Antisense oligodeoxynucleotide and ribozyme design

Antisense oligonucleotides targeting the RNA binding region of the NP gene inhibit replication of highly pathogenic avian influenza virus H5N1

The H5N1 avian influenza virus (AIV) causes widespread infections in bird and human respiratory tracts, and vaccines and drug therapy are limited in their effectiveness. Recent studies of AIV structures have been published and provide new targets for designing antiviral drugs such as antisense oligonucleotides (AS ODNs), which effectively inhibit gene replication. In this study, we designed and synthesized three AS ODNs (NP267, NP628, NP749) that were specific for the RNA binding region of nucleoprotein (NP) based on AIV structure. Results showed that all three AS ODNs could inhibit viral replication in MDCK cells. The NP628 showed the best antiviral effect of all through viral titers, quantitative RT-PCR and indirect immunofluorescence (IFA) assays. In addition, the liposome mediated NP628 could partially protect the mice from a lethal H5N1 influenza virus challenge. Moreover, the NP628 group had a lower viral titer and lung index in the infected mice when compared with the viral control. Our results showed that AS ODN targeting of the AIV NP gene could potently inhibit AIV H5N1 reproduction, thus, formulating a candidate for an emergent therapeutic drug for the pathogenic H5N1 influenza virus infection.

Antisense applications for biological control

Although Nature's antisense approaches are clearly impressive, this Perspectives article focuses on the experimental uses of antisense reagents (ASRs) for control of biological processes. ASRs comprise antisense oligonucleotides (ASOs), and their catalytically active counterparts ribozymes and DNAzymes, as well as small interfering RNAs (siRNAs). ASOs and ribozymes/DNAzymes target RNA molecules on the basis of Watson-Crick base pairing in sequence-specific manner. ASOs generally result in destruction of the target RNA by RNase-H mediated mechanisms, although they may also sterically block translation, also resulting in loss of protein production. Ribozymes and DNAzymes cleave target RNAs after base pairing via their antisense flanking arms. siRNAs, which contain both sense and antisense regions from a target RNA, can mediate target RNA destruction via RNAi and the RISC, although they can also function at the transcriptional level. A considerable number of ASRs (mostly ASOs) have progressed into clinical trials, although most have relatively long histories in Phase I/II settings. Clinical trial results are surprisingly difficult to find, although few ASRs appear to have yet established efficacy in Phase III levels. Evolution of ASRs has included: (a) Modifications to ASOs to render them nuclease resistant, with analogous modifications to siRNAs being developed; and (b) Development of strategies to select optimal sites for targeting. Perhaps the biggest barrier to effective therapies with ASRs is the "Delivery Problem." Various liposomal vehicles have been used for systemic delivery with some success, and recent modifications appear to enhance systemic delivery, at least to liver. Various nanoparticle formulations are now being developed which may also enhance delivery. Going forward, topical applications of ASRs would seem to have the best chances for success. In summary, modifications to ASRs to enhance stability, improve targeting, and incremental improvements in delivery vehicles continue to make ASRs attractive as molecular therapeutics, but their advance toward the bedside has been agonizingly slow.

Caspase-3 antisense oligodeoxynucleotides inhibit apoptosis in gamma-irradiated human leukemia HL-60 cells

To study the inhibitory effects of caspase-3 mRNA antisense oligodeoxynucleotides (ASODNs) on apoptosis, we designed four ASODNs targeting different regions of caspase-3 mRNA and transfected them into human leukemia HL-60 cells. The transfected cells were given 10 Gy gamma-irradiation followed by incubation for 18 h and measurement of apoptosis and caspase-3 expression. Our results showed that ASODN-2 targeting the 5' non-coding region of sites -62 to -46, and ASODN-3 targeting the 5' coding region of sites -1 to 16, both reduced apoptosis measured by gel electrophoresis and flow cytometry. Hoechst 33258 staining and TUNEL assay revealed that apoptotic indexes in the ASODN-2 and ASODN-3 groups were significantly lower than those in the untransfected and mismatched oligodeoxynucleotide (MODN) groups. Immunocytochemistry, Western blotting and RT-PCR showed that expression levels of caspase-3 protein and mRNA in both ASODN-2 and ASODN-3 groups were decreased compared with those in the untransfected and MODN groups. In conclusion, caspase-3 mRNA ASODNs can inhibit gamma-radiation-induced apoptosis of HL-60 cells and reduce expression of caspase-3 protein and mRNA. The results suggest that antisense approach may be useful for therapeutic treatment of certain neurodegenerative diseases in which apoptosis is involved.

Rat carotid arteriotomy: c-myc is involved in negative remodelling and apoptosis

OBJECTIVE

c-myc is the main proto-oncogene responsible for restenosis in cardiovascular surgery. The aim of our study was to evaluate the effects of c-myc antisense (AS) phosphorothioate oligodeoxynucleotides (ODNs) in the remodelling process induced by surgical carotid arteriotomy on an experimental rat model.

METHODS

Fifty-five rats with carotid stenosis and apoptosis induced by arteriotomy were submitted to gene expression analysis 4 h after surgery, to TUNEL assay 48 h after surgery and to histological analysis 30 days later.

RESULTS

AS ODNs induced a 60% decrease in target c-myc mRNA in injured carotid arteries compared to control sense and scrambled ODN-treated carotid arteries (P < 0.05). Histological evaluation revealed that stenosis stimulated by arteriotomy was mainly due to adventitial constrictive remodelling rather than to neointimal hyperplasia, observed only in a limited number of samples. Morphometric analysis showed that lumen area in c-myc AS ODN-treated carotid arteries was 35% greater than in control arteries (P < 0.05), whereas the media/lumen area ratio showed a 63% reduction in AS ODN-treated carotid arteries in comparison to control arteries (P < 0.05). Surgical injury affected the expression of apoptosis-related genes Bcl-2, Bax, Bcl-xL and Bcl-xS, inducing a mean 3.5-fold decrease in the Bcl-2/ Bax ratio and a 9-fold decrease in the Bcl-xL/S ratio 4 h after injury as compared with uninjured carotid arteries. TUNEL assay experiments revealed increased apoptosis in AS ODN-treated carotid arteries in comparison to control carotid arteries.

CONCLUSIONS

c-myc AS ODNs reduce the negative remodelling induced by arteriotomy. The imbalance between proliferative stimulus represented by surgery and the c-myc mRNA decrease induced greater apoptosis in AS ODN-treated carotid arteries without further affecting mRNA levels of Bcl-2, Bax, Bcl-xL and Bcl-xS genes.

Agents targeting c-Jun N-terminal kinase pathway as potential neuroprotectants

c-Jun N-terminal kinase (JNK) plays an integral role in neuronal death in multiple cell lines following a wide variety of stimuli and in a number of physiological functions that may be involved in human disease, including CNS diseases. In the past decades, many researchers in this field have found and reinforced the concept that prolonged activation of JNK signalling can induce neuronal cell death by both a transcriptional induction of death-promoting genes and modulation of the mitochondrial apoptosis pathways. Data are emerging to extend the understanding of the JNK signalling and confirm the possibility that targeting JNK signalling may offer an effective therapy for pathological conditions in the near future. This review will focus on the pro-apoptotic role of JNK signalling and updated pharmacological inhibitors of this pathway.

Toxicology of antisense therapeutics

Targeting unique mRNA molecules using antisense approaches, based on sequence specificity of double-stranded nucleic acid interactions should, in theory, allow for design of drugs with high specificity for intended targets. Antisense-induced degradation or inhibition of translation of a target mRNA is potentially capable of inhibiting the expression of any target protein. In fact, a large number of proteins of widely varied character have been successfully downregulated using an assortment of antisense-based approaches. The most prevalent approach has been to use antisense oligonucleotides (ASOs), which have progressed through the preclinical development stages including pharmacokinetics and toxicological studies. A small number of ASOs are currently in human clinical trials. These trials have highlighted several toxicities that are attributable to the chemical structure of the ASOs, and not to the particular ASO or target mRNA sequence. These include mild thrombocytopenia and hyperglycemia, activation of the complement and coagulation cascades, and hypotension. Dose-limiting toxicities have been related to hepatocellular degeneration leading to decreased levels of albumin and cholesterol. Despite these toxicities, which are generally mild and readily treatable with available standard medications, the clinical trials have clearly shown that ASOs can be safely administered to patients. Alternative chemistries of ASOs are also being pursued by many investigators to improve specificity and antisense efficacy and to reduce toxicity. In the design of ASOs for anticancer therapeutics in particular, the goal is often to enhance the cytotoxicity of traditional drugs toward cancer cells or to reduce the toxicity to normal cells to improve the therapeutic index of existing clinically relevant cancer chemotherapy drugs. We predict that use of antisense ASOs in combination with small molecule therapeutics against the target protein encoded by the antisense-targeted mRNA, or an alternate target in the same or a connected biological pathway, will likely be the most beneficial application of this emerging class of therapeutic agent.

Bcl2-low-expressing MCF7 cells undergo necrosis rather than apoptosis upon staurosporine treatment

We present a ribozyme-based strategy for studying the effects of Bcl2 down-regulation. The anti-bcl2 hammerhead ribozyme Rz-bcl2 was stably transfected into MCF7 cancer cells and the cleavage of Bcl2 mRNA was demonstrated using a new assay for cleavage product detection, while Western blot analysis showed a concomitant depletion of Bcl2 protein. Rz-bcl2-expressing cells were more sensitive to staurosporine than control cells. Moreover, both molecular and cellular read-outs indicated that staurosporine-induced cell death was necrosis rather than apoptosis in these cells. The study of the effects of Bcl2 down-regulation was extended to the global MCF7 protein expression profile, exploiting a proteomic approach. Two reference electro-pherograms of Rz-bcl2-transfected cells, one with the ribozyme in a catalytically active form and the other with the ribozyme in a catalytically inactive form, were obtained. When comparing the two-dimensional maps, 53 differentially expressed spots were found, four of which were identified by MALDI-TOF (matrix-assisted laser-desorption ionization-time-of-flight) MS as calreticulin, nucleophosmin, phosphoglycerate kinase and pyruvate kinase. How the up-regulation of these proteins might help to explain the modification of Bcl2 activity is discussed.

Fast and accurate determination of sites along the FUT2 in vitro transcript that are accessible to antisense oligonucleotides by application of secondary structure predictions and RNase H in combination with MALDI-TOF mass spectrometry

Alteration of gene expression by use of antisense oligonucleotides has considerable potential for therapeutic purposes and scientific studies. Although applied for almost 25 years, this technique is still associated with difficulties in finding antisense-effective regions along the target mRNA. This is mainly due to strong secondary structures preventing binding of antisense oligonucleotides and RNase H, playing a major role in antisense-mediated degradation of the mRNA. These difficulties make empirical testing of a large number of sequences complementary to various sites in the target mRNA a very lengthy and troublesome procedure. To overcome this problem, more recent strategies to find efficient antisense sites are based on secondary structure prediction and RNase H-dependent mechanisms. We were the first who directly combined these two strategies; antisense oligonucleotides complementary to predicted unpaired target mRNA regions were designed and hybridized to the corresponding RNAs. Incubation with RNase H led to cleavage of the RNA at the respective hybridization sites. Analysis of the RNA fragments by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, which has not been used in this context before, allowed exact determination of the cleavage site. Thus the technique described here is very promising when searching for effective antisense sites.

Inhibiting expression of specific genes in mammalian cells with 5' end-mutated U1 small nuclear RNAs targeted to terminal exons of pre-mRNA

Reducing or eliminating expression of a given gene is likely to require multiple methods to ensure coverage of all of the genes in a given mammalian cell. We and others [Furth, P. A., Choe, W. T., Rex, J. H., Byrne, J. C., and Baker, C. C. (1994) Mol. Cell. Biol. 14, 5278-5289] have previously shown that U1 small nuclear (sn) RNA, both natural or with 5' end mutations, can specifically inhibit reporter gene expression in mammalian cells. This inhibition occurs when the U1 snRNA 5' end base pairs near the polyadenylation signal of the reporter gene's pre-mRNA. This base pairing inhibits poly(A) tail addition, a key, nearly universal step in mRNA biosynthesis, resulting in degradation of the mRNA. Here we demonstrate that expression of endogenous mammalian genes can be efficiently inhibited by transiently or stably expressed 5' end-mutated U1 snRNA. Also, we determine the inhibitory mechanism and establish a set of rules to use this technique and to improve the efficiency of inhibition. Two U1 snRNAs base paired to a single pre-mRNA act synergistically, resulting in up to 700-fold inhibition of the expression of specific reporter genes and 25-fold inhibition of endogenous genes. Surprisingly, distance from the U1 snRNA binding site to the poly(A) signal is not critical for inhibition, instead the U1 snRNA must be targeted to the terminal exon of the pre-mRNA. This could reflect a disruption by the 5' end-mutated U1 snRNA of the definition of the terminal exon as described by the exon definition model.

Surgical injury of rat arteries: genetic control of the remodelling process

OBJECTIVES

Remodelling and restenosis are complex biological processes responsible for bypass and percutaneous transluminal coronary angioplasty failures which are likely to affect many hundreds of genes. We evaluated the effectiveness of topically applied antisense oligonucleotides in reducing the translation of the messenger RNA for the transcription factor c-myc and in reducing stenosis.

METHODS

Surgery was performed under sterile conditions; 60 Wistar-Kyoto male rats were anaesthetized by ketamine. The carotid arteries were isolated through a median incision in the anterior neck region. At the same point, 0.5 mm longitudinal incisions were performed. Haemostasis was obtained by an adventitial 8.0 stitch. Thirty animals were given 150 microg of c-myc antisense oligonucleotide (Group A) while the other 30 animals received 150 microg of c-myc control sense oligonucleotide (Group B). Oligo molecules were locally applied through 100 microl of 20% pluronic gel. Rats were sacrificed at 30 days; carotid arteries were explanted and stained. Qualitative histological analysis was performed in all cases; serial sections were made every 25 micro in seven consecutive rats for each group. Morphometric analysis was also performed, luminal and medial area values recorded and the ratio between the two areas calculated. Data from each animal were compared with the corresponding contralateral carotid artery and expressed as mean+/-standard deviation. Statistical comparison between the two groups was carried out by one-way ANOVA text.

RESULTS

Qualitative histological analysis showed marked remodelling with complete disarray of vessel wall, neointima accumulation and evidence of elastic fibres in the adventitia of all animals of Group B versus Group A. Morphometric analysis showed a significant reduction in the lumen area in Group A animals together with increased values of the medial area versus Group B animals. In addition, the ratio between the lumen and medial area was significantly higher in Group A than in Group B (2.61+/-0.18 versus 1.14+/-0.33, P<0.0001).

CONCLUSIONS

c-myc antisense oligonucleotides applied intraoperatively can reduce post-operative stenosis.

Advantages of antisense drugs for the treatment of oral diseases

For almost two decades, antisense oligonucleotides (AS-ON) have been used successfully to suppress and regulate gene expression in vitro and in vivo. They are, meanwhile, well established to serve as molecular tools for several biologic applications, from the study of single gene functions up to complex target gene validations. Based on an at least theoretically simple mode of action, the sequence-specific inhibition of mRNA functions after complex formation by Watson-Crick base pairing and presumably enzymatic degradation of the target mRNA, they obviously carry a high therapeutic potential for the treatment of human diseases. In recent years, a remarkable number of clinical trials have been initiated and performed to evaluate the therapeutic usefulness of antisense technology. However, after the successful development of the first antisense-based drug Vitravene (Isis Pharmaceutical Inc., Carlsbad, CA) in 1998, no second product has appeared on the market to date. Here, we describe substantial advantages for the development of antisense-based drugs against less severe oral diseases that represent novel but highly promising application fields of the technology.

Remote electronic control of DNA hybridization through inductive coupling to an attached metal nanocrystal antenna

Increasingly detailed structural and dynamic studies are highlighting the precision with which biomolecules execute often complex tasks at the molecular scale. The efficiency and versatility of these processes have inspired many attempts to mimic or harness them. To date, biomolecules have been used to perform computational operations and actuation, to construct artificial transcriptional loops that behave like simple circuit elements and to direct the assembly of nanocrystals. Further development of these approaches requires new tools for the physical and chemical manipulation of biological systems. Biomolecular activity has been triggered optically through the use of chromophores, but direct electronic control over biomolecular 'machinery' in a specific and fully reversible manner has not yet been achieved. Here we demonstrate remote electronic control over the hybridization behaviour of DNA molecules, by inductive coupling of a radio-frequency magnetic field to a metal nanocrystal covalently linked to DNA. Inductive coupling to the nanocrystal increases the local temperature of the bound DNA, thereby inducing denaturation while leaving surrounding molecules relatively unaffected. Moreover, because dissolved biomolecules dissipate heat in less than 50 picoseconds (ref. 16), the switching is fully reversible. Inductive heating of macroscopic samples is widely used, but the present approach should allow extension of this concept to the control of hybridization and thus of a broad range of biological functions on the molecular scale.