Sequence specific inhibition of human type II phospholipase A2 enzyme activity by phosphorothioate oligonucleotides

Nanotechnology and aptamers: applications in drug delivery

Nucleic acid ligands, also known as aptamers, are a class of macromolecules that are being used in several novel nanobiomedical applications. Aptamers are characterized by high affinity and specificity for their target, a versatile selection process, ease of chemical synthesis and a small physical size, which collectively make them attractive molecules for targeting diseases or as therapeutics. These properties will enable aptamers to facilitate innovative new nanotechnologies with applications in medicine. In this review, we will highlight recent developments in using aptamers in nanotechnology solutions for treating and diagnosing disease.

Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis

RNA interference can be considered as an antisense mechanism of action that utilizes a double-stranded RNase to promote hydrolysis of the target RNA. We have performed a comparative study of optimized antisense oligonucleotides designed to work by an RNA interference mechanism to oligonucleotides designed to work by an RNase H-dependent mechanism in human cells. The potency, maximal effectiveness, duration of action, and sequence specificity of optimized RNase H-dependent oligonucleotides and small interfering RNA (siRNA) oligonucleotide duplexes were evaluated and found to be comparable. Effects of base mismatches on activity were determined to be position-dependent for both siRNA oligonucleotides and RNase H-dependent oligonucleotides. In addition, we determined that the activity of both siRNA oligonucleotides and RNase H-dependent oligonucleotides is affected by the secondary structure of the target mRNA. To determine whether positions on target RNA identified as being susceptible for RNase H-mediated degradation would be coincident with siRNA target sites, we evaluated the effectiveness of siRNAs designed to bind the same position on the target mRNA as RNase H-dependent oligonucleotides. Examination of 80 siRNA oligonucleotide duplexes designed to bind to RNA from four distinct human genes revealed that, in general, activity correlated with the activity to RNase H-dependent oligonucleotides designed to the same site, although some exceptions were noted. The one major difference between the two strategies is that RNase H-dependent oligonucleotides were determined to be active when directed against targets in the pre-mRNA, whereas siRNAs were not. These results demonstrate that siRNA oligonucleotide- and RNase H-dependent antisense strategies are both valid strategies for evaluating function of genes in cell-based assays.

Efficiency of antisense oligonucleotide drug discovery

The costs for discovering and developing new drugs continue to escalate, with current estimates that the average cost is more than $800 million for each new drug brought to the market. Pharmaceutical companies are under enormous pressure to increase their efficiency for bringing new drugs to the market by third-party payers, shareholders, and their patients, and at the same time regulators are placing increased demands on the industry. To be successful in the future, pharmaceutical companies must change how they discover and develop new drugs. So far, new technologies have done little to increase overall efficiency of the industry and have added additional costs. Platform technologies such as monoclonal antibodies and antisense oligonucleotides have the potential of reducing costs for discovery of new drugs, in that many of the steps required for traditional small molecules can be skipped or streamlined. Additionally the success of identifying a drug candidate is much higher with platform technologies compared to small molecule drugs. This review will highlight some of the efficiencies of antisense oligonucleotide drug discovery compared to traditional drugs and will point out some of the current limitations of the technology.

Antisense oligonucleotide inhibition of type II phospholipase A2 expression, release and activity in vitro

Phospholipase A2 (PLA2) enzymes that regulate the release of arachidonic acid from cell membrane phospholipids represent a crucial rate-limiting step for the prostaglandin biosynthetic pathway. The aim of this study was to determine the mechanism of action and effects of type II PLA2 antisense oligonucleotides on type II PLA2 mRNA relative abundance, and the release of PLA2 enzymatic activity and prostaglandin F2alpha (PGF2alpha) in vitro. A human placental explant system was used to evaluate the effects of the type II PLA2 specific antisense oligonucleotides A (5'-GGGTGGGTATAGAAGGGCTCC-3', complementary to the base sequence 697-717 of the type II PLA2 gene) and B (5'-TTTTTGATTTGCTAATTGCTT-3', complementary to the base sequence 821-841 of the type II PLA2 gene). PLA2 activity released from explants was quantified by radiolabelled substrate assay using 14C-phosphatidylethanolamine (PE), and PGF2alpha content was analyzed by radioimmunoassay. Compared with control, the release of PLA2 activity and PGF2alpha was significantly reduced over the 24-h period by treatment with both antisense oligonucleotides (P< 0.05). At this concentration, type II PLA2 mRNA abundance was also significantly reduced by both antisense oligonucleotides A and B (P< 0.05). This data demonstrates the efficacy of antisense oligonucleotide inhibition of secretory PLA2 (sPLA2) expression and activity, and the contribution of sPLA2 to placental prostaglandin production.

Antisense therapy in cancer

This review discusses laboratory and clinical studies of antisense oligodeoxynucleotides as potential treatments for haematological malignancies and solid tumours. Mechanisms of action, pharmacokinetics, toxicities and potential clinical applications of these agents are described.

Inhibition of CD28 Expression by Oligonucleotide Decoys to the Regulatory Element in Exon 1 of the CD28 Gene

Ligation of CD28 provides a costimulatory signal essential for Ag-mediated T cell activation via the TCR. Previously we demonstrated that inhibition of human and murine CD28 expression by a guanosine (G)-rich oligonucleotide (ODN), GR1, led to immunosuppression in vitro and in vivo. The bioactivity of GR1 was dependent on a G-rich DNA sequence motif consisting of two G tetrads separated by four nucleotides, (G4N4G4). We have shown recently that a G-rich region, designated CD28GR, in exon 1 of the CD28 gene is such a motif and is a positive regulatory element that binds the transcription factors Sp1 and EGR-1. Here we showed that the bioactivity of GR1 and the related GR2 correlated with the sequence-specific formation of distinct nuclear protein complexes and a high degree of ODN secondary structure. In addition, these ODN blocked transcription factor binding to CD28GR (also in a sequence-specific manner) and prevented CD28GR from driving transcription of a reporter gene. Interestingly, GR1 potently inhibited CD28, but not the expression of other Sp1- and EGR-1-regulated genes, an effect associated with lower Sp1 protein binding affinity of GR1 and GR2 compared with that of canonical Sp1 sites. These data show that DNA sequences that contain the G-rich sequence motif, G4N4G4, such as GR1 and GR2, can functionally mimic the regulatory protein binding ability of CD28GR. Thus, GR1 and GR2 act as molecular decoys to selectively interfere with transcriptional regulation of the CD28 gene.

Antisense oligonucleotides: is the glass half full or half empty?

Antisense oligonucleotides are widely used as tools to explore the pharmacological effects of inhibiting expression of a selected gene product. In addition, they are being investigated as therapeutic agents for the treatment of viral infections, cancers, and inflammatory disorders. Proof that the pharmacological effects produced by the oligonucleotides are attributable to an antisense mechanism of action requires careful experimentation. Central to this problem is the finding that oligonucleotides are capable of interacting with and modulating function of specific proteins in both a sequence-independent and -dependent manner. Despite these undesired interactions, it has been possible to demonstrate that oligonucleotides are capable of binding to a specific RNA in cultured cells, or within tissues, resulting in selective reduction of the targeted gene product and pharmacological activity. In general, these oligonucleotides were identified after a selection process in which multiple oligonucleotides targeting different regions on the RNA were evaluated for direct inhibition of targeted gene product, resulting in the identification of a potent and selective oligonucleotide. Similar to other drug-receptor interactions, selection of the most potent inhibitor results in an increase in the signal-to-noise ratio, yielding increased confidence that activity observed is the result of a desired effect of the inhibitor. With careful selection, proper controls, and careful dose-response curves it is possible to utilize antisense oligonucleotides as effective research tools and potentially as therapeutic agents.

Contiguous four-guanosine sequence in c-myc antisense phosphorothioate oligonucleotides inhibits cell growth on human lung cancer cells: possible involvement of cell adhesion inhibition

A contiguous four-guanosine (4G) sequence in c-myc antisense phosphorothioate oligonucleotides caused an antiproliferative effect in smooth muscle cells. To investigate the antiproliferative effect of c-myc antisense oligonucleotides on human lung cancer cell lines, we synthesized oligonucleotides of various lengths and sequences, focusing on the contiguous four-guanosine (4G) sequence. While a c-myc antisense oligonucleotide (20AS1 (4G)) targeted to the translation initiation codon of c-myc mRNA inhibited cell growth of A549 cells by 69% at 10 microM, a scrambled oligonucleotide (20SCR1 (4G)) containing the contiguous four-guanosine (4G) sequence also inhibited cell growth by 72% at the same dose. Although treatment with either 20AS1 (4G) or 20SCR1 (4G) inhibited cell adhesion by 70% at 10 microM, expression of c-myc protein was significantly suppressed only by 20AS1 (4G) (62%), and was only weakly inhibited by 20SCR1 (4G) (32%). Furthermore, a small cell lung carcinoma cell line, Lu65, which can grow in suspension form, was highly resistant to 20AS1 (4G) treatment (IC50>20 microM). These results suggest that the cell growth inhibition by c-myc antisense oligonucleotides containing the contiguous four-guanosine (4G) sequence was possibly correlated with inhibition of cell adhesion, but not with inhibition of c-myc protein expression, via a sequence-specific non-antisense mechanism.

Purification and characterization of nuclear alkaline phospholipase A2 in rat ascites hepatoma cells

The alkaline phospholipase A2 (PLA2) was purified from nuclei of rat ascites hepatoma cells (AH7974) by column chromatography with a Sephacryl S-300 column and an immunoadsorbent using anti-group II PLA2 monoclonal antibody. From these two columns, the alkaline PLA2 was eluted in parallel with a 17-kDa protein which is reactive to another anti-group II PLA2 polyclonal antibody. Approximately 80% of nuclear PLA2 was inhibited by this antibody. The alkaline PLA2 was found in association with the chromatin fraction among subnuclear fractions. By an immunocytochemical staining, the nuclei of AH7974 were stained more strongly than other parts of cells with anti-group II PLA2 antiserum.

Guanine-rich oligonucleotide modified at the 5' terminal by dimethoxytrityl residue inhibits HIV-1 replication by specific interaction with the envelope glycoprotein

Previous studies have shown that a guanine-rich oligonucleotide SA-1042, DmTr-TGGGAGGTGGGTCTG, neutralizes HIV-1 infectivity, blocks syncytium formation and inhibits the binding of recombinant gp120 to immobilized soluble CD4 in vitro (Furukawa et al., 1994). We have now investigated the precise mode of action of SA-1042. We show here that SA-1042 specifically antagonizes the binding of anti-V3 loop antibodies or anti-CD4 binding-site antibodies to recombinant gp120, and also blocks the binding of an anti-V3 loop antibody to the V3 peptide (gp120IIIB: aa302-324). In contrast, SA-1042 does not inhibit gp120 binding of monoclonal antibodies directed to other regions of gp120, such as the conserved N-terminal regions (gp120IIIB: aa35-108 or gp120IIIB: aa72-130) or the C-terminal region (gp120IIIB: aa481-496). Furthermore, SA-1042 does not interfere with the binding of monoclonal antibodies directed to other molecules, gp41, CD4, CD11a, CD18, CD26, CD44 or CD54. These data suggest that SA-1042 exerts its antiviral effects by targeting the V3 loop as well as the CD4 binding site on gp120.

Recent status of the antisense oligonucleotide approaches in oncology

Antisense oligonucleotides designed to complement a region of a particular messenger RNA may inhibit gene expression potentially through sequence-specific hybridization. Their inhibiting effect has been shown in a variety of in vitro and in vivo models in oncology, whereas much rarer clinical trials have been carried out. Rigorous demonstration of in vitro and in vivo specific effects upon their targets is mandatory before their use as drugs in cancer therapy.

Bias in nucleotide composition of antisense oligonucleotides

In this study we investigated if specific sequence motifs occur with a higher frequency in antisense oligonucleotides than can be expected on the basis of the mRNA composition to get an impression of the importance of these motifs for antisense effects. Computer analysis of 206 antisense oligonucleotides extracted from the literature and from sequence databases, all targeted against human mRNA, was performed. We compared the sequence composition of these oligonucleotides with the average of 100 equally large and randomly selected sequences from sequence databases and of their target mRNA. We found that the frequency of sequence motifs containing GG, CCC, CC, GAC, and CG is significantly higher and TT and that TCC is significantly lower in antisense oligonucleotide sequences than in the randomly selected mRNA sequences. We conclude that there is a bias in the nucleotide composition of antisense oligonucleotides. Some of these biased sequence motifs have been reported to induce nonantisense effects mediated by protein binding. Further analysis of the biologic function of these motifs is necessary to investigate if they should be avoided or incorporated into future designs of therapeutic effective oligonucleotides.

The antiproliferative activity of c-myb and c-myc antisense oligonucleotides in smooth muscle cells is caused by a nonantisense mechanism

Smooth muscle cell (SMC) proliferation is thought to play a major role in vascular restenosis after angioplasty and is a serious complication of the procedure. Developing antisense (AS) oligonucleotides as therapeutics is attractive because of the potentially high specificity of binding to their targets, and several investigators have reported inhibition of SMC proliferation in vitro and in vivo by using AS strategies. We report here the results of our experiments on vascular SMCs using AS oligonucleotides directed toward c-myb and c-myc. We found that significant inhibition of SMC proliferation occurred with these specific AS sequences but that this inhibition was clearly not via a hybridization-dependent AS mechanism. Rather, inhibition was due to the presence of four contiguous guanosine residues in the oligonucleotide sequence. This was demonstrated in vitro in primary cultures of SMCs and in arteries ex vivo. The ex vivo model developed here provides a rapid and effective system in which to screen potential oligonucleotide drugs for restenosis. We have further explored the sequence requirements of this non-AS effect and determined that phosphorothioate oligonucleotides containing at least two sets of three or four consecutive guanosine residues inhibit SMC proliferation in vitro and ex vivo. These results suggest that previous AS data obtained using these and similar, contiguous guanosine-containing AS sequences be reevaluated and that there may be an additional class of nucleic acid compounds that have potential as antirestenosis therapeutics.

Helix-stabilizing agent, CC-1065, enhances suppression of translation by an antisense oligodeoxynucleotide

The antitumor antibiotic CC-1065 is known to bind at selected sequences in the minor groove of duplex nucleic acids and to hyperstabilize the duplexes against thermal melting. These properties suggested that CC-1065 may enhance translation inhibition by antisense oligonucleotides directed against a specific mRNA. A 585 bp mRNA transcript containing the equine infectious anemia virus (EIAV) S2 gene and a portion of the env gene was prepared. Also, a complementary 20 mer antisense oligodeoxynucleotide (5'-TGTTGGGTAATAGG-GGTTGA-3') was prepared against a target sequence in the mRNA located near the translational initiation sites of the overlapping S2 and env genes. The center of the target sequence had an expected CC-1065 recognition sequence (5'-UAUUA-3'). Translation in the presence of CC-1065 and antisense was markedly suppressed compared with that of antisense alone. Addition of a sense 20 mer strand, with or without CC-1065, had little or no effect on translation. CC-1065 and related compounds may be useful as ligands for enhancing the stability of sense-antisense duplexes and for promoting the inhibition of translation by antisense oligonucleotides.