Aptamer mediated siRNA delivery

Cell specific aptamer-photosensitizer conjugates as a molecular tool in photodynamic therapy

This paper describes the application of a molecular construct of a photosensitizer and an aptamer for photo-therapeutically targeting tumor cells. The key step in increasing selectivity in chemotherapeutic drugs is to create effective molecular platforms that could target cancer cells but not normal cells. Recently, we have developed a strategy via cell-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) to obtain cell specific aptamers using intact viable cells as targets to select aptamers that can recognize cell membrane proteins with high selectivity and excellent affinity. We have identified an aptamer TD05 that only recognizes Ramos cells, a Burkitt’s lymphoma cell line. Here, the high specificity of aptamers in target cell binding and an efficient phototherapy reagent, Ce6, are molecularly engineered to construct a highly selective Aptamer-photosensitizer conjugates (APS) to effectively destroy target cancer cells. Introduction of the APS conjugates followed by irradiation of light selectively destroyed target Ramos cells but not acute lymphoblastic leukemia and myeloid leukemia cell lines. This study demonstrates that the use of cancer specific aptamers conjugated to a photosensitizer will enhance the selectivity of photodynamic therapy. Coupled with the advantages of the cell-SELEX in generating multiple effective aptamers for diseased cell recognition, we will be able to develop highly efficient photosensitizer based therapeutical reagents for clinical applications.

Cell studies of a three-component antisense MORF/tat/Herceptin nanoparticle designed for improved tumor delivery

The three-component nanoparticle of this investigation consisted of an anti-type I regulatory subunit alpha of the cyclic AMP-dependent protein kinase A (RIalpha) antisense phosphorodiamidate morpholino (MORF) oligomer, a tat peptide and the anti-HER2 Herceptin antibody each biotinylated and each linked via streptavidin and tested in SUM190 (HER2+), SUM149 (HER2-) and SK-BR-3 (HER2+) cells in culture, using both radioactivity and fluorescent labels on the antisense and control sense MORF. Within the nanoparticle, the antibody provides specific binding to the target cells, the tat improves cellular delivery and the MORF provides the specific retention of the radioactivity in the target cell nucleus. The results show that within the nanoparticle, the Herceptin was still able to bind to its determinant; that the MORF escaped entrapment with its mRNA-binding ability preserved and that the tat maintained its carrier function. Fluorescence microscopy showed evidence of antisense MORF internalization, separation from Herceptin and migration to the nucleus. In conclusion, streptavidin appears to provide an easy means of mixing and matching components to improve the tumor-specific targeting, cell membrane transport, pharmacokinetics and other properties of antisense and other oligomers. Combining the three components of this investigation with streptavidin apparently did not interfere with the properties of each component in cell culture and significantly improved delivery.

RNAi for treating hepatitis B viral infection

Chronic hepatitis B virus (HBV) infection is one of the leading causes of liver cirrhosis and hepatocellular carcinoma (HCC). Current treatment strategies of HBV infection including the use of interferon (IFN)-α and nucleotide analogues such as lamivudine and adefovir have met with only partial success. Therefore, it is necessary to develop more effective antiviral therapies that can clear HBV infection with fewer side effects. RNA interference (RNAi), by which a small interfering RNA (siRNA) induces the gene silence at a post-transcriptional level, has the potential of treating HBV infection. The successful use of chemically synthesized siRNA, endogenous expression of small hairpin RNA (shRNA) or microRNA (miRNA) to silence the target gene make this technology towards a potentially rational therapeutics for HBV infection. However, several challenges including poor siRNA stability, inefficient cellular uptake, widespread biodistribution and non-specific effects need to be overcome. In this review, we discuss several strategies for improving the anti-HBV therapeutic efficacy of siRNAs, while avoiding their off-target effects and immunostimulation. There is an in-depth discussion on the (1) mechanisms of RNAi, (2) methods for siRNA/shRNA production, (3) barriers to RNAi-based therapies, and (4) delivery strategies of siRNA for treating HBV infection.

Facilitated in vivo synthesis of ribonucleic acid and protein via T7 RNA polymerase

Ribozyme and small interfering RNA (siRNA) now are widely used to suppress target genes bearing homologous sequences. In this study, commonly used cell lines (e.g., HEK, HeLa, H1299) were stably transfected with gene encoding T7 RNA polymerase. The cytoplasm-restricted transcription activity of T7 RNA polymerase confers a continuous and robust transcription from T7 promoter-containing oligonucleotide (ODN) template for siRNA or ribozyme and leads to 70 to 80% inhibition of the tested target genes. ODN template offers the advantages of being more stable and economical than synthetic or in vitro-transcribed siRNA or ribozyme. Compared with the use of siRNA/ribozyme-expressing plasmids, our system does not require procedures with preparations of recombinant plasmids and enrichment of transfected cells and can be applied to synthesize protein in which different levels of translation could be modulated via variations in the presence of polyA tail or internal ribosome entry site (IRES) in the T7-transcribed RNAs. The results of our current study provide a rapid and efficient system for the assay of in vivo synthesis and expression of RNAs and proteins.

Conjugation of nucleosides and oligonucleotides by [3+2] cycloaddition

A procedure is presented for copper(I)-catalyzed [3+2] cycloaddition of nucleosides and nucleotides in near-quantitative yield. Azido-alkyne cycloaddition was applied for the preparation of a range of adenosine dimers and derivatives with versatile functionality, as well as for the smooth condensation of two oligonucleotide strands. The described technology may find valuable application in the synthesis of oligonucleotide dimers and conjugates.

Nucleic acid aptamers for targeting of shRNA-based cancer therapeutics

Aptamers are nucleic acid ligands which have been validated to bind to epitopes with a specificity similar to that of monoclonal antibodies. Aptamers have been primarily investigated for their direct function in terms of inhibition of protein targets; however, recent evidence gives reason to actively explore aptamers as targeting moieties for delivery of anticancer therapeutics. Many aptamers have been developed to bind to extracellular membrane domains of proteins overexpressed on cancer cells and have the potential to be modified for use in targeting cancer therapeutics. The use of DNA vector-based short hairpin RNA (shRNA) for RNA interference (RNAi) is a precise means for the disruption of target gene expression but its clinical usage in cancer is limited by obstacles related to delivery into cancer cells. Nucleic acid aptamers are attractive candidates for targeting of shRNA therapies. Their small size, ease of production and modification, and high specificity are valued attributes in comparison to other targeting moieties currently being tested. Here we review the development of aptamers directed to PSMA, Nucleolin, HER-3, RET, TN-C, and MUC1 and focus on their potential for use in targeting of shRNA-based cancer therapeutics.

MicroRNAs in disease and potential therapeutic applications

MicroRNAs (miRNAs) are 21-24 nucleotide (nt) duplex RNAs that are created from precursor transcripts by subsequent processing steps mediated by members of the RNAseIII family, Drosha and Dicer. One of the two strands is incorporated into the active sites of the Argonaute family of proteins, where it serves as a guide for Watson-Crick base pairing with complementary sequences in target messenger RNAs (mRNAs). In mammals, the majority of miRNAs guide the RNA-induced silencing complex (RISC) to the 3' untranslated regions (UTRs) of mRNA targets, with the consequence that translation of the target mRNAs is inhibited. The importance of miRNAs in normal cellular development and metabolism is only now being realized. miRNA deficiencies or excesses have been correlated with a number of clinically important diseases ranging from myocardial infarction to cancers. The loss or gain of miRNA function can be caused by a single point mutation in either the miRNA or its target or by epigenetic silencing of primary miRNA transcription units. This review summarizes miRNA biogenesis and biology, explores the potential roles miRNAs can play in a variety of diseases, and suggests some therapeutic applications for restoring or inhibiting miRNA function.

The versatility of oligonucleotides as potential therapeutics

Oligonucleotides can in a variety of ways inhibit gene expression by interfering with translation. Oligonucleotides that are complementary to a target mRNA, antisense oligonucleotides, can prevent translation either by cleaving the target or by physically blocking the process. Additionally, oligonucleotides can correct the undesired splicing of pre-mRNA. RNA interference using double-stranded oligoribonucleotides also results in cleavage of the target mRNA. Catalytically competent ribozymes and DNAzymes can have the same effect. Even with no RNA as target, oligonucleotides can be selected as aptamers to bind to any protein to inhibit its activity. Moreover, oligonucleotides can act as decoys particularly for transcription factors to prevent binding to the promoter. A different mode of action is the activation of Toll-like receptors to induce an immune response. Several pathways for drug development are still in their infancy, for example microRNAs and antagomirs.

Interfering with disease: a progress report on siRNA-based therapeutics

RNA interference (RNAi) has rapidly advanced since its initial discovery to form the basis of a new class of therapeutics. De Fougerolles and colleagues discuss the challenges in the development of RNAi-based therapeutics, focusing on lead identification/optimization and effective delivery, and review the latest clinical results.

RNA interference (RNAi) quietly crept into biological research in the 1990s when unexpected gene-silencing phenomena in plants and flatworms first perplexed scientists. Following the demonstration of RNAi in mammalian cells in 2001, it was quickly realized that this highly specific mechanism of sequence-specific gene silencing might be harnessed to develop a new class of drugs that interfere with disease-causing or disease-promoting genes. Here we discuss the considerations that go into developing RNAi-based therapeutics starting from in vitro lead design and identification, to in vivo pre-clinical drug delivery and testing. We conclude by reviewing the latest clinical experience with RNAi therapeutics.

Targeted quantum dot conjugates for siRNA delivery

Treatment of human diseases such as cancer generally involves the sequential use of diagnostic tools and therapeutic modalities. Multifunctional platforms combining therapeutic and diagnostic imaging functions in a single vehicle promise to change this paradigm. in particular, nanoparticle-based multifunctional platforms offer the potential to improve the pharmacokinetics of drug formulations, while providing attachment sites for diagnostic imaging and disease targeting features. We have applied these principles to the delivery of small interfering RNA (siRNA) therapeutics, where systemic delivery is hampered by rapid excretion and nontargeted tissue distribution. Using a PEGlyated quantum dot (QD) core as a scaffold, siRNA and tumor-homing peptides (F3) were conjugated to functional groups on the particle's surface. We found that the homing peptide was required for targeted internalization by tumor cells, and that siRNA cargo could be coattached without affecting the function of the peptide. Using an EGFP model system, the role of conjugation chemistry was investigated, with siRNA attached to the particle by disulfide cross-linkers showing greater silencing efficiency than when attached by a nonreducible thioether linkage. Since each particle contains a limited number of attachment sites, we further explored the tradeoff between number of F3 peptides and the number of siRNA per particle, leading to an optimized formulation. Delivery of these F3/siRNA-QDs to EGFP-transfected HeLa cells and release from their endosomal entrapment led to significant knockdown of EGFP signal. By designing the siRNA sequence against a therapeutic target (e.g., oncogene) instead of EGFP, this technology may be ultimately adapted to simultaneously treat and image metastatic cancer.

Simplified preparation via streptavidin of antisense oligomers/carriers nanoparticles showing improved cellular delivery in culture

OBJECTIVE

Carriers are increasingly now viewed as helpful or even essential to improve cellular uptake in connection with antisense tumor targeting and other applications requiring transmembrane delivery of oligomers. Evaluation of many of the large number of available and potentially useful carriers is limited only by the complexities of preparing the oligomer/carriers by covalent conjugation. However, using streptavidin as a linker between biotinylated carriers and biotinylated antisense oligomers would require only simple mixing for preparation. The goal of this study was to evaluate the preparation and cell accumulation in culture of carrier/streptavidin nanoparticle of an antisense phosphorodiamide morpholino (MORF) oligomer.

METHODS

The model carriers were cholesterol, a 10 mer HIV-tat peptide, and a 10 mer polyarginine, each having been reported elsewhere to improve cellular delivery of oligomers. The model antisense oligomer was the 25 mer MORF targeting the survivin mRNA. The accumulations of the antisense MORF/carrier nanoparticle were compared to the sense MORF/carrier, to the carrier-free nanoparticles, and to the naked antisense MORF in the survivin-expressing MCF-7 cells. The MORFs and peptides were purchased biotinylated, while the cholesterol was biotinylated in-house. In all cases, the 99mTc radiolabel was placed on the oligomers. Cell studies were performed at low nM concentration as required for antisense imaging applications and at 37 degrees C primarily in 1% FBS.

RESULTS

Each radiolabeled oligomer/streptavidin/carrier nanoparticle was successfully prepared by careful mixing at a 1:1 molar ratio. As evidence of carrier participation, the radiolabeled MORF showed increased accumulation in cells when incubated as the nanoparticle compared to the carrier-free nanoparticle and by as much as a factor of 11. Accumulation of the antisense MORF/streptavidin/tat nanoparticle was significantly higher than the sense MORF/streptavidin/tat nanoparticle as evidence of specific antisense targeting.

CONCLUSIONS

The preparation of oligomer/carrier nanoparticles was greatly simplified over covalent conjugations by using streptavidin as a linker. Furthermore, our results suggest that the addition of streptavidin did not interfere with the cellular delivery function of the tat, polyarginine, or cholesterol carriers nor with the specific antisense mRNA binding function of the MORF oligomer.

Gene therapy progress and prospects: RNA aptamers

Aptamers are oligonucleotides evolved in vitro or in nature to bind target ligands with high affinity and specificity. They are emerging as powerful tools in the fields of therapeutics, drug development, target validation and diagnostics. Aptamers are attractive alternatives to antibody- and small-molecule-based therapeutics owing to their stability, low toxicity, low immunogenicity and improved safety. With the recent approval of the first aptamer drug Macugen by the US FDA, there is great impetus to develop therapeutic aptamers that can target a wide array of disease states. The recent demonstration that aptamer activity can be reversed by the administration of a simple antidote greatly enhances the potential value of aptamers as therapeutic agents.

Gene therapy for stroke: 2006 overview

Gene therapy is a promising approach for treatment of stroke and other cerebrovascular diseases, although it may take many years to realize. Gene therapy could occur prior to a stroke (eg, to stabilize atherosclerotic plaques) and/or following a stroke (eg, to prevent vasospasm after subarachnoid hemorrhage or reduce injury to neurons by ischemic insult). We have transferred the gene coding for vasoactive calcitonin gene-related peptide via cerebrospinal fluid, and demonstrated attenuation of vasospasm after SAH. Transfer of neuroprotective genes or small interfering RNA for neurotoxic genes has good potential for ischemic stroke. In this brief report, we review recent developments in experimental gene therapy for stroke. Fundamental advances, including development of safer, more specific gene transfer vectors, are discussed.

Hydrophobization and bioconjugation for enhanced siRNA delivery and targeting

RNA interference (RNAi) is an evolutionarily conserved process by which double-stranded small interfering RNA (siRNA) induces sequence-specific, post-transcriptional gene silencing. Unlike other mRNA targeting strategies, RNAi takes advantage of the physiological gene silencing machinery. The potential use of siRNA as therapeutic agents has attracted great attention as a novel approach for treating severe and chronic diseases. RNAi can be achieved by either delivery of chemically synthesized siRNAs or endogenous expression of small hairpin RNA, siRNA, and microRNA (miRNA). However, the relatively high dose of siRNA required for gene silencing limits its therapeutic applications. This review discusses several strategies to improve therapeutic efficacy as well as to abrogate off-target effects and immunostimulation caused by siRNAs. There is an in-depth discussion on various issues related to the (1) mechanisms of RNAi, (2) methods of siRNA production, (3) barriers to RNAi-based therapies, (4) biodistribution, (5) design of siRNA molecules, (6) chemical modification and bioconjugation, (7) complex formation with lipids and polymers, (8) encapsulation into lipid particles, and (9) target specificity for enhanced therapeutic effectiveness.

Strategies for silencing human disease using RNA interference

Since the first description of RNA interference (RNAi) in animals less than a decade ago, there has been rapid progress towards its use as a therapeutic modality against human diseases. Advances in our understanding of the mechanisms of RNAi and studies of RNAi in vivo indicate that RNAi-based therapies might soon provide a powerful new arsenal against pathogens and diseases for which treatment options are currently limited. Recent findings have highlighted both promise and challenges in using RNAi for therapeutic applications. Design and delivery strategies for RNAi effector molecules must be carefully considered to address safety concerns and to ensure effective, successful treatment of human diseases.

Administration in non-human primates of escalating intravenous doses of targeted nanoparticles containing ribonucleotide reductase subunit M2 siRNA

The results of administering escalating, i.v. doses of targeted nanoparticles containing a siRNA targeting the M2 subunit of ribonucleotide reductase to non-human primates are reported. The nanoparticles consist of a synthetic delivery system that uses a linear, cyclodextrin-containing polycation, transferrin (Tf) protein targeting ligand, and siRNA. When administered to cynomolgus monkeys at doses of 3 and 9 mg siRNA/kg, the nanoparticles are well tolerated. At 27 mg siRNA/kg, elevated levels of blood urea nitrogen and creatinine are observed that are indicative of kidney toxicity. Mild elevations in alanine amino transferase and aspartate transaminase at this dose level indicate that the liver is also affected to some extent. Analysis of complement factors does not reveal any changes that are clearly attributable to dosing with the nanoparticle formulation. Detection of increased IL-6 levels in all animals at 27 mg siRNA/kg and increased IFN-gamma in one animal indicate that this high dose level produces a mild immune response. Overall, no clinical signs of toxicity clearly attributable to treatment are observed. The multiple administrations spanning a period of 17-18 days enable assessment of antibody formation against the human Tf component of the formulation. Low titers of anti-Tf antibodies are detected, but this response is not associated with any manifestations of a hypersensitivity reaction upon readministration of the targeted nanoparticle. Taken together, the data presented show that multiple, systemic doses of targeted nanoparticles containing nonchemically modified siRNA can safely be administered to non-human primates.

Synthetic RNA circuits

Natural and engineered RNA 'parts' can perform a variety of functions, including hybridizing to targets, binding ligands and undergoing programmed conformational changes, and catalyzing reactions. These RNA parts can in turn be assembled into synthetic genetic circuits that regulate gene expression by acting either in cis or in trans on mRNAs. As more parts are discovered and engineered, it should be increasingly possible to create synthetic RNA circuits that are able to carry out complex logical operations in cells, either superimposed on or autonomous to extant gene regulation.

Comparison of different strategies to select aptamers against a transmembrane protein target

Binding of aptamers is dependent on their target conformation, which in turn is conditioned by the target's environment. Therefore, selection of aptamers against the active forms of membrane proteins could require their correct membrane insertion in order to maintain their native conformation. Here, we compare different SELEX strategies to identify aptamers against the mutated form of the membrane receptor tyrosine kinase RET(C634Y). (1) selections S1 and S2 against living cells transformed to express the protein yielded a minority of RET-targeted aptamers while the bulk of aptamers recognized more abundant membrane proteins, suggesting that a high level of expression of the target protein is crucial to allow the isolation of aptamers at cell surface; (2) selection S3 against the purified extracellular moiety of RET yielded aptamers unable to recognize RET expressed at the cell membrane; (3) crossover selections S4 and S5 alternating cells and recombinant RET enhanced the enrichment of the aptamers directed against RET; however, these aptamers displayed a weaker affinity for Ret than those obtained with S1 and S2. In our case, using transformed cell lines as the partitioning matrix during SELEX appears to be essential in order to obtain aptamers able to recognize the RET receptor tyrosine kinase in its physiologic environment.