MicroRNA Expression Analysis: Next-Generation Sequencing

MicroRNAs in Corneal Diseases: Emerging Roles as Biomarkers, Regulators, and Therapeutics

MicroRNAs (miRNAs) are conserved, short, non-coding RNAs that play a crucial role in regulating gene expression. Emerging evidence suggests that miRNAs are closely involved in the pathophysiology of various corneal diseases, particularly in regulating corneal wound healing, inflammation and neovascularization. In this review, we summarized the recent progress of miRNAs in corneal diseases, especially focused on their application as diagnostic biomarkers, regulators of cell biology, and therapeutic targets. Recent advances in miRNA detection technology have made it possible to analyze minimal miRNAs in samples such as tears or exosomes, further enhancing the ability to identify disease-specific miRNA profiles and providing potential objective indicators for the early diagnosis of disease. Meanwhile, we summarized the mechanisms and pathways of multiple miRNAs in regulating various biological processes of corneal cells, as well as the advantages of studying miRNA compared to proteins or genes. Furthermore, we explore the potential of miRNAs-based therapies, especially introduce various miRNA delivery systems and challenges associated with clinical translation. This review highlights the need for further research to harness the full potential of miRNAs in treating various corneal diseases.

The role of microRNA in the regulation of hepatic metabolism and energy-expensive processes in the hibernating dormouse

The garden dormouse (Eliomys quercinus) is a fat-storing mammal that undergoes annual periods of hibernation to mitigate the effects of food scarcity, low ambient temperatures, and reduced photoperiod that characterize winter. Like other hibernating species, this animal suppresses its metabolic rate by downregulating nonessential genes and processes in order to prolong available energy stores and limit waste accumulation throughout the season. MicroRNAs (miRNAs) are short, single-stranded, noncoding RNAs that bind to mRNA and mediate post-transcriptional suppression, making miRNA ideal for modulating widespread changes in gene expression, including global downregulation typified by metabolic rate depression. Using next-generation sequencing, we analyzed an RNA-seq dataset to determine which miRNAs are differentially regulated during hibernation in the dormouse liver. We found that the expression of 19 miRNAs was altered during hibernation; however, only one major miRNA (miR-34a-5p) remained significantly downregulated after correcting for false discovery rate. Gene Ontology, KEGG Pathway Analysis, and DIANA-miRPath predicted that energy metabolism, nuclear-related functions such as histone binding, chromatin- and chromosomal binding, and the cell cycle are processes that may be differentially regulated during hibernation due to miRNA regulation. Taken together, our data suggest that miRNA influence appears to be strongly directed toward suppressing energy-intensive processes in the nucleus hence contributing to extend the animal's endogenous fuel reserves for the duration of hibernation.

Preanalytical, analytical and postanalytical considerations in circulating microRNAs measurement

Microribonucleic acids (miRNAs) have emerged as a new category of biomarkers for many human diseases like cancer, cardiovascular and neurodegenerative disorders. MicroRNAs can be detected in various body fluids including blood, urine and cerebrospinal fluid. However, the literature contains conflicting results for circulating miRNAs, which is the main barrier to using miRNAs as non-invasive biomarkers. This variability in results is largely due to differences between studies in sample processing methodology, miRNA quantification and result normalization. The purpose of this review is to describe the various preanalytical, analytical and postanalytical factors that can impact miRNA detection accuracy and to propose recommendations for the standardization of circulating miRNAs measurement.

Experimental MicroRNA Detection Methods

MicroRNAs (miRNAs) are considerably small yet highly important riboregulators involved in nearly all cellular processes. Due to their critical roles in posttranscriptional regulation of gene expression, they have the potential to be used as biomarkers in addition to their use as drug targets. Although computational approaches speed up the initial genomewide identification of putative miRNAs, experimental approaches are essential for further validation and functional analyses of differentially expressed miRNAs. Therefore, sensitive, specific, and cost-effective microRNA detection methods are imperative for both individual and multiplex analysis of miRNA expression in different tissues and during different developmental stages. There are a number of well-established miRNA detection methods that can be exploited depending on the comprehensiveness of the study (individual miRNA versus multiplex analysis), the availability of the sample and the location and intracellular concentration of miRNAs. This review aims to highlight not only traditional but also novel strategies that are widely used in experimental identification and quantification of microRNAs.

MiR-144-3p Inhibits BMSC Proliferation and Osteogenic Differentiation Via Targeting FZD4 in Steroid-Associated Osteonecrosis

BACKGROUND

MicroRNAs have recently been recognized to be engaged in the development of bone diseases.

OBJECTIVE

This study was performed to elucidate the effects of miR-144-3p on proliferation and osteogenesis of mesenchymal stem cells (MSCs) from the patients with steroid-associated osteonecrosis (ONFH) and its related mechanism.

METHOD

The expression level of miR-144-3p in the MSCs from the proximal femur of the patients was examined by Real-time PCR. The cell proliferation ability was assayed by MTT. The differentiation ability of MSCs was assayed by Alizarin Red S (ARS) staining. The interaction between miR-144-3p and frizzled4 (FZD4) was investigated by Real-time PCR, western blot and luciferase reporter assay.

RESULTS

ONFH samples had the obviously high expression of miR-144-3p compared to the control. MiR-144-3p had a negative effect on the proliferation and osteogenesis of MSCs. Via targeting FZD4, miR-144-3p decreased β-catenin nuclear translocation, the transcription of RUNX2 and COL1A1. Over-expression of FZD4 partially reversed miR-144-3p-induced decrease in the proliferation and osteogenesis of MSCs.

CONCLUSION

MiR-144-3p might play an important role in the development of ONFH and might be used as a novel class of therapeutic targets for this disease.

MiR-217 promotes cell proliferation and osteogenic differentiation of BMSCs by targeting DKK1 in steroid-associated osteonecrosis

MicroRNAs (miRNAs) have recently been recognized to play an important role in bone-associated diseases. This study aims to explore the expression profile and biological function of miR-217, which is known to be related to tumor cell proliferation and migration, to the proliferation and osteogenic differentiation of MSCs from the patients with steroid-associated osteonecrosis (ONFH). Bone marrow was obtained from the proximal femur of 10 patients with ONFH and 10 patients with femoral neck fractures. Bone marrow-derived mesenchymal stem cells (MSCs) were isolated and cultured. The expression profile, biological function of miR-217 and the interaction between miR-217 and DKK1 were assayed using cell viability measurement, western blot, Real-time PCR, luciferase reporter assay, Alizarin Red S (ARS) staining. We noted that the expression level of miR-217 was significantly decreased in the ONFH samples compared to the control samples (P < 0.0001). By targeting DKK1, miR-217 promoted nuclear translocation of β-catenin, increased expression of RUNX2, COL1A1 and obviously promoted the proliferation and differentiation of MSCs. Restoring the expression of DKK1 in the MSCs partially reversed the role of miR-217. These findings suggest that miR-217 promotes cell proliferation and osteogenic differentiation by inhibiting DKK1 during the development of steroid-associated osteonecrosis.