Gene targeting for gene therapy: prospects

Current Transport Systems and Clinical Applications for Small Interfering RNA (siRNA) Drugs

Small interfering RNAs (siRNAs) are an attractive new agent with potential as a therapeutic tool because of its ability to inhibit specific genes for many conditions, including viral infections and cancers. However, despite this potential, many challenges remain, including off-target effects, difficulties with delivery, immune responses, and toxicity. Traditional genetic vectors do not guarantee that siRNAs will silence genes in vivo. Rational design strategies, such as chemical modification, viral vectors, and non-viral vectors, including cationic liposomes, polymers, nanocarriers, and bioconjugated siRNAs, provide important opportunities to overcome these challenges. We summarize the results of research into vector delivery of siRNAs as a therapeutic agent from their design to clinical trials in ophthalmic diseases, cancers, respiratory diseases, and liver virus infections. Finally, we discuss the current state of siRNA delivery methods and the need for greater understanding of the requirements.

Therapeutic plasmid DNA versus siRNA delivery: common and different tasks for synthetic carriers

Gene therapy offers great opportunities for the treatment of severe diseases including cancer. In recent years the design of synthetic carriers for nucleic acid delivery has become a research field of increasing interest. Studies on the delivery of plasmid DNA (pDNA) have brought up a variety of gene delivery vehicles. The more recently emerged gene silencing strategy by the intracellular delivery of small interfering RNA (siRNA) takes benefit from existing expertise in pDNA transfer. Despite common properties however, delivery of siRNA also faces distinct challenges due to apparent differences in size, stability of the formed nucleic acid complexes, the location and mechanism of action. This review emphasizes the common aspects and main differences between pDNA and siRNA delivery, taking into consideration a wide spectrum of polymer-based, lipidic and peptide carriers. Challenges and opportunities which result from these differences as well as the recent progress made in the optimization of carrier design are presented.

Role of chromatin structure in integration of helper-dependent adenoviral vectors containing the beta-globin locus control region

We constructed helper-dependent, fiber-chimeric adenoviral vectors that efficiently transduce human hematopoietic stem cells. We found that vectors carrying a 23-kb fragment of the beta-globin locus control region (LCR) flanked by adeno-associated virus inverted terminal repeats (Ad.LCR) preferentially integrated into the chromosomal beta-globin LCR of human erythroid Mo7e cells. We hypothesized that this targeted integration involves beta-globin LCR-specific chromatin structures. Chromatin immunoprecipitation assays of the beta-globin LCR revealed active chromatin within, and immediately downstream of, DNase hypersensitivity region 2 (HS2) in erythroid Mo7e cells, but not in nonerythroid cells. Importantly, most of the Ad.LCR integrations in Mo7e cells were found within this area. We provide further data indicating tethering of incoming Ad.LCR genomes to the chromosomal LCR. We also provide data that suggest a role for active chromatin in AAV Rep78-mediated Ad.LCR integration. Our findings support a new strategy for achieving targeted integration through chromatin tethering of vector DNA.

Polymer-based siRNA delivery: Perspectives on the fundamental and phenomenological distinctions from polymer-based DNA delivery

Gene therapy holds tremendous promise in the treatment of many genetic and acquired diseases. The future of gene therapy in humans, however, is contingent upon the discovery of safe and effective carriers of genetic material. Polymers represent a class of materials that can be extensively modified to meet the needs of a particular gene delivery system. A variety of polymer formulations have been proposed in the literature as potential carriers, most of which facilitate gene delivery by encapsulating, and in some cases, condensing nucleic acids into nano-sized particles which can then be taken up by cells. Crucial to successful delivery of the gene to a cell is the polymer's ability to protect its contents from degradation in the extracellular environment. A well-designed carrier will also promote cellular uptake and intracellular release of the nucleic acid. In the past, a common approach to gene therapy has been to transfect cells with a polymer-encapsulated DNA plasmid designed to replace a defective gene in the target-cell genome. Within the last few years, however, RNA interference (RNAi) has emerged as a novel therapeutic pathway by which harmful genes can be "silenced" by delivering complementary short interfering RNA (siRNA) to target cells. siRNA delivery facilitated by polymers, although very promising, suffers from many of the same limitations as DNA delivery. This review will (1) highlight the similarities and differences between these two methods of gene therapy and (2) discuss how some of the remaining challenges in siRNA delivery facilitated by polymers can be addressed by applying knowledge from the longer-studied problem of DNA delivery.

A novel single step double positive double negative selection strategy for β-globin gene replacement

beta-Thalassemias are a heterogeneous group of autosomal recessive disorders, characterized by reduced or absence of the beta-globin chain production by the affected alleles. Transplantation of genetically corrected autologous hematopoietic stem cell (HSC) is an attractive approach for treatment of these disorders. Gene targeting (homologous recombination) has many desirable features for gene therapy due to its ability to target the mutant genes and restore their normal expression. In the present study, a specific gene construct for beta-globin gene replacement was constructed consisting of: two homologous stems including, upstream and downstream regions of beta-globin gene, beta-globin gene lying between hygromycin and neomycin resistant genes as positive selection markers and thymidine kinase expression cassettes at both termini as negative selection marker. All segments were subcloned into pBGGT vector. The final plasmid was checked by sequencing and named as pFBGGT. Mammalian cell line COS-7 was transfected with linear plasmid by lipofection followed by positive and negative selection. DNA of the selected cells was analyzed by PCR and sequencing to confirm the occurrence of homologous recombination. In this novel strategy gene replacement was achieved in one step and by a single construct.

In vitro functional correction of the mutation responsible for murine severe combined immune deficiency by small fragment homologous replacement

A homologous recombination (HR) approach for site-specific correction of mutations would be highly desirable for the treatment of genetic disorders if recombination efficiencies were sufficiently high as to permit a biological effect. Using a T cell thymoma line derived from severe combined immunodeficient (SCID) mice with a point mutation in the gene encoding the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), we have shown that short DNA fragments (SDFs; 621 bases) can provide genotypic and functional correction of these cells. Double-stranded SDFs (dsSDFs) or single-stranded SDFs (ssSDFs) were designed to span the wild-type sequence of exon 85 in the DNA-PKcs gene and part of the 3' and 5' flanking intron regions. SCID cells were nucleofected with both single- and double-stranded wild-type SDF sequences. Corrected cells were selected on the basis of protection from radiation hypersensitivity that occurs as a consequence of the SCID mutation. Correction was mediated by both SDF forms (double and single stranded). These results indicate that SDFs can correct point mutations by HR with the possibility of harnessing ionizing radiation (IR) as a selection method to eliminate noncorrected cells and enrich for corrected SCID radioresistant cells.

A capsid-modified helper-dependent adenovirus vector containing the beta-globin locus control region displays a nonrandom integration pattern and allows stable, erythroid-specific gene expression

Gene therapy for hemoglobinopathies requires efficient gene transfer into hematopoietic stem cells and high-level erythroid-specific gene expression. Toward this goal, we constructed a helper-dependent adenovirus vector carrying the beta-globin locus control region (LCR) to drive green fluorescent protein (GFP) expression, whereby the LCR-GFP cassette is flanked by adeno-associated virus (AAV) inverted terminal repeats (Ad.LCR-beta-GFP). This vector possesses the adenovirus type 35 fiber knob that allows efficient infection of hematopoietic cells. Transduction and vector integration studies were performed in MO7e cells, a growth factor-dependent CD34(+) erythroleukemic cell line, and in cord blood-derived human CD34(+) cells. Stable transduction of MO7e cells with Ad.LCR-beta-GFP was more efficient and less subject to position effects and silencing than transduction with a vector that did not contain the beta-globin LCR. Analysis of integration sites indicated that Ad.LCR-beta-GFP integration in MO7e cells was not random but tethered to chromosome 11, specifically to the globin LCR. More than 10% of analyzed integration sites were within the chromosomal beta-globin LCR. None of the Ad.LCR-beta-GFP integrations occurred in exons. The integration pattern of a helper-dependent vector that contained X-chromosomal stuffer DNA was different from that of the beta-globin LCR-containing vector. Infection of primary CD34(+) cells with Ad.LCR-beta-GFP did not affect the clonogenic capacity of CD34(+) cells. Transduction of CD34(+) cells with Ad.LCR-beta-GFP resulted in vector integration and erythroid lineage-specific GFP expression.

Functional correction of episomal mutations with short DNA fragments and RNA-DNA oligonucleotides

BACKGROUND

Gene correction is an alternative approach to replacement gene therapy. By correcting mutations within the genome, some of the barriers to effective gene therapy are avoided. Homologous nucleic acid sequences can correct mutations by inducing recombination or mismatch repair. Recently, encouraging data have been presented using both short DNA fragments (SDFs) and RNA-DNA oligonucleotides (RDOs) in experimental strategies to realize clinical gene correction.

METHODS

The delivery of labelled SDFs and RDOs to a variety of cell lines was tested using both FACS analysis and confocal microscopy. A GFP-based reporter system was constructed, containing a nonsense mutation, to allow quantitation of gene correction in living cells. This reporter was used to compare efficiencies of functional gene correction using SDFs and RDOs in arange of mammalian cell lines.

RESULTS

The delivery experiments highlight the inefficient delivery of SDFs and RDOs to the nucleus using polyethylenimine (PEI) transfection. This study compared the episomal correction efficiency of the reporter plasmid mediated by SDFs and RDOs within different cell types; low levels of functional correction were detected in cell culture.

CONCLUSIONS

Whilst delivery of PEI-complexed SDFs or RDOs to the cell is highly effective, nuclear entry appears to be a limiting factor. SDFs elicited episomal GFP correction across a range of cell lines, whereas RDOs only corrected the reporter in a cell line that overexpresses RAD51.

Stem cells in tissue engineering

The concept of producing 'spare parts' of the body for replacement of damaged or lost organs lies at the core of the varied biotechnological practices referred to generally as tissue engineering. Use of postnatal stem cells has the potential to significantly alter the perspective of tissue engineering. Successful long-term restoration of continuously self-renewing tissues such as skin, for example, depends on the use of extensively self-renewing stem cells. The identification and isolation of stem cells from a number of tissues provides appropriate targets for prospective gene therapies.

Chromosomal integration pattern of a helper-dependent minimal adenovirus vector with a selectable marker inserted into a 27.4-kilobase genomic stuffer

Helper-dependent minimal adenovirus vectors are promising tools for gene transfer and therapy because of their high capacity and the absence of immunostimulatory or cytotoxic viral genes. In order to characterize this new vector system with respect to its integrative properties, the integration pattern of a minimal adenovirus vector with a neo(r) gene inserted centrally into a noncoding 27.4-kb genomic stuffer element derived from the human X chromosome after infection of a sex chromosome aneuploid (X0) human glioblastoma cell line was studied. Our results indicate that even extensive homologies and abundant chromosomal repeat elements present in the vector did not lead to integration of the vector via homologous or homology-mediated mechanisms. Instead, integration occurred primarily by insertion of a monomer with no or little loss of sequences at the vector ends, apparently at random sites, which is very similar to E1 deletion adenovirus vectors. It is therefore unlikely that the incorporation of stuffer elements derived from human genomic DNA, which were shown to allow long-term transgene expression in vivo in a number of studies, leads to an enhanced risk of insertional mutagenesis. Furthermore, our findings indicate that the potential of minimal adenovirus vectors as tools for targeted insertion and gene targeting is limited despite the possibility of incorporating long stretches of homologous sequences. However, we found an enhanced efficiency of stable neo(r) transduction of the minimal adenovirus vector compared to an E1 deletion adenovirus vector, possibly caused by the absence of potential growth-inhibitory viral genes. Complete integration of the vector and tolerance of the integrated vector sequences by the cell might indicate a potential use of these vectors as tools for stable transfer of (large) genes.

Bone marrow stromal stem cells: nature, biology, and potential applications

Bone marrow stromal cells are progenitors of skeletal tissue components such as bone, cartilage, the hematopoiesis-supporting stroma, and adipocytes. In addition, they may be experimentally induced to undergo unorthodox differentiation, possibly forming neural and myogenic cells. As such, they represent an important paradigm of post-natal nonhematopoietic stem cells, and an easy source for potential therapeutic use. Along with an overview of the basics of their biology, we discuss here their potential nature as components of the vascular wall, and the prospects for their use in local and systemic transplantation and gene therapy.

Manipulating the mammalian genome by homologous recombination

Gene targeting in mammalian cells has proven invaluable in biotechnology, in studies of gene structure and function, and in understanding chromosome dynamics. It also offers a potential tool for gene-therapeutic applications. Two limitations constrain the current technology: the low rate of homologous recombination in mammalian cells and the high rate of random (nontargeted) integration of the vector DNA. Here we consider possible ways to overcome these limitations within the framework of our present understanding of recombination mechanisms and machinery. Several studies suggest that transient alteration of the levels of recombination proteins, by overexpression or interference with expression, may be able to increase homologous recombination or decrease random integration, and we present a list of candidate genes. We consider potentially beneficial modifications to the vector DNA and discuss the effects of methods of DNA delivery on targeting efficiency. Finally, we present work showing that gene-specific DNA damage can stimulate local homologous recombination, and we discuss recent results with two general methodologies--chimeric nucleases and triplex-forming oligonucleotides--for stimulating recombination in cells.

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.

Gene therapy and molecular approaches to the treatment of hereditary muscular disorders

Gene therapy for inherited muscle disease is an active area of research and development. Initial emphasis has been on gene replacement but alternative approaches are increasingly being considered in order to overcome difficulties, such as the immune rejection of transduced cells, the need for appropriate and tissue-specific control of expression, and the requirement for systemic spread in some conditions. However, the most significant obstacles to the clinical success of gene therapy are still the lack of efficiency and accuracy of gene medicine delivery.