Gene repair and transposon-mediated gene therapy

Insertion and Deletion Mismatches Distant from the Target Position Improve Gene Correction with a Tailed Duplex

A 5'-tailed duplex (TD) DNA corrects a base-substitution mutation. In this study, the effects of insertion and deletion (indel) mismatches distant from the target position on the gene correction were examined. Three target plasmid DNAs with and without indel mismatches ∼330 bases distant from the correction target position were prepared, and introduced into HeLa cells together with the TD. The indel mismatches improved the gene correction efficiency and specificity without sequence conversions at the indel mismatch site. These results suggested that the gene correction efficiency and specificity are increased when an appropriate second mismatch is introduced into the TD fragment.

Correction of frameshift mutations with tailed duplex DNAs

Tailed duplex (TD) DNAs, prepared by annealing an oligonucleotide to a several-hundred-base single-stranded (ss) DNA fragment, correct a base-substitution mutation with high efficiency. In the present study, the abilities of TD fragments to correct single-base insertion and deletion mutations were examined, using hygromycin-resistance and enhanced green fluorescent protein fusion (Hyg-EGFP) genes inactivated by +G and -C frameshift mutations. The 5'-TD and 3'-TD DNA fragments were co-transfected with plasmid DNA containing the inactivated Hyg-EGFP gene into CHO-K1 cells, and the gene correction efficiencies were determined by introducing the plasmid DNA recovered from the transfected cells into Escherichia coli cells. In contrast to their efficiencies for the substitution mutation, the gene correction abilities of the TD fragments were relatively low. The correction efficiencies by the TD fragments were apparently higher than that by a ss DNA fragment, one of the DNA fragments employed for gene correction. These results suggest that the TD fragments have the potential to correct frameshift mutations, although further improvement is required.

Keratin 14-null cells as a model to test the efficacy of gene therapy approaches in epithelial cells

Skin fragility disorders caused by keratin mutations are incurable, and a better understanding of their etiology is needed to find new ways to improve and treat these conditions. The best-studied skin fragility disorder is epidermolysis bullosa simplex (EBS), an autosomal dominant condition caused by mutations in keratin 5 (K5) or K14. To analyze disease mechanisms and develop gene therapy strategies, we have used keratinocyte cell lines derived from EBS patients as model systems. Here, we describe two cell lines established from EBS patients with K14-null mutations. We analyze the responses of these cells to stress assays previously shown to discriminate between wild-type and keratin-mutant keratinocytes, to directly evaluate the efficacy of rescuing K14-null cells by supplementation with wild-type K14 complementary DNA (cDNA). The K14-null cells show elevated levels of stress correlating with reduced normal keratin function. By transfecting wild-type K14 into these cells, we demonstrate "proof of principle" that an add-back approach can significantly rescue the normal keratinocyte behavior profile. These K14-null cell lines provide a disease model for studying the effects of keratin ablation in EBS patients and to test the efficacy of gene add-back and other therapy approaches in keratinocytes.

Improved gene correction efficiency with a tailed duplex DNA fragment

A 606-base single-stranded (ss) DNA fragment, prepared by restriction enzyme digestion of ss phagemid DNA, corrects a hygromycin resistance and enhanced green fluorescent protein (Hyg-EGFP) fusion gene more efficiently than a PCR fragment, which is the conventional type of DNA fragment used in gene correction. Here, a tailed duplex, obtained by annealing an oligonucleotide to the ss DNA fragment, was used in the correction. The tailed duplex may be a good substrate for the RAD51 protein, an important enzyme in homologous recombination, which could be the gene correction pathway. The annealing of the oligonucleotides enhanced the correction efficiency of the Hyg-EGFP gene, especially when annealed in the 3'-region of the ss DNA fragment. Both the length and backbone structure of the oligonucleotides affected the gene correction efficiency. This type of gene correction device was also effective for another target gene, the rpsL gene. The results obtained in this study indicate that tailed duplex DNA fragments are effective nucleic acids for gene correction.

Cftr gene targeting in mouse embryonic stem cells mediated by Small Fragment Homologous Replacement (SFHR)

Different gene targeting approaches have been developed to modify endogenous genomic DNA in both human and mouse cells. Briefly, the process involves the targeting of a specific mutation in situ leading to the gene correction and the restoration of a normal gene function. Most of these protocols with therapeutic potential are oligonucleotide based, and rely on endogenous enzymatic pathways. One gene targeting approach, "Small Fragment Homologous Replacement (SFHR)", has been found to be effective in modifying genomic DNA. This approach uses small DNA fragments (SDF) to target specific genomic loci and induce sequence and subsequent phenotypic alterations. This study shows that SFHR can stably introduce a 3-bp deletion (deltaF508, the most frequent cystic fibrosis (CF) mutation) into the Cftr (CF Transmembrane Conductance Regulator) locus in the mouse embryonic stem (ES) cell genome. After transfection of deltaF508-SDF into murine ES cells, SFHR-mediated modification was evaluated at the molecular levels on DNA and mRNA obtained from transfected ES cells. About 12% of transcript corresponding to deleted allele was detected, while 60% of the electroporated cells completely lost any measurable CFTR-dependent chloride efflux. The data indicate that the SFHR technique can be used to effectively target and modify genomic sequences in ES cells. Once the SFHR-modified ES cells differentiate into different cell lineages they can be useful for elucidating tissue-specific gene function and for the development of transplantation-based cellular and therapeutic protocols.

Sleeping beauty transposase has an affinity for heterochromatin conformation

The Sleeping Beauty (SB) transposase reconstructed from salmonid fish has high transposition activity in mammals and has been a useful tool for insertional mutagenesis and gene delivery. However, the transposition efficiency has varied significantly among studies. Our previous study demonstrated that the introduction of methylation into the SB transposon enhanced transposition, suggesting that transposition efficiency is influenced by the epigenetic status of the transposon region. Here, we examined the influence of the chromatin status on SB transposition in mouse embryonic stem cells. Heterochromatin conformation was introduced into the SB transposon by using a tetracycline-controlled transrepressor (tTR) protein, consisting of a tetracycline repressor (TetR) fused to the Kruppel-associated box (KRAB) domain of human KOX1 through tetracycline operator (tetO) sequences. The excision frequency of the SB transposon, which is the first step of the transposition event, was enhanced by approximately 100-fold. SB transposase was found to be colocalized with intense DAPI (4',6'-diamidino-2-phenylindole) staining and with the HP1 family by biochemical fractionation analyses. Furthermore, chromatin immunoprecipitation analysis revealed that SB transposase was recruited to tTR-induced heterochromatic regions. These data suggest that the high affinity of SB transposase for heterochromatin conformation leads to enhancement of SB transposition efficiency.

Delivery and mechanistic considerations for the production of knock-in mice by single-stranded oligonucleotide gene targeting

Single-stranded oligodeoxynucleotide (ssODN) gene targeting may facilitate animal model creation and gene repair therapy. Lipofection of ssODN can introduce point mutations into target genes. However, typical efficiencies in mouse embryonic stem cells (ESC) are <10(-4), leaving corrections too rare to effectively identify. We developed ESC lines with an integrated mutant neomycin resistance gene (Tyr22Ter). After targeting with ssODN, repaired cells survive selection in G418. Correction efficiencies varied with different lipofection procedures, clonal lines, and ssODN designs, ranging from 1 to 100 corrections per million cells plated. Uptake studies using cell sorting of Cy5-labelled ssODN showed 40% of the corrections concentrated in the best transfected 22% of cells. Four different basepair mismatches were tested and results show that the base-specificity of the mismatch is critical. Dual mismatch ssODN also showed mismatch preferences. These ESC lines may facilitate development of improved ssODN targeting technologies for either animal production or ex vivo gene therapy.

Bioregulators as prototypic nontraditional threat agents

Bioregulators are naturally occurring organic compounds that regulate a multitude of biologic processes. Under natural circumstances, bioregulators are synthesized in minute quantities in a variety of living organisms and are essential for physiologic homeostasis. In the wrong hands, these compounds have the capability to be used as nontraditional threat agents that are covered by the prohibitions of the Chemical Weapons Convention and the Biological and Toxin Weapons Convention. Unlike traditional biowarfare/bioterrorism agents that have a latency period of hours to days,the onset of action of bioregulators may occur within minutes after host exposure. Concerns regarding the potential misuse of bioregulators for nefarious purposes relate to the ability of these nontraditional agents to induce profound physiologic effects.

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Physical incorporation of a single-stranded oligodeoxynucleotide during targeted repair of a human chromosomal locus

BACKGROUND

Targeted gene repair is an attractive method to correct point-mutated genes at their natural chromosomal sites, but it is still rather inefficient. As revealed by earlier studies, successful gene correction requires a productive interaction of the repair molecule with the target locus. The work here set out to investigate whether DNA repair, e.g., mismatch repair, or a direct incorporation of the correction molecule follows as the step upon the initial interaction.

METHODS

Single-stranded 21mer oligodeoxynucleotides (ODNs) of sense orientation were directed towards point-mutated enhanced green fluorescence protein transgene loci in HEK-293-derived cell clones. First gene repair assays compared ODNs carrying the canonical termini 5'-phosphate and 3'-OH with their respective variants harbouring non-canonical termini (5'-OH, 3'-H). Second, a protocol was established to allow efficient recovery of integrated short biotin-labelled ODNs from the genomes of gene-corrected cells using streptavidin-coated beads in order to test directly whether transfected ODNs become bona fide parts of the target locus DNA.

RESULTS

Oligodeoxynucleotides with canonical termini were about 34-fold more efficient than their counterparts carrying non-canonical termini in a phosphorothioate-modified backbone. Furthermore, biotinylated fragments were successfully recovered from genomic DNAs of gene-corrected cells.

CONCLUSIONS

The experiment showed that ODNs are incorporated into a mammalian genome. This unravels one early repair step and also sets an unexpected example of genome dynamics possibly relevant to other ODN-based cell techniques.

Role of protein tyrosine phosphatases in cancer

Protein phosphorylation and dephosphorylation are complex enzymatic reactions that are performed by the concerted action of protein kinases and phosphatases, respectively. Deregulation of such coordination due to loss or gain of a single component of the process can result in disease conditions that include, but are not limited to, neoplastic transformation, developmental, autoimmune, and metabolic disorders. Unlike many protein tyrosine kinases that function as oncoproteins, protein tyrosine phosphatases (PTPs) could impart positive or negative effect on cell proliferation. Although past studies have suggested a potential role for PTPs in cancer, the molecular mechanisms of the altered activity/level of these enzymes and the pathological manifestations of these modifications in diseases, particularly in cancer, have not been critically analyzed. This chapter is a comprehensive survey of the alterations of PTPs and the implications of the growth, proliferation, and apoptosis phenotypes attributable to the altered function of this family of phosphatases in cancer. Further, the potential applications of different therapeutic approaches to rectify the adverse effects of alterations in expression of the phosphatase genes and of the phosphatase activity in cancer are discussed.

Gene therapy for autosomal dominant disorders of keratin

Dominant mutations that interfere with the assembly of keratin filaments cause painful and disfiguring epidermal diseases like pachyonychia congenita and epidermolysis bullosa simplex. Genetic therapies for such diseases must either suppress the production of the toxic proteins or correct the genetic defect in the chromosome. Because epidermal skin cells may be genetically modified in tissue culture or in situ, gene correction is a legitimate goal for keratin diseases. In addition, recent innovations, such as RNA interference in animals, make an RNA knockdown approach plausible in the near future. Although agents of RNA reduction (small interfering RNA, ribozymes, triplex oligonucleotides, or antisense DNA) can be delivered as nucleotides, the impermeability of the skin to large charged molecules presents a serious impediment. Using viral vectors to deliver genes for selective inhibitors of gene expression presents an attractive alternative for long-term treatment of genetic disease in the skin.

Factors affecting SFHR gene correction efficiency with single-stranded DNA fragment

A 606-nt single-stranded (ss) DNA fragment, prepared by restriction enzyme digestion of ss phagemid DNA, improves the gene correction efficiency by 12-fold as compared with a PCR fragment, which is the conventional type of fragment used in the small fragment homologous replacement method [H. Tsuchiya, H. Harashima, H. Kamiya, Increased SFHR gene correction efficiency with sense single-stranded DNA, J. Gene Med. 7 (2005) 486-493]. To reveal the characteristic features of this gene correction with the ss DNA fragment, the effects on the gene correction in CHO-K1 cells of the chain length, 5'-phosphate, adenine methylation, and transcription were studied. Moreover, the possibility that the ss DNA fragment is integrated into the target DNA was examined with a radioactively labeled ss DNA fragment. The presence of methylated adenine, but not the 5'-phosphate, enhanced the gene correction efficiency, and the optimal length of the ss DNA fragment (approximately 600 nt) was determined. Transcription of the target gene did not affect the gene correction efficiency. In addition, the target DNA recovered from the transfected CHO-K1 cells was radioactive. The results obtained in this study indicate that length and adenine methylation were important factors affecting the gene correction efficiency, and that the ss DNA fragment was integrated into the double-stranded target DNA.

Misleading gene conversion frequencies due to a PCR artifact using small fragment homologous replacement

Recent studies have reported successful correction of the most common F508del mutation in cystic fibrosis (CF) airway epithelial cells by small fragment homologous replacement (SFHR). We wished to apply the SFHR methodology to our CF bronchial epithelial cells, of compound heterozygous genotype (F508del/W1282X), in which nucleic acid transfer was previously optimized by electroporation. Using a PCR-based detection methodology, with one of the primers located outside the SFHR homology region, we obtained SFHR dose-dependent F508del to wild-type CFTR gene conversion frequencies reaching 30%. However, the increased wild-type/F508del CFTR allele ratio was transient, vanishing at 5 days posttransfection. Furthermore, we have been unable to reproduce the SFHR-mediated repair of the F508del mutation in our cellular model when both detection primers were located outside the SFHR homology region. A thorough reexamination of our initial detection strategy revealed that a false positive result was originated from a PCR artifact created by the SFHR fragment itself. Thus, nonamplifiable detection methods, such as Southern blotting, protein analysis, or functional assays, should be performed, whenever possible, to correctly assess gene conversion frequencies.

In vivo alteration of the keratin 17 gene in hair follicles by oligonucleotide-directed gene targeting

Using intradermal injection of a chimeric RNA-DNA oligonucleotide (RDO) or a single-stranded oligonucleotide (ssODN) into murine skin, we attempted to make a dominant mutation (R94p) in the conserve alpha-helical domain of keratin 17 (K17), the same mutation found in pachyononychia congenichia type 2 (PC-2) patients with phenotypes ranging from twisted hair and multiple pilosebaceous cysts. Both K17A-RDO and -ssODN contained a single base mismatch (CGC to CCC) to alter the normal K17 sequence to cause an amino acid substitution (R94P). The complexes consisting of oligonucleotides and cationic liposomes were injected to C57B1/6 murine skin at 2 and 5 day after birth. Histological examination of skin biopsies at postnatal day 8 from several mice showed consistent twisted hair shafts or broken hair follicles at the sebaceous gland level and occasional rupture of the hair bulb or epidermal cyst-like changes. In the injected area, the number of full anagen hair follicles decrease by 50%. Injection of the control oligonucleotide, identical to K17A-RDO but containing no mismatch to the normal sequence, did not result in any detectable abnormality. The frequency of gene alteration was lower than 3%, according to the restriction fragment length polymorphism (RFLP) analysis of the genomic DNA isolated by dissection of hair follicles from slides. Although intradermal injection of K17A-RDO or K17-ssODN caused a dominant mutation in K17 affecting hair growth and morphology, these phenotypic changes were transient either due to the compensation of K17 by other keratins or the replacement of the mutated cells by normal surrounding cells during hair growth.

Prospects for gene therapy in the fragile X syndrome

"If politics is the art of the possible, research is the art of the soluble. Both are immensely practical-minded affairs." P. B. Medawar.Gene therapy is unarguably the definitive way to treat, and possibly cure, genetic diseases. A straightforward concept in theory, in practice it has proven difficult to realize, even when directed to easily accessed somatic cell systems. Gene therapy for diseases in which the central nervous system (CNS) is the target organ presents even greater challenges and diverse vectors and brain delivery approaches are under investigation. We argue that in the case of the fragile X syndrome the approach most likely to have a chance of being effective should consist of a small, diffusible vector derived from the adeno-associated virus, carrying an FMR1 cDNA comprising the 5' promoter region and the 3' untranslated region of the gene, delivered to the entire brain by osmotic blood-brain barrier disruption. The approach can be tested in Fmr1 knockout mice, although changes in their neurobehavioral abnormalities may be difficult to evaluate. A defect in the expression of GABA(A) receptors in these mice-if shown to be a direct consequence of the Fmr1 defect-promises to be a more readily assessable marker of restored FMRp function on gene transfer.

Functional improvement of mutant keratin cells on addition of desmin: an alternative approach to gene therapy for dominant diseases

A major challenge to the concept of gene therapy for dominant disorders is the silencing or repairing of the mutant allele. Supplementation therapy is an alternative approach that aims to bypass the defective gene by inducing the expression of another gene, with similar function but not susceptible to the disrupting effect of the mutant one. Epidermolysis bullosa simplex (EBS) is a genetic skin fragility disorder caused by mutations in the genes for keratins K5 or K14, the intermediate filaments present in the basal cells of the epidermis. Keratin diseases are nearly all dominant in their inheritance. In cultured keratinocytes, mutant keratin renders cells more sensitive to a variety of stress stimuli such as osmotic shock, heat shock or scratch wounding. Using a 'severe' disease cell culture model system, we demonstrate reversion towards wild-type responses to stress after transfection with human desmin, an intermediate filament protein normally expressed in muscle cells. Such a supplementation therapy approach could be widely applicable to patients with related individual mutations and would avoid some of the financial obstacles to gene therapy for rare diseases.

Transposon-based strategies for microbial functional genomics and proteomics

Transposons are mobile genetic elements that can relocate from one genomic location to another. As well as modulating gene expression and contributing to genome plasticity and evolution, transposons are remarkably diverse molecular tools for both whole-genome and single-gene studies in bacteria, yeast, and other microorganisms. Efficient but simple in vitro transposition reactions now allow the mutational analysis of previously recalcitrant microorganisms. Transposon-based signature-tagged mutagenesis and genetic footprinting strategies have pinpointed essential genes and genes that are crucial for the infectivity of a variety of human and other pathogens. Individual proteins and protein complexes can be dissected by transposon-mediated scanning linker mutagenesis. These and other transposon-based approaches have reaffirmed the usefulness of these elements as simple yet highly effective mutagens for both functional genomic and proteomic studies of microorganisms.

Transgene manipulation in zebrafish by using recombinases

Although much remains to be done, our results to date suggest that efficient and precise genome engineering in zebrafish will be possible in the future by using Cre recombinase and SB transposase in combination with their respective target sites. In this study, we provide the first evidence that Cre recombinase can mediate effective site-specific deletion of transgenes in zebrafish. We found that the efficiency of target site utilization could approach 100%, independent of whether the target site was provided transiently by injection or stably within an integrated transgene. Microinjection of Cre mRNA appeared to be slightly more effective for this purpose than microinjection of Cre-expressing plasmid DNA. Our work has not yet progressed to the point where SB-mediated mobilization of our transgene constructs would be observed. However, a recent report has demonstrated that SB can enhance transgenesis rates sixfold over conventional methods by efficiently mediating multiple single-copy insertion of transgenes into the zebrafish genome (Davidson et al., 2003). Therefore, it seems likely that a combined system should eventually allow both SB-mediated transgene mobilization and Cre-mediated transgene modification. Our goal is to validate methods for the precise reengineering of the zebrafish genome by using a combination of Cre-loxP and SB transposon systems. These methods can be used to delete, replace, or mobilize large pieces of DNA or to modify the genome only when and where required by the investigator. For example, it should be possible to deliver particular RNAi genes to well-expressed chromosomal loci and then exchange them easily with alternative RNAi genes for the specific suppression of alternative targets. As a nonviral vector for gene therapy, the transposon component allows for the possibility of highly efficient integration, whereas the Cre-loxP component can target the integration and/or exchange of foreign DNA into specific sites within the genome. The specificity and efficiency of this system also make it ideal for applications in which precise genome modifications are required (e.g., stock improvement). Future work should establish whether alternative recombination systems (e.g., phiC31 integrase) can improve the utility of this system. After the fish system is fully established, it would be interesting to explore its application to genome engineering in other organisms.

Gene therapy for gastric cancer: A review

Gastric cancer is common in China, and its early diagnosis and treatment are difficult. In recent years great progress has been achieved in gene therapy, and a wide array of gene therapy systems for gastric cancer has been investigated. The present article deals with the general principles of gene therapy and then focuses on how these principles may be applied to gastric cancer.

Sequence-specific modification of genomic DNA by small DNA fragments

Small DNA fragments have been used to modify endogenous genomic DNA in both human and mouse cells. This strategy for sequence-specific modification or genomic editing, known as small-fragment homologous replacement (SFHR), has yet to be characterized in terms of its underlying mechanisms. Genotypic and phenotypic analyses following SFHR have shown specific modification of disease-causing genetic loci associated with cystic fibrosis, beta-thalassemia, and Duchenne muscular dystrophy, suggesting that SFHR has potential as a therapeutic modality for the treatment of monogenic inherited disease.

An important role for RUNX3 in human L1 transcription and retrotransposition

LINE-1s (long interspersed nuclear elements-1) are abundant non-LTR retrotransposons that comprise 17% of the human genome. The 5' untranslated region (5'UTR) of human L1 (L1Hs) houses a poorly understood internal promoter. Here we report that mutations at a putative runt-domain transcription factor (RUNX) site (+83 to +101) in the 5'UTR decreased L1Hs transcription and retrotransposition in cell culture-based assays. Exogenous expression of RUNX3, but not the other two RUNX family members, RUNX1 and RUNX2, increased L1Hs transcription and retrotransposition, which were otherwise decreased by siRNAs targeting RUNX3 and a dominant negative RUNX. Further more, the specific interaction between RUNX3 and its binding site was demonstrated by an electrophoretic mobility shift assay (EMSA) using an anti-RUNX3 antibody. Interestingly, RUNX3 may also regulate the antisense promoter activity of L1Hs 5'UTR via another putative RUNX site (+526 to +508), as revealed by site-directed mutations and exogenous expression of RUNX factors. Our results indicate an important role for RUNX3 in L1Hs retrotransposition as well as transcription from its 5'UTR in both sense and antisense directions, and they should contribute to our understanding of the mechanism underlying L1Hs retrotransposition and its impact on the expression of adjacent cellular genes.

Genotype, obesity and cardiovascular disease--has technical and social advancement outstripped evolution?

Teleologically, our ancestors were highly adapted hunter-gatherers. In recent history, the environment in which Homo sapiens exists has altered drastically and humans are exposed to environments for which the hunter-gatherer genotype is ill-suited. The adoption of a sedentary Western lifestyle, and the case of obtaining food of a high calorific content imposed upon a thrifty genotype, have resulted in the current global epidemic of obesity, Type 2 diabetes and the Metabolic Syndrome. The ramification of this epidemic is that cardiovascular disease is becoming a global healthcare problem, which will have its greatest impact on the developing nations. A global strategy is required to reduce the impact of the Western lifestyle on the health of developing nations and prevent obesity and Type 2 diabetes. Such an approach needs to be culturally sensitive, integrated, and multidisciplinary and involve a range of interventions that work at the individual and community levels. If lifestyle measures fail, then pharmacological intervention may be necessary. For this, novel agents such as dual PPARalpha/gamma agonists may be the therapy of the future.

Suitability of oligonucleotide-mediated cystic fibrosis gene repair in airway epithelial cells

BACKGROUND

Non-viral vector-mediated targeted gene repair could become a useful alternative to classical gene addition strategies. The methodology guarantees a physiologically regulated and persistent expression of the repaired gene, with reported gene conversion and phenotypic correction efficiencies approaching 40-50% in some in vitro and in vivo models of disease. This is particularly important for cystic fibrosis (CF) because of its complex pathophysiology and the cellular heterogeneity of the cystic fibrosis transmembrane conductance regulator (CFTR) gene expression and function in the lung.

METHODS

A cell-free biochemical assay was applied to assess the ability of CF airway epithelial cells to support chimeraplast-mediated repair. In addition, a methodology allowing the relative quantification of the percentage of W1282X mutation repair in a heterozygous background using the PCR/oligonucleotide ligation assay (PCR/OLA) was developed. The performance of different chimeraplast and short single-stranded oligonucleotide structures delivered by non-viral vectors and electroporation was evaluated.

RESULTS

Chimeraplast-mediated repair competency was corroborated in CF airway epithelial cells. However, their repair activity was about 5-fold lower than that found in liver cells. Moreover, regardless of the corrector oligonucleotide structure applied to our CF bronchial epithelial cells, of compound heterozygous genotype (F508del/W1282X), the percentage of their resulting wild-type allele in the W1282X (exon 20) locus of the CFTR gene was not significantly different from that of the control untreated cells by our PCR/OLA assay (confidence interval at 95% +/- 4 allele wild-type).

CONCLUSIONS

Oligonucleotide-mediated CFTR gene repair is an inefficient process in CF airway epithelial cells. Further improvements in oligonucleotide structure, nuclear delivery and/or the capability for mismatch repair stimulation will be necessary to achieve therapeutic levels of mutation correction in these cells.

Sustainable correction of junctional epidermolysis bullosa via transposon-mediated nonviral gene transfer

Sustainable correction of severe human genetic disorders of self-renewing tissues, such as the blistering skin disease junctional epidermolysis bullosa (JEB), is facilitated by stable genomic integration of therapeutic genes into somatic tissue stem cells. While integrating viral vectors can achieve this, they suffer from logistical and biosafety concerns. To circumvent these limitations, we used the Sleeping Beauty transposable element to integrate the LAMB3 cDNA into genomes of epidermal holoclones from six unrelated JEB patients. These cells regenerate human JEB skin that is normalized at the level of laminin 5 protein expression, hemidesmosome formation and blistering. Transposon-mediated gene delivery therefore affords an opportunity for stable gene delivery in JEB and other human diseases.

Transcription affects formation and processing of intermediates in oligonucleotide-mediated gene alteration

The role of transcription in oligonucleotide (ODN)-directed gene modification has been investigated in mammalian cells. The importance of transcription is demonstrated using mammalian cell lines with varying degrees of transcription of the mutant LacZ reporter gene, residing in both episome and chromosome. Gene correction occurs more efficiently when the target gene is actively transcribed and antisense ODN is more active than sense ODN. Using an approach that combines biochemical studies with a cell-based assay to measure the functional activity of intermediates it is shown that a joint molecule, consisting of supercoiled DNA and homologous ODN targeted to correct the mutated base, is a functional intermediate in the gene repair process. Furthermore, this approach showed that a resected joint molecule is a downstream intermediate of the D-loop. These results indicate that the primary reason for efficient gene repair exhibited by the antisense ODN is its increased accessibility to the non-transcribed strand, and as a consequence an increased formation of intermediate during active transcription. Moreover, the processing of intermediates was also affected by transcription, suggesting that ODN-directed gene repair may be linked to transcription-coupled repair. Thus, transcription plays an important role in ODN-directed gene repair by affecting the formation and processing of key intermediates.

[Homologous recombination and gene targeting]

Gene therapy and the production of mutated cell lines or model animals both require the development of efficient, controlled gene-targeting strategies. Classical approaches are based on the ability of cells to use homologous recombination to integrate exogenous DNA into their own genome. The low frequency of homologous recombination in mammalian cells leads to inefficient targeting. Here, we review the limiting steps of classical approaches and the new strategies developed to improve the efficiency of homologous recombination in gene-targeting experiments.

Current status of gene therapy for inherited lung diseases

Gene therapy as a treatment modality for pulmonary disorders has attracted significant interest over the past decade. Since the initiation of the first clinical trials for cystic fibrosis lung disease using recombinant adenovirus in the early 1990s, the field has encountered numerous obstacles including vector inflammation, inefficient delivery, and vector production. Despite these obstacles, enthusiasm for lung gene therapy remains high. In part, this enthusiasm is fueled through the diligence of numerous researchers whose studies continue to reveal great potential of new gene transfer vectors that demonstrate increased tropism for airway epithelia. Several newly identified serotypes of adeno-associated virus have demonstrated substantial promise in animal models and will likely surface soon in clinical trials. Furthermore, an increased understanding of vector biology has also led to the development of new technologies to enhance the efficiency and selectivity of gene delivery to the lung. Although the promise of gene therapy to the lung has yet to be realized, the recent concentrated efforts in the field that focus on the basic virology of vector development will undoubtedly reap great rewards over the next decade in treating lung diseases.

Highly efficient, large volume flow electroporation

Electroporation is widely used to transfect and load cells with various molecules. Traditional electroporation using a static mode is typically restricted to volumes less than 1 mL, which limits its use in clinical and industrial bioprocessing applications. Here we report efficient, large volume transfection results by using a scalable-volume electroporation system. Suspended (Jurkat) and adherent cells (10T1/2 and Huh-7) were tested. A large macromolecule, FITC-conjugated dextran (MW=500 kD) was used to measure cell uptake, while a plasmid carrying the gene coding for enhanced green fluorescence protein (eGFP) was used to quantitate the flow electrotransfection efficiency as determined by flow cytometry. The flow electroloading efficiency of FITC-dextran was >90%, while the cell viability was highly maintained (>90%). High flow electrotransfection efficiency (up to 75%) and cell viability (up to 90%) were obtained with processing volumes ranging from 1.5 to 50 mL. No significant difference of electrotransfection efficiency was observed between flow and static electrotransfection. When 50 mL of cell volume was processed and samples collected at different time points during electroporation, the transgene expression and cell viability results were identical. We also demonstrated that DNA plasmid containing EBNA1-OriP elements from Epstein-Barr virus were more efficient in transgene expression than standard plasmid without the elements (at least 500 too 1000-fold increase in expression level). Finally, to examine the feasibility of utilizing flow electrotransfected cells as a gene delivery vehicle, 10T1/2 cells were transfected with a DNA plasmid containing the gene coding for mIL12. mIL12 transfected cells were injected subcutaneously into mice, and produced functional mIL12, as demonstrated by anti-angiogenic activity. This is the first demonstration of efficient, large volume, flow electroporation and the in vivo efficacy of flow electrotransfected cells. This technology may be useful for clinical gene therapy and large-scale bioprocesses.

Participation of the melanocortin-1 receptor in the UV control of pigmentation

The cloning of the melanocortin-1 receptor (MC1R) gene from human melanocytes and the demonstration that these cells respond to the melanocortins alpha-melanocyte stimulating hormone (alpha-MSH) and adrenocorticotropic hormone (ACTH) with increased proliferation and melanogenesis have renewed the interest in investigation the physiological role of these hormones in regulating human pigmentation. Alpha-melanocyte stimulating hormone and ACTH are both synthesized in the human epidermis, and their synthesis is upregulated by exposure to ultraviolet radiation (UVR). Activation of the MC1R by ligand binding results in stimulation of cAMP formation, which is a principal mechanism for inducing melanogenesis. The increase in cAMP is required for the pigmentary response of human melanocytes to UVR, and for allowing them to overcome the UVR-induced G1 arrest. Treatment of human melanocytes with alpha-MSH increases eumelanin synthesis, an effect that is expected to enhance photoprotection of the skin. Population studies have revealed more than 20 allelic variants of the MC1R gene. Some of these variants are overexpressed in individuals with skin type I or II, red hair, and poor tanning ability. Future studies will aim at further exploration of the role of these variants in MC1R function, and in determining constitutive human pigmentation, the response to sun exposure, and possibly the susceptibility to skin cancer.