Therapeutic potential and mechanism of action of oligonucleotides and ribozymes

Polymersome delivery of siRNA and antisense oligonucleotides

siRNA and antisense oligonucleotides, AON, have similar size and negative charge and are often packaged for in vitro delivery with cationic lipids or polymers-but exposed positive charge is problematic in vivo. Here we demonstrate loading and functional delivery of RNAi and AON with non-ionic, nano-transforming polymersomes. These degradable carriers are taken up passively by cultured cells after which the vesicles transform into micelles that allow endolysosomal escape and delivery of either siRNA into cytosol for mRNA knockdown or else AON into the nucleus for exon skipping within pre-mRNA. Polymersome-mediated knockdown appears as efficient as common cationic-lipid transfection and about half as effective as Lenti-virus after sustained selection. For AON, initial results also show that intramuscular injection into a mouse model of muscular dystrophy leads to the expected protein expression, which occurs along the entire length of muscle. The lack of cationic groups in antisense polymersomes together with initial tests of efficacy suggests broader utility of these non-viral carriers.

Apoptosis: a novel therapeutic tool?

Apoptosis is a genetically programmed cell death mechanism that appears to occur in all multicellular organisms. It is a normal process that serves to maintain cellular homeostasis. However, in many diseases there is a disruption in the equilibrium between cell proliferation and cell death that contributes directly to the disease. In these cases, a possible therapeutic intervention would be to restore the skewed equilibrium by pushing it in the desired direction through the use of pharmacological agents or genetic approaches. These observations have instigated substantial research in the field of apoptosis, resulting in an increasingly detailed analysis of the molecular mechanisms and the sequence of events that occur in this cell death pathway. In addition, by trying to understand this pathway, several potential therapeutic agents have arisen from those used in chemo-, radio-, and cytokine therapy. While these agents have been relatively successful, it is rare that their effect is complete. Thus, the search continues for a strategy to conquer those cells that are resistant to these regimens. Genetic approaches are novel and have been shown to be quite successful in several in vitro and animal models. They also tend to have low toxicity. It is believed that using a more traditional front-line approach of therapy, supplemented by appropriate genetic intervention, will allow substantial increases in the efficacy of treatment, while at the same time introducing little or no additional toxicity.

Mechanistic studies on acyl-transferase ribozymes and beyond

In vitro selection has allowed the isolation of many new ribozymes that are able to catalyze an ever-widening array of chemical transformations. Mechanistic studies on these selected ribozymes have provided valuable insight into the methods that RNA can invoke to overcome different catalytic tasks. We focus on the methods employed in these mechanistic studies using the acyl-transferase family of selected ribozymes as well-studied reference systems. Chemical and biochemical techniques have been used in tandem in order to draw conclusions on the various modes of catalysis employed by the different family members. In turn, this type of mechanistic information may provide a means for the redesign and optimization of existing ribozymes or the basis for new selection systems for more powerful RNA catalysts.

Substrate specificity and reaction kinetics of an X-motif ribozyme

The X-motif is an in vitro-selected ribozyme that catalyzes RNA cleavage by an internal phosphoester transfer reaction. This ribozyme class is distinguished by the fact that it emerged as the dominant clone among at least 12 different classes of ribozymes when in vitro selection was conducted to favor the isolation of high-speed catalysts. We have examined the structural and kinetic properties of the X-motif in order to provide a framework for its application as an RNA-cleaving agent and to explore how this ribozyme catalyzes phosphoester transfer with a predicted rate constant that is similar to those exhibited by the four natural self-cleaving ribozymes. The secondary structure of the X-motif includes four stem elements that form a central unpaired junction. In a bimolecular format, two of these base-paired arms define the substrate specificity of the ribozyme and can be changed to target different RNAs for cleavage. The requirements for nucleotide identity at the cleavage site are GD, where D = G, A, or U and cleavage occurs between the two nucleotides. The ribozyme has an absolute requirement for a divalent cation cofactor and exhibits kinetic behavior that is consistent with the obligate binding of at least two metal ions.

Down-regulation of alpha v/beta 3 integrin via misrouting to lysosomes by overexpression of a beta 3Lamp1 fusion protein

We present a general strategy for the dominant negative reduction in the levels of type-1 membrane-bound heterodimeric proteins within the secretory pathway through fusion of the soluble ectodomain of one of the partners to the transmembrane-cytosolic tail of the lysosomal protein Lamp1. Thus, in human embryonic kidney (HEK)-293 cells, overexpression of an integrin beta 3Lamp1 chimera resulted in a drastic reduction of its endogenous partner, the integrin alpha v subunit. The mechanism involves the formation in the endoplasmic reticulum of a alpha v/beta 3Lamp1 complex that is subsequently sorted towards a lysosomal/endosomal degradation pathway. The specificity of this approach is afforded by the invariance in the levels of the endogenous integrins alpha 5 and beta1 as compared with control cells. Conversely overexpression of integrin beta 3 in HEK-293 cells led to an increased level of alpha v beta 3 at the cell surface. Functionally beta 3Lamp1 and beta 3 overexpressors exhibit decreased and increased adhesion to vitronectin, respectively, as well as diminished cellular aggregation. The application of this technology should enable the analysis of the functional importance of homodimers or heterodimers in the cell types of choice and the identification of novel partner proteins by proteomic approaches.

Subcellular trafficking of antisense oligonucleotides and down-regulation of bcl-2 gene expression in human melanoma cells using a fusogenic liposome delivery system

Antisense oligonucleotides (ODN) targeted to specific genes have shown considerable potential as therapeutic agents. The polyanionic charges carried by these molecules, however, present a barrier to efficient cellular uptake and consequently their biological effects on gene regulation are compromised. To overcome this obstacle, a rationally designed carrier system is desirable for antisense delivery. This carrier should assist antisense ODN penetrate the cell membrane and, once inside the cell, then release the ODN and make them available for target binding. We have developed a carrier formulation employing programmable fusogenic vesicles (PFV) as the antisense delivery mediator. This study investigates the intracellular fate of PFV-ODN and bioavailability of antisense ODN to cells. The subcellular distribution of PFV and ODN was examined by monitoring the trafficking of FITC-labeled ODN and rhodamine/phosphatidylethanolamine (Rh-PE)-labeled PFV using confocal microscopy. Fluorescently tagged ODN were first co-localized with the liposomal carrier in the cytoplasm, presumably in endosome/lysosome compartments, shortly after incubation of PFV-ODN with HEK 293 and 518A2 cells. Between 24 and 48 h incubation, however, separation of FITC-ODN from the carrier and subsequent accumulation in the nucleus was observed. In contrast, the Rh-PE label was localized to the cell cytoplasm. The enhanced cellular uptake achieved using the PFV carrier, compared to incubation of free ODN with cells, and subsequent release of ODN from the carrier resulted in significant down-regulation of mRNA expression. Specifically, G3139, an antisense construct targeting the apoptotic antagonist gene bcl-2, was examined in the human melanoma cell line 518A2. Upon exposure to PFV-encapsulated G3139, cells displayed a time-dependent reduction in bcl-2 message levels. The bcl-2 mRNA level was reduced by 50% after 24 h treatment and by approximately 80% after 72 h when compared to cells treated with free G3139, empty PFV or PFV-G3622, a control ODN sequence. Our results establish that ODN can be released from PFV after intracellular uptake and can then migrate to the nucleus and selectively down-regulate target mRNA.

The use of synthetic polymers for delivery of therapeutic antisense oligodeoxynucleotides

Developed over the past two decades, the antisense strategy has become a technology of recognised therapeutic potential, and many of the problems raised earlier in its application have been solved to varying extents. However, the adequate delivery of antisense oligodeoxynucleotides to individual cells remains an important and inordinately difficult challenge. Synthetic polymers appeared on this scene in the middle 1980s, and there is a surprisingly large variety used or proposed so far as agents for delivery of oligodeoxynucleotides. After discussing the principles of antisense strategy, certain aspects of the ingestion of macromolecules by cells, and the present situation of delivery procedures, this article analyses in detail the attempts to use synthetic polymers as carrier matrices and or cell membrane permeabilisation agents for delivery of antisense oligodeoxynucleotides. Structural aspects of various polymers, as well as the results, promises and limitations of their use are critically evaluated.

Programmable fusogenic vesicles for intracellular delivery of antisense oligodeoxynucleotides: enhanced cellular uptake and biological effects

Programmable fusogenic vesicles (PFV) are liposomes composed of non-bilayer lipid components stabilized by the inclusion of an exchangeable poly(ethylene glycol) (PEG)-lipid conjugate. Vesicle destabilization by loss of the PEG-lipid results in recovery of the inherent fusogenic character. As a result, PFV can be designed to display a long circulation lifetime after i.v. administration, high accumulation at disease sites and full bioavailability of an encapsulated compound. In the present study, we investigated the potential application of PFV as carriers for intracellular delivery of antisense oligodeoxynucleotides (ODN). Antisense phosphorothioate ODN were encapsulated into PFV containing dioleoylphosphatidylethanolamine, cholesterol, dioleyldimethylammonium chloride and PEG-ceramides with different carbon chain length (C(8), C(14) and C(20)). In vitro fluorescent microscopy and flow cytometry analysis demonstrated that PFV containing PEG-ceramide C(14) provided enhanced intracellular delivery of FITC-labelled antisense ODN compared to PFV displaying faster or slower rates of destabilization (containing PEG-ceramide C(8) or C(20), respectively). Therapeutic efficacy of PFV-encapsulated antisense ODN against two proto-oncogenes, c-myc and bcl-2, was examined in various cell lines. At antisense concentrations of 0.5 microM, no significant downregulation of c-myc mRNA levels was observed in HEK293, B16 and MCA207 cells. However, treatment of 518A2 melanoma cells with PFV-encapsulated antisense targeting bcl-2 at concentrations of 0.5 microM and 1.0 microM resulted in reduced bcl-2 mRNA level by about 20% and 25% after 48 h incubation. Free antisense ODN did not affect bcl-2 mRNA expression at the concentrations used in this study and encapsulated control antisense (reverse polarity) led to a non-specific increase in mRNA levels. Our results suggest that PFV carriers displaying appropriate rates of destabilization have the potential to act as intracellular delivery vehicles and may improve the bioavailability and potency of antisense oligonucleotides.

Peritoneal colonization by human pancreatic cancer cells is inhibited by antisense FUT3 sequence

Several alpha(1,3/1,4) fucosyltransferases expressed in human pancreatic cancer cells can participate in the biosynthesis of cell surface sialyl-Lewis a and sialyl-Lewis x antigens that contribute to hematogenous metastatis. Previously, we observed a significant increase of the alpha(1,4) fucosyltransferase activity in tumoral pancreatic cell lines, suggesting that FUT3 could be involved in the sialyl-Lewis antigen expression. Therefore, we invalidated the expression of FUT3 by expressing FUT3 antisense sequence in the human pancreatic tumor BxPC-3 cell line, which expresses the alpha(1,4) fucosyltransferase activity and harbors the cell surface sialyl-Lewis antigens. The decrease of FUT3 transcript after transfection of antisense cDNA of FUT3 in these cells results in a substantial reduction of sialyl-Lewis antigen expression on cell surface. This decreased antigen expression was associated with an inhibition of adhesive properties to E-selectin and a decrease of metastatic power of FUT3 antisense-transfected BxPC-3 cells as tested in nude mice. Our study provides evidence that the expression level of FUT3 may regulate the expression of sialyl-Lewis a and sialyl-Lewis x surface antigens and consequently could play an important role in metastatic properties of human pancreatic cancer cells.

Peritoneal colonization by human pancreatic cancer cells is inhibited by antisense FUT3 sequence

Several alpha(1,3/1,4) fucosyltransferases expressed in human pancreatic cancer cells can participate in the biosynthesis of cell surface sialyl-Lewis a and sialyl-Lewis x antigens that contribute to hematogenous metastatis. Previously, we observed a significant increase of the alpha(1,4) fucosyltransferase activity in tumoral pancreatic cell lines, suggesting that FUT3 could be involved in the sialyl-Lewis antigen expression. Therefore, we invalidated the expression of FUT3 by expressing FUT3 antisense sequence in the human pancreatic tumor BxPC-3 cell line, which expresses the alpha(1,4) fucosyltransferase activity and harbors the cell surface sialyl-Lewis antigens. The decrease of FUT3 transcript after transfection of antisense cDNA of FUT3 in these cells results in a substantial reduction of sialyl-Lewis antigen expression on cell surface. This decreased antigen expression was associated with an inhibition of adhesive properties to E-selectin and a decrease of metastatic power of FUT3 antisense-transfected BxPC-3 cells as tested in nude mice. Our study provides evidence that the expression level of FUT3 may regulate the expression of sialyl-Lewis a and sialyl-Lewis x surface antigens and consequently could play an important role in metastatic properties of human pancreatic cancer cells.

Influence of mRNA self-structure on hybridization: computational tools for antisense sequence selection

Antisense targeting, an innovative technology based on preventing biosynthesis through sequence-specific hybridization of mRNA to synthetic oligodeoxynucleotides (ODNs), is used to selectively and transiently downregulate the expression of any gene product. Its potential applications are both investigative (neurobiology and related disciplines) and therapeutic (oncology, virology, genetic diseases), and several antisense-based drugs are currently undergoing clinical trials. However, the reported efficiencies vary and there is still a lack of clarity in the underlying mechanisms of action. A critical factor of antisense efficiency is the issue of target site selection, as both mRNA and ODN molecules exhibit a significant amount of highly heterogeneous self-structure and the region selected for targeting may well be sterically or energetically inaccessible. Because of the prohibitively large chain length, mRNA structural information is not accessible by X-ray crystallography or NMR, making a modeling approach indispensable. I outline how the latest molecular modeling techniques can be employed to establish the secondary (2D) and tertiary (3D) structures into which a given mRNA folds during and after transcription. The aim should be to integrate 2D prediction results achieved by (a) free-energy minimization, (b) kinetic folding simulations, (c) iterative population breeding by genetic algorithms, and (d) phylogenetic comparison techniques. These results can form the input of a 3D structure prediction paradigm based on constraint-satisfying programming, governed by experimental molecular mechanical constraints, and refined by molecular dynamics simulations. Finally, the automated docking (by simulated annealing) of ODN molecules to the mRNA structure can provide information about the accessibility of target mRNA regions for hybridization. To date, the great majority of studies that employ antisense as a tool select their target sequences more or less randomly. Although the wealth of molecular interactions that take place within a cell makes complete predictability unrealistic, the kind of information that can be extracted from such techniques is of relevance to every application of antisense technology, both investigative and therapeutic.

Cathepsin-B fusion proteins misroute secretory protein partners such as the proprotein convertase PC2-7B2 complex toward the lysosomal degradation pathways

A general strategy is presented for the dominant negative reduction in the levels of heterodimeric soluble proteins within the secretory pathway through fusion of one of its partners C-terminal to the lysosomal enzyme cathepsin B (CB). Stable transfectants of CB-7B2 chimeras in AT20 cells result in a drastic reduction of the endogenous levels of its partner, the proprotein convertase PC2. This dominant negative suppressive effect requires active CB. It was partially reversed by NH(4)Cl, the cell-permeable CB inhibitor CA-074Me, but not by the proteasome inhibitor Lactacystin, suggesting the potential participation of the lysosomal/endosomal degradative pathway in this process.

Retrovirus-mediated delivery of HPV16 E7 antisense RNA inhibited tumorigenicity of CaSki cells

OBJECTIVE

In cervical cancer, high-risk human papillomavirus (HPV) genes are expressed solely in cancerous cells and have been proposed to be the most important etiological factors for cervical cancer, thus making them suitable targets for gene therapy. In this study, we aim to inactivate the HPV16 E7 in CaSki cells and test the possibility of reducing the tumorigenicity of these cells.

METHODS

The full-length HPV16 E7 cDNA was cloned in the pBabe-puro or pWZL-Hygro retrovirus vector in reverse orientation and was stably transfected into CaSki cells by replication-defective retrovirus infection giving rise to CaSki-E7AS and CaSki-E7AS2X cells. Immunoprecipitation/Western analysis and real-time RT-PCR were performed to document the levels of HPV16 E7 gene product. Flow cytometry was performed to study changes in the cell cycle in response to reduced E7 protein. The expression of bcl-2, RB, and E2F-1 was studied using Western blot analysis. Tumorigenicity of CaSki, CaSki-E7AS, and CaSki-E7AS2X cells was assayed with subepidermal tumor growth in nude mice.

RESULTS

We have documented that the delivery of the antisense gene construct resulted in the reduction of HPV16 E7 protein expression and cell proliferation in CaSki cells. Furthermore, we demonstrated that these changes were accompanied by cell cycle arrest, up-regulation of RB, and down-regulation of E2F-1 and bcl-2 proteins. More importantly, dose-dependent transduction of the antisense HPV16E7 construct was able to inhibit and/or retard the tumorigenicity of CaSki cells in vivo.

CONCLUSIONS

Down-regulation of HPV16 E7 with antisense RNA is beneficial in reducing the tumorigenicity of CaSki cells and can potentially be useful for HPV-associated malignancy gene therapy.

New role for tRNA and its fragment purified from human urinary bladder carcinoma conditioned medium: inhibition of endothelial cell growth

The growth of endothelial cells is necessary for angiogenesis, which in turn is required for later steps of tumor progression. In an attempt to purify new modulators of endothelial cell growth from the conditioned medium of human urinary bladder carcinoma cells, we isolated a small and stable oligonucleotide containing 10 to 16 bases. This oligonucleotide inhibited the growth of endothelial cells in vitro and was identified as a fragment of transfer RNA (tRNA). When unfractionated bovine tRNA was added to the cell culture, it specifically inhibited growth of endothelial cells, but not smooth muscle cells, bovine kidney cells, 3T3 fibroblasts, and several cancer cell lines. In contrast, ribosomal RNA, total yeast RNA, and single nucleosides from tRNA hydrolysate had no effect. These results demonstrate a new role for tRNA and its fragment as a selective endothelial cell inhibitor in vitro.