Antagonism of microRNA function in zebrafish embryos by using locked nucleic acid enzymes (LNAzymes)

DNAzymes: Expanding the Potential of Nucleic Acid Therapeutics

Nucleic acids drugs have been proven in the clinic as a powerful modality to treat inherited and acquired diseases. However, key challenges including drug stability, renal clearance, cellular uptake, and movement across biological barriers (foremost the blood-brain barrier) limit the translation and clinical efficacy of nucleic acid-based therapies, both systemically and in the central nervous system. In this study we provide an overview of an emerging class of nucleic acid therapeutic, called DNAzymes. In particular, we review the use of chemical modifications and carrier molecules for the stabilization and/or delivery of DNAzymes in cell and animal models. Although this review focuses on DNAzymes, the strategies described are broadly applicable to most nucleic acid technologies. This review should serve as a general guide for selecting chemical modifications to improve the therapeutic performance of DNAzymes.

miR-181a regulates the host immune response against Schistosoma japonicum infection through the TLR4 receptor pathway

Background

Schistosomiasis japonica is a serious zoonotic parasitic disease. Preliminary studies have shown that the expression of microRNA-181a (miR-181a) in the liver, lung and spleen tissues of susceptible host BALB/c mice and resistant host reed vole (Microtus fortis) 10 days post-infection (dpi) with Schistosoma japonicum was significantly different from pre-infection levels. This difference suggests the possibility that miR-181a expression may be related to the regulation of the hosts’ early immune response against S. japonicum infection and thereby affect the development and survival of parasites in their final hosts.

Methods

BALB/c mice, M. fortis, Toll-like receptor 4 (TLR4)-deficient mice and wild-type mice (C57BL/6) were infected with S. japonicum, and differences in miR-181a expression between BALB/c mice and M. fortis over different time points post-infection (0, 3, 7, 10 and 14 dpi) were compared. MiR-181a mimic, miR-181a inhibitor and irrelevant miRNA, as well as lipopolysaccharide (LPS), a TLR4 receptor ligand, were used to transfect mouse RAW264.7 macrophages. The expression levels of the TLR4 pathway-related cytokines interleukin (IL)-1β, tumor necrosis factor α (TNF-α) and IL-6 were detected by quantitative PCR analysis.

Results

The expression of miR-181a was significantly upregulated in the serum and liver of mice infected with S. japonicum and downregulated in the serum and liver of M. fortis. T-helper cell (Th1)-type cytokines, such as TNF-α, IL-6 and IL-1β, and Th2-type cytokines, such as IL-10 and IL-4, were differentially expressed in M. fortis and BALB/c mice in the early stage of infection. The expression level of miR-181a in the serum was threefold higher in TLR4-deficient mice than in wild-type mice 10 dpi with S. japonicum. The expression of IL-1β, TNF-α and IL-6 decreased in RAW264.7 cells transfected with miR-181a mimic and increased in cells transfected with miR-181a inhibitor. miR-181a expression was downregulated and the expressions of TLR4 and three TLR4 pathway-related cytokines (IL-1β, IL-6, and TNF-α) were upregulated in RAW264.7 macrophages stimulated with the TLR4 receptor ligand LPS.

Conclusion

These results suggest the possibility of mutual regulation between miR-181a and the TLR4 signaling pathway during S. japonicum infection. miR-181a may regulate the expression of pro-inflammatory factors through the TLR4 receptor pathway and participate in the immunomodulatory effect of anti-S. japonicum infection.

Graphical abstract

Targeted and direct intracellular delivery of native DNAzymes enables highly specific gene silencing

DNAzymes exhibit high potential as gene silencing agents for therapeutic applications. Such purposes, however, are significantly challenged by the targeted and successful delivery of unmodified DNAzymes into cells with minimal side effects. Here, we set out to formulate and demonstrate a new stimuli-responsive and constrained aptamer/DNAzyme (Apt/Dz) catenane nanostructure for highly specific gene silencing. The rational design of the Apt/Dz catenane nanostructure with the respective integration of the aptamer sequence and the completely closed catenane format enables both the targeted capability and significantly improved nuclease resistance, facilitating the stable and targeted delivery of unmodified Dz into cancer cells. Moreover, the Dz enzymatic activity in the constrained structure can only be conditionally regulated by the specific intracellular mRNA sequences to silence the target gene with highly reduced side effects. Results show that the Apt/Dz catenane nanostructure can effectively inhibit the expression of the target gene and the proliferation of cancer cells with high specificity.

LncRNAs regulating stemness in aging

One of the most outstanding observations from next-generation sequencing approaches was that only 1.5% of our genes code for proteins. The biggest part is transcribed but give rise to different families of RNAs without coding potential. The functional relevance of these abundant transcripts remains far from elucidated. Among them are the long non-coding RNAs (lncRNAs), a relatively large and heterogeneous group of RNAs shown to be highly tissue-specific, indicating a prominent role in processes controlling cellular identity. In particular, lncRNAs have been linked to both stemness properties and detrimental pathways regulating the aging process, being novel players in the intricate network guiding tissue homeostasis. Here, we summarize the up-to-date information on the role of lncRNAs that affect stemness and hence impact upon aging, highlighting the likelihood that lncRNAs may represent an unexploited reservoir of potential therapeutic targets for reprogramming applications and aging-related diseases.

Zebrafish: A Premier Vertebrate Model for Biomedical Research in Indian Scenario

The zebrafish (Danio rerio) is a versatile model organism that has been used in biomedical research for several decades to study a wide range of biological phenomena. There are many technical advantages of using zebrafish over other vertebrate models. They are readily available, hardy, easy, and inexpensive to maintain in the laboratory, have a short life cycle, and have excellent fecundity. Due to its optical clarity and reproducible capabilities, it has become one of the predominant models of human genetic diseases. Zebrafish research has made rapid strides in the United States and Europe, but in India the field is at an early stage and many researchers still remain unaware of the full research potential of this tiny fish. The zebrafish model system was introduced into India in the early 2000s. Up to now, more than 200 scientific referred articles have been published by Indian researchers. This review gives an overview of the current state of knowledge for zebrafish research in India, with the aim of promoting wider utilization of zebrafish for high level biological studies.

HDL and microRNA therapeutics in cardiovascular disease

microRNAs (miRNA) are small non-coding RNAs (sRNA) that post-transcriptionally regulate gene (mRNA) expression and are implicated in many biological processes and diseases. Many miRNAs have been reported to be altered in cardiovascular disease (CVD); both cellular and extracellular miRNA levels are affected by hypercholesterolemia and atherosclerosis. We and other groups have reported that lipoproteins transport miRNAs in circulation and these lipoprotein signatures are significantly altered in hypercholesterolemia and coronary artery disease (CAD). Extracellular miRNAs are a new class of potential biomarkers for CVD; however, they may also be new drug targets as high-density lipoproteins (HDL) transfer functional miRNAs to recipient cells in an endocrine-like form of intercellular communication that likely suppresses vascular inflammation. Recently, RNA-based drugs have emerged as the next frontier in drug therapy, and there are many miRNA inhibitors and mimics in clinical development. Here, we discuss specific miRNA drug targets and how their manipulation may impact CVD. We also address the potential for manipulating HDL-miRNA levels to treat CVD and the use of HDL as a delivery vehicle for RNA and chemical drugs. Finally, we outline the current and future challenges for HDL and miRNA-based therapeutics for the prevention and treatment of CVD.

Nonconventional chemical inhibitors of microRNA: therapeutic scope

MicroRNAs (miRNAs) are a class of genomically encoded small RNA molecules (∼22nts in length), which regulate gene expression post transcriptionally. miRNAs are implicated in several diseases, thus modulation of miRNA is of prime importance. Small molecules offer a non-conventional alternative to do so.

Hepatitis C virus gene-specific locked nucleic acid enzyme significantly inhibits C gene expression in vitro

AIM: To investigate the inhibitory effects of locked nucleic acid enzyme targeting the hepatitis C virus (HCV) C gene on HCV RNA replication and expression in HepG2.9706 cells.

METHODS: The sequences encoding DNAzyme, thiolmodificated DNAzyme and LNAzyme targeting the HCV C gene were designed and synthesized. The following experimental groups were set up: lipo-DNAzyme, lipo-S-DNAzyme, lipo-LNAzyme, blank control, empty liposomes, and lipo-random-LNAzyme. Transfection was performed using cationic liposomes. The level of HCV RNA and luciferase gene expression in supernatants were tested by real-time fluorescent quantitative PCR and chemiluminescence technique 24, 48 and 96 h after treatment, respectively. Cytotoxicity of LNAzyme was evaluated by MTT assay.

RESULTS: Significant down-regulation of HCV RNA replication and luciferase gene expression was noted in the lipo-LNAzyme group, lipo-DNAzyme group and lipo-S-DNAzyme group compared with the control group (P < 0.05 for all). Relative to the lipo-DNAzyme group and lipo-S-DNAzyme group, the average inhibition rates in the lipo-LNAzyme group were 47.55% and 52.44%, respectively. With the prolongation of the treatment time, the inhibition rate increased. At 96 h, HCR RNA replication and fluorescent protein expression were significantly lower than those before treatment in the lipo-LNAzyme group (P < 0.01 for both), and the average inhibition rates were 79.40% and 84.05%, respectively. No obvious toxicity was observed.

CONCLUSION: LNAzyme has a significant inhibitory effect on HCV C gene replication and expression in vitro, which is stronger than that of the thiolmodificated DNAzyme.

Regulatory mechanisms of long noncoding RNAs in vertebrate central nervous system development and function

Long noncoding RNAs (lncRNAs) have emerged as an important class of molecules that regulate gene expression at epigenetic, transcriptional, and post-transcriptional levels through a wide array of mechanisms. This regulation is of particular importance in the central nervous system (CNS), where precise modulation of gene expression is required for proper neuronal and glial production, connection and function. There are relatively few functional studies that characterize lncRNA mechanisms, but possible functions can often be inferred based on existing examples and the lncRNA's relative genomic position. In this review, we will discuss mechanisms of lncRNAs as predicted by genomic contexts and the possible impact on CNS development, function, and disease pathogenesis. There is no doubt that investigation of the mechanistic role of lncRNAs will open a new and exciting direction in studying CNS development and function.