p and 375-3p were found to be downregulated in the stomach and upregulated in the hypothalamus (p < 0.001), whereas miR-320-3p was upregulated in the duodenum. After early weaning, miR-320-3p and miR-375-3p were downregulated in the stomach and the duodenum, but upregulated in the hypothalamus and the hippocampus. Combination of miR-320-3p/DOSP with early weaning enhanced miR-320-3p and chromogranin A expression in the duodenum. In the female brain stem, miR-320-3p, miR-504, and miR-16-5p levels were all upregulated. Investigating the oral miRNA-320-3p loads in the duodenal cell lineage paved the way for designing new therapeutics to avoid unexpected long-term impacts on the brain.

CircKMT2E Participates in Osteoarthritis through Promotes Apoptosis of Chondrocytes Via Sponging miR-140-5p to Activate TLR4

Objective

To explore the latent pathogenesis of circRNAs in osteoarthritis (OA), as well as their function mechanism.

Methods

The murine chondrocytes with and without OA were involved and used for in-depth sequencing. Herein, we carried out subsequent bioinformatics analysis to disclose the expression pattern, characteristics of circRNAs based on gene ontology, and the KEGG pathway analyses. Then sequencing data were used to deduce the interaction between circRNA and miRNA. The potential miRNA response elements for the annotated circRNAs and relevant target genes were forecasted on the basis of TargetScan and miRanda. For chondrocytes, the effect of the overexpression of the screened circRNA for apoptosis was spotted by flow cytometry as well as Western Blot.

Results

466 diverse circRNAs in the 23,787 spotted circRNAs were both significantly and differentially transcribed. CircKMT2E was upregulated more than two folds in chondrocytes with OA compared with normal tissues, exhibiting an expression trend opposite to miR-140-5p. We disclosed that circKMT2E could possess mutual effect with miR-140-5p by way of AGO proteins. Thus, circKMT2E was verified to have functioned as a molecular sponge targeting miR-140-5p. Therefore, circKMT2E may be at work in the pathogenesis of OA. Further, the sponge connection between circKMT2E and miR-140-5p was proved on the basis of a dual-luciferase reporter assay. Besides, miR-140-5p was speculated can bind TLR4 by bioinformatics analysis. Further PCR analysis found the relative expression level of TLR4, caspase-3, and Bax in the OA groups presented significant upregulation. Overexpression of circKMT2E can promote apoptosis of chondrocytes.

Conclusion

The upregulation of circKMT2E is involved in the chondrocyte apoptosis of the pathogenesis of OA through activation of TLR4 by the sponge function of miR-140-5p.