MicroRNA-derived fragment length polymorphism assay

Research on the inhibition for aseptic loosening of artificial joints by Sr-doped calcium polyphosphate (SCPP)in vivo

Aseptic loosening of artificial joints is the most common complication after artificial joint replacement. Finding the solution to tackle aseptic loosening of artificial joints is a focus in bone and joint surgery research field.In vitrostudies of Sr-doped calcium polyphosphate (SCPP) have found by our team that it could promote osteoblast proliferation and inhibit osteoclast activity, and it has a potential inhibitory effect on aseptic loosening by suppressing the expression of receptor activator of nuclear factor-κ B ligand and improving the expression of OPG. The present study aims to confirm the conclusionin vitroby the mean of animal experiment. The Ti rod prosthesis coated with SCPP, calcium polyphosphate (CPP), and Ultra-high molecular weight polyethylene (UHMWPE were implanted in the femur (the internal surface of bone tunnel was also coated with SCPP, CPP and UHMWPE respectively). Radiography (x-rays, micro-CT), histochemistry (Hematoxylin-eosin staining (HE), methylene blue-acid fuchsin, Von Kossa histological staining), molecular biology (alkaline phosphatase and TRAP5b factors, Mir21-5p and Mir 26a-5p) were performed to analyzed the effects of SCPP within 20 weeks. The Radiography results showed that osteolysis with various severity occurred in all groups, and SCPP group had the mildest osteolysis. Histochemistry results showed that arthritis was milder in SCPP and CPP groups, while the bone formation in SCPP group was most significant. Its bone reconstruction effect was the best as well. The Molecular biology results showed that the bone reconstruction was out-sync in each group. Compared with other groups, the bone resorption occurred at the latest and the bone resorption time was the shortest in experimental animals of SCPP group. All results indicated that SCPP could promote osteoblast activity and bone reconstruction, improve the integration of bone interface between prosthesis and base bone, reduce osteoclast activity and shorten the osteoclast action time at the implantation sitein vivo. Thus, it could postpone or alleviate the occurrence and development of aseptic looseningin vivo. Therefore, SCPP could be a promising material for the construction of artificial joints with the ability to resist aseptic loosening.

LncRNA NEAT1 activates MyD88/NF-κB pathway in bronchopneumonia through targeting miR-155-5p

BACKGROUND

Bronchopneumonia is a disease of the respiratory tract. It leads to other complications and endangers life and health. Long non-coding RNA (lncRNA) participates in the occurrence and development of bronchopneumonia. Nuclear paraspeckle assembly transcript 1 (NEAT1) plays a key role in inflammatory diseases, but the function of NEAT1 in bronchopneumonia remains unclear.

METHODS

RT-qPCR and Western blotting were performed to determine genes and proteins expressions. MTT was applied to test cell viability. Cell apoptosis was detected by flow cytometry. RIP was used to investigate the correlation between NEAT1 and miR-155-5p. The interaction between miR-155-5p and NEAT1 or MyD88 was evaluated by the dual-luciferase reporter gene.

RESULTS

NEAT1 and MyD88 were upregulated in BEAS-2B cells by LPS, while miR-155-5p was downregulated. Knockdown of NEAT1 inhibited LPS-induced BEAS-2B cells growth inhibition by inhibiting the apoptosis. In addition, NEAT1 silencing suppressed LPS-induced inflammatory responses in BEAS-2B cells via suppression of TNF-α, IL-1β, IL-6, and IL-18. Meanwhile, NEAT1 is directly bound to miR-155-5p to regulate MyD88/NF-κB axis, and overexpression of miR-155-5p increased cell proliferation and suppressed inflammatory factors expression levels and cell apoptosis. Furthermore, sh-NEAT1-induced inhibition of BEAS-2B cells injury was partially reversed by miR-155-5p inhibitor or MyD88 overexpression.

CONCLUSION

NEAT1 silencing suppressed LPS-induced BEAS-2B cells injury and inflammation by the mediation of miR-155-5p/MyD88/NF-κB axis. Thus, our study might shed new light on exploring the new strategies for the treatment of bronchopneumonia.

Evaluation of methodologies for microRNA biomarker detection by next generation sequencing

In recent years, microRNAs (miRNAs) in tissues and biofluids have emerged as a new class of promising biomarkers for numerous diseases. Blood-based biomarkers are particularly desirable since serum or plasma is easily accessible and can be sampled repeatedly. To comprehensively explore the biomarker potential of miRNAs, sensitive, accurate and cost-efficient miRNA profiling techniques are required. Next generation sequencing (NGS) is emerging as the preferred method for miRNA profiling; offering high sensitivity, single-nucleotide resolution and the possibility to profile a considerable number of samples in parallel. Despite the excitement about miRNA biomarkers, challenges associated with insufficient characterization of the sequencing library preparation efficacy, precision and method-related quantification bias have not been addressed in detail and are generally underappreciated in the wider research community. Here, we have tested in parallel four commercially available small RNA sequencing kits against a cohort of samples comprised of human plasma, human serum, murine brain tissue and a reference library containing ~ 950 synthetic miRNAs. We discuss the advantages and limits of these methodologies for massive parallel microRNAs profiling. This work can serve as guideline for choosing an adequate library preparation method, based on sensitivity, specificity and accuracy of miRNA quantification, workflow convenience and potential for automation.

Quantification of MicroRNAs in human aqueous humor by miRFLP assay

MiRNAs are expressed in a tissue-specific fashion in the eyes and changes in miRNAs levels in aqueous humor (AH) may reflect the function of the eye and eye disease. Due to the low concentration of total miRNA in human aqueous humor, high volume of sample is required for RNA extraction prior to routine quantification such as RT-qPCR. However, limited volume of AH could be collected through surgery because of the characteristic of the eye. In addition, inefficiency of RNA-extraction kits could affect target miRNA quantification dramatically. AH-direct miRFLP assay was developed for quantification of target miRNAs in human aqueous humor samples. For the first time, accurate miRNA quantification in human AH was achieved with microliter scale sample loading. Higher copy numbers of target miRNAs were obtained in direct detection than in RNA-extraction solution. It indicates that AH-direct miRFLP assay was able to quantify target miRNAs more accurately with no requirement for RNA-extraction to avoid sampling variability.

Small and Smaller-sRNAs and MicroRNAs in the Regulation of Toxin Gene Expression in Prokaryotic Cells: A Mini-Review

Non-coding small RNAs (sRNAs) have been identified in the wide range of bacteria (also pathogenic species) and found to play an important role in the regulation of many processes, including toxin gene expression. The best characterized prokaryotic sRNAs regulate gene expression by base pairing with mRNA targets and fall into two broad classes: cis-encoded sRNAs (also called antisense RNA) and trans-acting sRNAs. Molecules from the second class are frequently considered as the most related to eukaryotic microRNAs. Interestingly, typical microRNA-size RNA molecules have also been reported in prokaryotic cells, although they have received little attention up to now. In this work we have collected information about all three types of small prokaryotic RNAs in the context of the regulation of toxin gene expression.

A DNA Circuit for IsomiR Detection

A synthetic DNA oligonucleotide has been programmed to function as a biological circuit to detect 5'-IsomiRs. The circuit consists of two integrated DNA switches. The first is "activated" when a DNA probe is enzymatically modified by a reverse transcriptase that incorporates nucleotides complementary to the 5'-region of a microRNA (miRNA). Addition of the correct number and sequence of nucleotides enables the probe to assemble into an asymmetric DNA hairpin. The reconfigured hairpin probe then primes an internal polymerisation reaction, resulting in the synthesis of a symmetrical DNA hairpin. This activates the second switch, which then initiates the amplification of reverse-transcribed miRNA through a continuous cycle of DNA nicking and polymerisation. The DNA circuit enables sensitive and rapid detection of femtomoles of a miRNA transcript under isothermal conditions.

Translating extracellular microRNA into clinical biomarkers for drug-induced toxicity: from high-throughput profiling to validation

Over the past 5 years, extracellular microRNAs (miRNAs) are being vigorously explored as injury biomarkers, including drug-induced cardiotoxicity, hepatotoxicity and nephrotoxicity. Currently, the development of miRNAs as clinical biomarkers has been hindered by the lack of standardization. Therefore, extracellular miRNA-based biomarkers have not been embraced as diagnostic tools. Each platform has its strengths and weaknesses when working with low-input-amount RNA samples from body fluids; the selection of a miRNA quantification approach should be based on the study design. The following review provides a summary of the extracellular miRNA release and stability in body fluids, performances of different miRNA quantification platforms, existing clinical gold standards for drug-induced tissue damage and translation of the miRNA biomarkers from the nonclinical to clinical setting.