Design of Effective Primary MicroRNA Mimics With Different Basal Stem Conformations

Premature MicroRNA-Based Therapeutic: A "One-Two Punch" against Cancers

Simple Summary

The current understanding of miRNA biology is greatly derived from studies on the guide strands and the passenger strands, also called miRNAs*, which are considered as carriers with no sense for long periods. As such, various studies alter the expression of guide strands by manipulating the expression of their primary transcripts or precursors, both of which are premature miRNAs. In this situation, the regulatory miRNA* species may interfere with the phenotypic interpretation against the target miRNA. However, such methods could manipulate the expression of two functionally synergistic miRNAs of the same precursor, leading to therapeutic potential against various diseases, including cancers. Premature miRNAs represent an underappreciated target reservoir and provide molecular targets for “one-two punch” against cancers. Examples of targetable miRNA precursors and available targeting strategies are provided in this review.

Abstract

Up-to-date knowledge regarding the biogenesis and functioning of microRNAs (miRNAs) has provided a much more comprehensive and concrete view of miRNA biology than anyone ever expected. Diverse genetic origins and biogenesis pathways leading to functional miRNAs converge on the synthesis of ≈21-nucleotide RNA duplex, almost all of which are processed from long premature sequences in a DICER- and/or DROSHA-dependent manner. Formerly, it was assumed that one mature strand of the duplex is preferentially selected for entry into the silencing complex, and the paired passenger strands (miRNA*) are subjected to degradation. However, given the consolidated evidence of substantial regulatory activity of miRNA* species, currently, this preconception has been overturned. Here, we see the caveat and opportunity toward exogenously manipulating the expression of premature miRNA, leading to simultaneous upregulation or downregulation of dual regulatory strands due to altered expressions. The caveat is the overlooked miRNA* interference while manipulating the expression of a target miRNA at the premature stage, wherein lies the opportunity. If the dual strands of a pre-miRNA function synergistically, the overlooked miRNA* interference may inversely optimize the therapeutic performance. Insightfully, targeting the premature miRNAs may serve as the “one-two punch” against diseases, especially cancers, and this has been discussed in detail in this review.

Generating DNA Expression Cassettes Encoding Multimeric Artificial MicroRNA Precursors

RNA interference (RNAi) is a promising tool for the treatment of chronic viral infection, such as that caused by the hepatitis B virus (HBV). RNAi activators, including expressed primary microRNA (pri-miRNA) mimics, can effectively silence viral gene expression and thereby inhibit viral replication. Here we describe a protocol for the design, generation and functional assessment of cassettes encoding effective single and multimeric pri-miRNA mimics. Artificial miRNAs targeting viral genes can be identified in silico and used to design corresponding pri-miRNA mimics. A two-step generation and TA cloning protocol can be used to produce single mimics, while the strategic use of restriction sites enables concatenation of mimics in a sub-cloning protocol. Basic gene silencing function of pri-miRNA mimics in cell culture can then be assessed using a dual luciferase assay and appropriate minimal targets. The methods described here for the generation of effective pri-miRNA mimics targeting HBV can be applied in the silencing of other viral or endogenous genes.

Efficient Knockdown and Lack of Passenger Strand Activity by Dicer-Independent shRNAs Expressed from Pol II-Driven MicroRNA Scaffolds

The expression of short hairpin RNAs (shRNAs) may result in unwanted activity from the co-processed passenger strand. Recent studies have shown that shortening the stem of conventional shRNAs abolishes passenger strand release. These Dicer-independent shRNAs, expressed from RNA polymerase III (Pol III) promoters, rely on Ago2 processing in resemblance to miR-451. Using strand-specific reporters, we tested two designs, and our results support the loss of passenger strand activity. We demonstrate that artificial primary microRNA (pri-miRNA) transcripts, expressed from Pol II promoters, can potently silence a gene of choice. Among six different scaffolds tested, miR-324 and miR-451 were readily re-targeted to direct efficient knockdown from either a CMV or a U1 snRNA promoter. Importantly, the miR-shRNAs have no passenger strand activity and remain active in Dicer-knockout cells. Our vectors are straightforward to design, as we replace the pre-miR-324 or -451 sequences with a Dicer-independent shRNA mimicking miR-451 with unpaired A-C nucleotides at the base. The use of Pol II promoters allows for controlled expression, while the inclusion of pri-miRNA sequences likely requires Drosha processing and, as such, mimics microRNA biogenesis. Since this improved and tunable system bypasses the requirement for Dicer activity and abolishes passenger strand activity completely, it will likely prove favorable in both research and therapeutic applications in terms of versatility and enhanced safety.

The Role of miRNAs in Common Inflammatory Arthropathies: Osteoarthritis and Gouty Arthritis

MicroRNAs (miRNAs) are small, non-coding RNA species that are highly evolutionarily conserved, from higher invertebrates to man. Up to 1000 miRNAs have been identified in human cells thus far, where they are key regulators of the expression of numerous targets at the post-transcriptional level. They are implicated in various processes, including cell differentiation, metabolism, and inflammation. An expanding list of miRNAs is known to be involved in the pathogenesis of common, non-autoimmune inflammatory diseases. Interestingly, osteoarthritis (OA) is now being conceptualized as a metabolic disease, as there is a correlation among hyperuricemia and metabolic syndrome (MetS). Experimental evidence suggests that metabolic deregulation is a commonality between these different pathological entities, and that miRNAs are key players in the modulation of metabolic routes. In light of these findings, this review discusses the role of miRNAs in OA and gouty arthritis, as well as the possible therapeutic targetability of miRNAs in these diseases.