RNAi and microRNAs: From animal models to disease therapy

RNA-targeted therapeutics in cancer clinical trials: Current status and future directions

Recent advances in RNA delivery and target selection provide unprecedented opportunities for cancer treatment, especially for cancers that are particularly hard to treat with existing drugs. Small interfering RNAs, microRNAs, and antisense oligonucleotides are the most widely used strategies for silencing gene expression. In this review, we summarize how these approaches were used to develop drugs targeting RNA in human cells. Then, we review the current state of clinical trials of these agents for different types of cancer and outcomes from published data. Finally, we discuss lessons learned from completed studies and future directions for this class of drugs.

Nucleic Acids-Based Nanotechnology

Nanobiotechnology is emerging as a valuable field that integrates research from science and technology to create novel nanodevices and nanostructures with various applications in modern nanotechnology. Applications of nanobiotechnology are employed in biomedical and pharmaceutical research, biosensoring, nanofluidics, self-assembly of nanostructures, nanopharmaceutics, molecular computing, and others. It has been proven that nucleic acids are a very suitable medium for self-assembly of diverse nanostructures and catalytic nanodevices for various applications. In this chapter, the authors discuss various applications of nucleic-based nanotechnology. The areas discussed here include building nanostructures using DNA oligonucleodite, self-assembly of integrated RNA-based nanodevices for molecular computing and diagnostics, antibacterial drug discovery, exogenous control of gene expression, and gene silencing.

Gene expression profiling of Atlantic cod (Gadus morhua) embryogenesis using microarray

Atlantic cod (Gadus morhua) is a fish species of high importance, as a key species in a range of Northern ecosystems, in fisheries, and as an emerging species in aquaculture. So far, little is known about the transcriptional activity during early developmental stages of Atlantic cod. Hence, we decided to use a cDNA microarray covering 7,000 genes to analyze the temporal activity of the transcriptome during cod embryogenesis. Twelve different embryonic time points were selected, covering major developmental stages and processes such as maternally derived mRNA, blastula, gastrula, segmentation, hatching, and first-feeding larval stage. The microarray analysis revealed a highly dynamic transcriptional profile, showing for the first time the differential expression of thousands of known and unknown genes during Atlantic cod embryogenesis. These initial findings will serve as an important baseline for future in-depth studies of candidate genes involved in development, reproductive control, disease resistance, growth, nutrient digestion, and metabolism.

PLP/DM20 expression and turnover in a transgenic mouse model of Pelizaeus-Merzbacher disease

The most common cause of Pelizaeus-Merzbacher (PMD) is due to duplication of the PLP1 gene but it is unclear how increased gene dosage affects PLP turnover and causes dysmyelination. We have studied the dynamics of PLP/DM20 in a transgenic mouse model of PMD with increased gene dosage of the proteolipid protein gene (Plp1). The turnover of PLP/DM20 were investigated using an ex-vivo brain slice system and cultured oligodendrocytes. Homozygous mice have reduced PLP translation, markedly enhanced PLP degradation, and markedly reduced incorporation of PLP into myelin. Proteasome inhibition (MG132) prevented the enhanced degradation. Numerous autophagic vesicles are present in homozygous transgenic mice that may influence protein dynamics. Surprisingly, promoting autophagy with rapamycin decreases the degradation of nascent PLP suggesting autophagic vacuoles serve as a cellular storage compartment. We suggest that there are multiple subcellular fates of PLP/DM20 when overexpressed: the vast majority being degraded by the proteasome, a proportion sequestered into autophagic vacuoles, probably fused with endolysosomes, and only a small proportion entering the myelin sheath, where its association with lipid rafts is perturbed. Transgenic oligodendrocytes have fewer membrane sheets and this phenotype is improved with siRNA-mediated knockdown of PLP expression that promotes the formation of MBP+ myelin-like sheets. This finding suggests that RNAi technology is in principle applicable to improve CNS myelination when compromised by PLP/DM20 overexpression.

Chitosan/siRNA nanoparticles biofunctionalize nerve implants and enable neurite outgrowth

Microstructured 20 μm thick polymer filaments used as nerve implants were loaded with chitosan/siRNA nanoparticles to promote nerve regeneration and ensure local delivery of nanotherapeutics. The stable nanoparticles were rapidly internalized by cells and did not affect cell viability. Target mRNA was successfully reduced by 65-75% and neurite outgrowth was enhanced even in an inhibitory environment. This work, thus, supports the application of nanobiofunctionalized implants as a novel approach for spinal cord and nerve repair.

A new approach for therapeutic use by RNA interference in the brain

RNA interference (RNAi) is a gene silencing phenomenon that is induced by ribonucleoprotein complexes containing 21-28 nucleotides (nt) of double-stranded RNA (si/miRNA). Although this phenomenon occurs in an inherent manner, it can also be induced in an artificially manipulated manner. Recently, the understanding of RNAi mechanisms has progressed from that in plants to that in mammals. As RNAi is a highly efficient and readily available procedure to knockdown specific targets, it can possibly be used as a new technique providing many researchers and clinicians with opportunities for its experimental use and prospective clinical application. Consequently, there has been a rush of elucidation of the effective sequences of siRNAs used for the knockdown of the targets in many fields, including neuroscience and experiments for neurological disorders. However, in many cases, it is difficult to effectively introduce si/miRNA into cells without causing injury to the recipient cells. Apart from the off-target effects and the pathogenic property of si/miRNA per se, which are designed and produced, the possibility and intensity of cell injury by RNAi depends on the method employed for the introduction of si/miRNA. Possible methods include si/miRNA delivery systems using liposome, polyethylenimine (PEI), electroporation, and viral infection. Currently, various methods for delivering si/miRNA into cells have been developed and challenged. Here, I review the advantages, disadvantages, and perspective of employing the RNAi procedure in the brain. Given that the disadvantages of RNAi can be overcome, the clinical application of RNAi technologies may be useful in realizing the elimination of pathogenic genes not only in the brain, but also in the other organs in the near future.

Large-scale sequence analyses of Atlantic cod

The Atlantic cod (Gadus morhua) is a key species in the North Atlantic ecosystem and commercial fisheries, with increasing aquacultural production in several countries. A Norwegian effort to sequence the complete 0.9Gbp genome by the 454 pyrosequencing technology has been initiated and is in progress. Here we review recent progress in large-scale sequence analyses of the nuclear genome, the mitochondrial genome and genome-wide microRNA identification in the Atlantic cod. The nuclear genome will be de novo sequenced with 25 times oversampling. A total of 120 mitochondrial genomes, sampled from several locations in the North Atlantic, are being completely sequenced by Sanger technology in a high-throughput pipeline. These sequences will be included in a new database for maternal marker reference of Atlantic cod diversity. High-throughput 454 sequencing, as well as Evolutionary Image Array (EvoArray) informatics, is used to investigate the complete set of expressed microRNAs and corresponding mRNA targets in various developmental stages and tissues. Information about microRNA profiles will be essential in the understanding of transcriptome complexity and regulation. Finally, developments and perspectives of Atlantic cod aquaculture are discussed in the light of next-generation high-throughput sequence technologies.

MicroRNA-9 directs late organizer activity of the midbrain-hindbrain boundary

The midbrain-hindbrain boundary (MHB) is a long-lasting organizing center in the vertebrate neural tube that is both necessary and sufficient for the ordered development of midbrain and anterior hindbrain (midbrain-hindbrain domain, MH). The MHB also coincides with a pool of progenitor cells that contributes neurons to the entire MH. Here we show that the organizing activity and progenitor state of the MHB are co-regulated by a single microRNA, miR-9, during late embryonic development in zebrafish. Endogenous miR-9 expression, initiated at late stages, selectively spares the MHB. Gain- and loss-of-function studies, in silico predictions and sensor assays in vivo demonstrate that miR-9 targets several components of the Fgf signaling pathway, thereby delimiting the organizing activity of the MHB. In addition, miR-9 promotes progression of neurogenesis in the MH, defining the MHB progenitor pool. Together, these findings highlight a previously unknown mechanism by which a single microRNA fine-tunes late MHB coherence via its co-regulation of patterning activities and neurogenesis.

A tightly regulated Pol III promoter for synthesis of miRNA genes in tandem

A compelling tool for functional genetics is to silence the expression of multiple related genes concomitantly and reversibly. Such a tool will accelerate the understanding on gene interaction in signaling pathway and the development of comprehensive animal models for human diseases. Multiple gene silencing may be achieved by concurrent expression of multiple miRNA from a Pol II promoter. By comparison, Pol III promoters possess greater capacity to synthesize RNA of high yield and are consisted of compact elements and simple terminators to be convenient for handling. The miRNA-induced gene silencing is a dose-dependent event, and thus, Pol III promoter as a miRNA driver increases the chance to induce phenotypes subsequent to the gene silencing. As a Pol III promoter, endogenous U6 promoter synthesizes small nuclear RNA of high yield and is commonly adapted for miRNA synthesis. Whether U6 promoter is effective to synthesize multiple miRNA in tandem remains to be determined. This study exploited a possibility to express multiple miRNA genes from U6 promoter and also tested the inducibility of varying types of Tet-regulatable U6 promoters. With miR-30a backbone, two miRNA genes were functionally and efficiently expressed from a U6 promoter. The transcriptional activity of Tet-regulatable U6 promoter was tightly regulated by Tetracycline system after sufficient repeats of Tetracycline Operator sequence were introduced within the promoter regions and also between U6 promoter and miRNA gene. This newly developed U6 miRNA system would make multi-gene silencing efficient and reversible.

[Relevance of microRNA-s in neoplastic diseases]

MicroRNA molecules consisting of 19-23 nucleotides influence numerous basic physiological and pathophysiological processes as endogenous mediators of RNA interference. These molecules are capable of specifically inhibiting the translation of messenger RNA molecules, but in some cases also promote the degradation of mRNA-s. Altered microRNA expression profiles were noted in several human diseases, most data, however, are known for neoplasms. Characteristic microRNA profiles are known both in solid and haematologic malignancies. MicroRNA profiles enable the distinction of benign follicular adenomas from follicular neoplasms of the thyroid. The micro-RNA expression patterns could be associated with the clinical behaviour of certain neoplasms (e.g. lung tumours and chronic lymphocytic leukemia) as well. It is possible that small molecular weight RNA-s may be used for therapeutical purposes in the future.

Energizing miRNA research: a review of the role of miRNAs in lipid metabolism, with a prediction that miR-103/107 regulates human metabolic pathways

MicroRNAs (miRNAs) are powerful regulators of gene expression. Although first discovered in worm larvae, miRNAs play fundamental biological roles-including in humans-well beyond development. MiRNAs participate in the regulation of metabolism (including lipid metabolism) for all animal species studied. A review of the fascinating and fast-growing literature on miRNA regulation of metabolism can be parsed into three main categories: (1) adipocyte biochemistry and cell fate determination; (2) regulation of metabolic biochemistry in invertebrates; and (3) regulation of metabolic biochemistry in mammals. Most research into the 'function' of a given miRNA in metabolic pathways has concentrated on a given miRNA acting upon a particular 'target' mRNA. Whereas in some biological contexts the effects of a given miRNA:mRNA pair may predominate, this might not be the case generally. In order to provide an example of how a single miRNA could regulate multiple 'target' mRNAs or even entire human metabolic pathways, we include a discussion of metabolic pathways that are predicted to be regulated by the miRNA paralogs, miR-103 and miR-107. These miRNAs, which exist in vertebrate genomes within introns of the pantothenate kinase (PANK) genes, are predicted by bioinformatics to affect multiple mRNA targets in pathways that involve cellular Acetyl-CoA and lipid levels. Significantly, PANK enzymes also affect these pathways, so the miRNA and 'host' gene may act synergistically. These predictions require experimental verification. In conclusion, a review of the literature on miRNA regulation of metabolism leads us believe that the future will provide researchers with many additional energizing revelations.