Antisense RNA gene therapy for studying and modulating biological processes

Small antisense RNA to cyclin D1 generated by pre-tRNA splicing inhibits growth of human hepatoma cells

Introns are present in some human pre-tRNAs. They are spliced out during the maturation processes of pre-tRNAs in a way that is irrelevant to their specific nucleotide sequences. This unique characteristic of tRNA splicing can be used for generation of small antisense RNAs by replacing the intron sequences with corresponding antisense sequences. In this work, the intron sequence of human pre-tRNAtyr gene was replaced with a 20 bp antisense sequence targeted to the 5' coding region of cyclin D1, a molecule that was over-expressed in many malignant proliferating cells. Under the control of U6 SnRNA promoter to further enhance transcription efficiency of the modified pre-tRNAtyr gene and subsequent antisense generation, the antisense RNA exhibited obvious suppression of cyclin D1 expression in H22 hepatoma cells. The growth of H22-transplanted tumors in mice was significantly inhibited when treated with naked plasmid DNA harboring the cyclin D1 antisense RNA generating cassette. Such tumor growth inhibition might be due to apoptosis caused by reduced cyclin D1 expression as revealed by immunohistochemical analysis of tumor samples.

DNA targeting of rhinal cortex D2 receptor protein reversibly blocks learning of cues that predict reward

When schedules of several operant trials must be successfully completed to obtain a reward, monkeys quickly learn to adjust their behavioral performance by using visual cues that signal how many trials have been completed and how many remain in the current schedule. Bilateral rhinal (perirhinal and entorhinal) cortex ablations irreversibly prevent this learning. Here, we apply a recombinant DNA technique to investigate the role of dopamine D2 receptor in rhinal cortex for this type of learning. Rhinal cortex was injected with a DNA construct that significantly decreased D2 receptor ligand binding and temporarily produced the same profound learning deficit seen after ablation. However, unlike after ablation, the D2 receptor-targeted, DNA-treated monkeys recovered cue-related learning after 11-19 weeks. Injecting a DNA construct that decreased N-methyl-d-aspartate but not D2 receptor ligand binding did not interfere with learning associations between the cues and the schedules. A second D2 receptor-targeted DNA treatment administered after either recovery from a first D2 receptor-targeted DNA treatment (one monkey), after N-methyl-d-aspartate receptor-targeted DNA treatment (two monkeys), or after a vector control treatment (one monkey) also induced a learning deficit of similar duration. These results suggest that the D2 receptor in primate rhinal cortex is essential for learning to relate the visual cues to the schedules. The specificity of the receptor manipulation reported here suggests that this approach could be generalized in this or other brain pathways to relate molecular mechanisms to cognitive functions.

Short-term cytotoxic effects and long-term instability of RNAi delivered using lentiviral vectors

Background

RNA interference (RNAi) can potently reduce target gene expression in mammalian cells and is in wide use for loss-of-function studies. Several recent reports have demonstrated that short double-stranded RNAs (dsRNAs), used to mediate RNAi, can also induce an interferon-based response resulting in changes in the expression of many interferon-responsive genes. Off-target gene silencing has also been described, bringing into question the validity of certain RNAi-based approaches for studying gene function. We have targeted the plasminogen activator inhibitor-2 (PAI-2 or SERPINB2) mRNA using lentiviral vectors for delivery of U6 promoter-driven PAI-2-targeted short hairpin RNA (shRNA) expression. PAI-2 is reported to have anti-apoptotic activity, thus reduction of endogenous expression may be expected to make cells more sensitive to programmed cell death.

Results

As expected, we encountered a cytotoxic phenotype when targeting the PAI-2 mRNA with vector-derived shRNA. However, this predicted phenotype was a potent non-specific effect of shRNA expression, as functional overexpression of the target protein failed to rescue the phenotype. By decreasing the shRNA length or modifying its sequence we maintained PAI-2 silencing and reduced, but did not eliminate, cytotoxicity. ShRNA of 21 complementary nucleotides (21 mers) or more increased expression of the oligoadenylate synthase-1 (OAS1) interferon-responsive gene. 19 mer shRNA had no effect on OAS1 expression but long-term selective pressure on cell growth was observed. By lowering lentiviral vector titre we were able to reduce both expression of shRNA and induction of OAS1, without a major impact on the efficacy of gene silencing.

Conclusions

Our data demonstrate a rapid cytotoxic effect of shRNAs expressed in human tumor cell lines. There appears to be a cut-off of 21 complementary nucleotides below which there is no interferon response while target gene silencing is maintained. Cytotoxicity or OAS1 induction could be reduced by changing shRNA sequence or vector titre, but stable gene silencing could not be maintained in extended cell culture despite persistent marker gene expression from the RNAi-inducing transgene cassette. These results underscore the necessity of careful controls for immediate and long-term RNAi use in mammalian cell systems.

In vitro surfactant protein B deficiency inhibits lamellar body formation

Surfactant protein (SP) B is essential for normal pulmonary surfactant activity and lamellar body genesis in type 2 cells. However, the role of SP-B in lamellar body genesis is poorly understood. We developed an adenovirus vector expressing antisense SP-B as an alternative in vitro model of SP-B deficiency to begin to explore the role of SP-B in lamellar body genesis. RT-PCR analysis revealed that antisense SP-B expression interfered with translation of endogenous SP-B mRNA. Antisense SP-B expression resulted in reliable in vitro reproduction of many features of SP-B deficiency, including absent mature SP-B and decreased lamellar bodies and SP-C. Light and electron microscopy demonstrated significant reductions in lamellar body number. Western blotting revealed a significant reduction in mature 8-kD SP-B protein and decreased mature SP-C. Our data indicate that antisense SP-B can be effectively used to replicate the SP-B-deficient type 2 cell phenotype in vitro, and provides an attractive alternative to transgenic models for the further study of the role of SP-B in lamellar body genesis.

Gene therapy approaches to HIV infection

The HIV pandemic represents a new challenge to biomedical research. What began as a handful of recognized cases among homosexual men in the US has become a global pandemic of such proportions that it clearly ranks as one of the most destructive viral scourges in history. In the past few years new treatments and drugs have been developed and tested, but the development of a new generation of therapies remains a major priority, because of the lack of chemotherapeutic drugs or vaccines that show long-term efficacy in vivo. Recently, gene therapeutic strategies for the treatment of patients with HIV infection have received increased attention because they are able to offer the possibility of simultaneously targeting multiple sites in the HIV genome, thereby minimizing the production of resistant virus. Recombinant genes for gene therapy can be classified as expressing interfering proteins (intracellular antibodies, dominant negative proteins) or interfering RNAs (antisense RNAs, ribozymes, RNA decoys). The latter group offers the advantage of avoiding the stimulation of host immune response which might progressively decrease the efficacy of proteins. The stumbling block to achieving lasting antiviral effects is still represented by the lack of efficient gene transfer techniques capable of generating persistent transgene expression and a high number of transduced cells relative to untransduced cells. Novel delivery vectors, such as lentiviruses, might overcome some of these shortcomings. The use of recombinant genes to generate immunity is a very promising concept that is rapidly expanding. Since the immune system can significantly amplify the response to tiny amounts of antigen, DNA vaccines can indeed be delivered by exploiting traditional gene therapy approaches without the need of high transduction efficiency.

Viral vector producing antisense RNA restores myotonic dystrophy myoblast functions

Myotonic dystrophy (DM1) is caused by the expansion of a trinucleotide repeat (CTG) located in the 3'untranslated region of the myotonic dystrophy protein kinase gene, for which currently there is no effective treatment. The data available suggest that misregulation of RNA homeostasis may play a major role in DM1 muscle pathogenesis. This indicates that the specific targeting of the mutant DMPK transcripts is essential to raise the rationale basis for the development of a specific gene therapy for DM1. We have produced a retrovirus which expresses a 149-bp antisense RNA complementary to the (CUG)13 repeats and to the 110-bp region following the repeats sequence to increase the specificity. This construct was introduced into human DM1 myoblasts, resulting in a preferential decrease in mutant DMPK transcripts, and effective restoration of human DM1 myoblast functions such as myoblast fusion and the uptake of glucose. It was previously shown that delay of muscle differentiation and insulin resistance in DM1 are associated with misregulation of CUGBP1 protein levels. The analysis of CUGBP1 levels and activity in DM1 cells expressing the antisense RNA indicated a correction of CUGBP1 expression in infected DM1 cells. We therefore show that current antisense RNA delivered in vitro using a retrovirus is not only capable of inhibiting mutant DMPK transcripts, but also can ameliorate dystrophic muscle pathology at the cellular levels.

Construction of antisense RNA expression plasmid for u-PAR and its transfection to highly invasive PC-3M cell subclones

To evaluate the specific inhibition of antisense u-PAR on the u-PAR expressions in highly invasive cell subclones and to determine its blocking function in the invasion by those cells, a cDNA fragment of u-PAR obtained by RT-PCR was inserted into a plasmid vector named pcDNA3 in antisense orientation. Then the antisense u-PAR recombinant was transfected into highly invasive cell subclones. The u-PAR expression in neo-resistant cells was examined by RT-PCR and immunohistochemical assay. Compared to the control cells, the content of mRNA and protein of u-PAR in transfected cells decreased sharply, and the rate of inhibition was 53% and 73%, respectively, indicating that an antisense u-PAR might have played a specific inhibitory role in its expression in the cells, which may provide a good cell model for making further investigation of the inhibitory effects of the antisense u-PAR on invasion in highly invasive cell subclones of human prostate carcinoma.

Hammerhead ribozymes for target validation

Expensive failures in the pharmaceutical industry might be avoided by target validation at an early stage. Often, the full consequences of inhibiting a chosen drug target do not emerge until late in the development process. One option is to use hammerhead ribozymes as highly specific ribonucleases targeted exclusively at the mRNA encoding the target protein. The first part of this review is concerned with the mechanism and design of hammerhead ribozymes. This includes the chemistry of their action, specificity of cleavage and ability to discriminate between different mRNAs and selection of suitable cleavage sites. In considering their use for target validation, hammerhead ribozymes are divided into two categories. Endogenous ribozymes are transcribed inside the cell where they act whilst exogenous are introduced into the cell from outside. Exogenous ribozymes are synthesised chemically and must be protected against cellular nucleases. Information is provided on transfection methods and vectors that have been used with endogenous ribozymes as well as synthesis and chemical modification of exogenous ribozymes. Of proteins inhibited in cells or whole organisms, those in animal experiments are emphasised. Comparisons are made with other approaches, especially the use of antisense oligonucleotides or RNA.

Gene therapy

With recent advances in molecular biology, the ability to transfer genes to patients is becoming a reality. Ongoing clinical trials using gene transfer techniques have illustrated the potential and pitfalls of this new therapeutic modality for the treatment of a wide variety of disorders. While these techniques are not currently a part of routine clinical practice, it is only a matter of time until some form of gene therapy is approved for general use in the clinic. This review highlights some of the basic methods used in current gene therapy protocols. The objective of this review is to familiarize practitioners with these concepts so they can more effectively follow the progress of this emerging technology and better inform their patients.

Restoration of vancomycin susceptibility in Enterococcus faecalis by antiresistance determinant gene transfer

We assessed the ability of gene transfer to reverse vancomycin resistance in class A (VanA) glycopeptide-resistant Enterococcus faecalis. Recombinant shuttle vectors containing a vanH promoter-vanA antisense gene cassette fully restored vancomycin susceptibility through a combined transcriptional activator binding domain decoy and inducible vanA antisense RNA effect.

The impact of genomics on therapeutic drug development

Genomics can be defined as a set of related technologies that are focused on the discovery of genes implicated in human disease. Although many of the estimated 100,000 genes in the human genome have been at least partially identified by nucleotide sequence, elucidation of biological function has been achieved for only a small percentage of these. An even smaller percentage of genes discovered by these methodologies have become valid drug targets. This review discusses the various genomics technologies and their likelihood of yielding therapeutic drugs. Emerging advances in microarray "chip" technology have allowed the parallel analysis of gene expression patterns for thousands of genes simultaneously. Sequence information derived from the genomes of many individuals is leading to the rapid discovery of single nucleotide polymorphisms or SNPs. Detection of these human polymorphisms will fuel the discipline of pharmacogenomics, resulting in an increase in the success of clinical trials, the rescue of drugs that have previously failed in clinical trials because of adverse reactions from patient subpopulations, and ultimately, in the development of more personalized drug therapies. The impending identification of all human genes will signal the end of the structural genomics phase and usher in the function genomics phase. Technologies have already begun to move toward high-throughput elucidation of gene relationships, interactions and, it is hoped, toward their functions.

The ABC transporter genes of Plasmodium falciparum and drug resistance

The seminal observations that (a) chloroquine-resistant Plasmodium falciparum strains accumulate less drug than more sensitive parasites, and (b) chloroquine resistance could be modulated in vitro by the classic multidrug-resistance (MDR) modulator verapamil, suggested not only that parasite resistance to multiple drugs may be similar to the MDR phenotype described in mammalian cancer cells, but that homologous proteins may be involved. These findings prompted search for MDR-like genes in the parasite. To date, three full-length ABC transporter genes have been isolated from P. falciparum: two P-glycoprotein-like homologues, pfmdr1 and pfmdr2, and a homologue of the yeast GCN20 gene, pfgcn20.

Effects of altered cyclophilin A expression on growth and differentiation of human and mouse neuronal cells

1. Cyclophilin A (CyP-A), a soluble cytoplasmic immunophilin, is known for its involvement in T cell differentiation and proliferation. Although CyP-A has a pivotal role in the immune response, it is most highly concentrated in brain, where its functions are largely unknown. 2. We reported previously that a murine neuroblastoma (NB-P2) cell line can partially differentiate into neurons when treated with cyclosporin A (CyS-A), implicating a role for CyP-A in neuronal differentiation (Hovland et al. [1999]. Neurochem. Int. 3:229-235). 3. The role of CyP-A in regulating neuronal growth and differentiation is not well defined. To investigate this, we first tested the utility of retroviral-mediated gene transfer and expression in human embryonic brain (HEB) and NB-P2 cells. Second, we examined the effects of retroviral-mediated overexpression or antisense-mediated reduction of CyP-A in HEB and NB-P2 cells. 4. Our data show that retroviral vectors are efficient for stable gene transfer and expression in both cell lines. Moreover, neither overexpression nor reduction of CyP-A expression in NB-P2 cells altered the growth rate or induced differentiation. More importantly, the up-or down-regulation of CyP-A expression did not affect the magnitude of cAMP-induced NB-P2 differentiation. However, overexpression of CyP-A increased the growth rate of HEB cells. 5. In summary, the utility of retroviral vectors for stable gene expression in human embryonic brain and murine neuroblastoma cells was shown. Furthermore, a novel role for CyP-A in augmenting the proliferation of human embryonic brain cells was demonstrated in vitro.

Antisense imaging: where are we now?

The field of antisense targeting is changing rapidly as additional results from in vitro studies and animal and patient trials become available. While these developments apply primarily to antisense chemotherapy, many have implications for antisense imaging and radiotherapy. It may now be profitable to reconsider antisense imaging in the light of these recent developments. With the benefit of further insight, it may be possible to predict which antisense mechanisms will be preferable for antisense imaging. It is also possible to consider the influences of carriers (vectors) on the targeting of antisense DNA and whether this might improve imaging. Furthermore, estimates showing only low mRNA steady-state copy numbers per cell may be reconsidered in refining predictions of tissue counting rates. Finally, recent results suggest that radiolabeling antisense DNAs may not adversely influence the targeting properties of antisense DNAs.

Cutaneous gene therapy. Principles and prospects

As investigators continue to close the gap between basic research and clinical science, gene therapy is becoming of increasing interest to the dermatologist. Most notably, recent advances in gene-based cancer therapy, DNA vaccination, and molecular pharmacology have opened new avenues for investigation beyond those of the traditional gene replacement applications. Different gene delivery systems are currently being tested, each with specific advantages and disadvantages. This article summarizes some of the principles of gene therapy and its applications to cutaneous diseases.