RecET driven chromosomal gene targeting to generate a RecA deficient Escherichia coli strain for Cre mediated production of minicircle DNA

Evaluation of DNA Vaccine Candidates against Foot-and-Mouth Disease Virus in Cattle

We evaluated four DNA vaccine candidates for their ability to produce virus-like particles (VLPs) and elicit a protective immune response against Foot-and-mouth disease virus (FMDV) in cattle. Two traditional DNA plasmids and two DNA minicircle constructs were evaluated. Both the pTarget O1P1-3C plasmid and O1P1-3C minicircle encoded a wild-type FMDV 3C protease to process the P1-2A polypeptide, whereas the O1P1-HIV-3C^T minicircle used an HIV-1 ribosomal frameshift to down-regulate expression of a mutant 3C protease. A modified pTarget plasmid with a reduced backbone size, mpTarget O1P1-3C^LT, used a 3C protease containing two mutations reported to enhance expression. All constructs produced mature FMDV P1 cleavage products in transfected cells, as seen by western blot analysis. Three constructs, O1P1-3C minicircles, pTarget O1P1-3C, and mpTarget O1P1-3C^LT plasmids, produced intracellular VLP crystalline arrays detected by electron microscopy. Despite VLP formation in vitro, none of the DNA vaccine candidates elicited protection from clinical disease when administered independently. Administration of pTarget O1P1-3C plasmid enhanced neutralizing antibody titers when used as a priming dose prior to administration of a conditionally licensed adenovirus-vectored FMD vaccine. Further work is needed to develop these DNA plasmid-based constructs into standalone FMD vaccines in cattle.

Construction and Evaluation of Recombinant Pseudorabies Virus Expressing African Swine Fever Virus Antigen Genes

African swine fever (ASF) is a highly contact infectious disease caused by the African swine fever virus (ASFV). The extremely complex structure and infection mechanism make it difficult to control the spread of ASFV and develop the vaccine. The ASFV genome is huge with many antigenic genes. Among them, CP204L (p30), CP530R (pp62), E183L (p54), B646L (p72), and EP402R (CD2v) are involved in the process of the virus cycle, with strong immunogenicity and the ability to induce the body to produce neutralizing antibodies. In this study, the recombinant virus rBartha-K61-pASFV that expresses the above ASFV antigen genes was constructed by Red/ET recombineering technology using pseudorabies virus (PRV) vaccine strain Bartha-K61. Western blot analysis showed that the ASFV antigen gene was expressed and the recombinant virus showed good genetic stability and proliferation characteristics in 15 continuous generations on porcine kidney (PK15) cells. The results of immunoassay of piglets and mice showed that rBartha-K61-pASFV had good immunogenicity and could induce higher antibody levels in the body. Therefore, PRV was a promising viral vector for expressing the ASFV antigen gene, and all the experiments in this study laid a foundation for the further development of a new viral vector vaccine of ASFV.

Transgenic DNA modules with pre-programmed self-destruction: Universal molecular devices to escape 'genetic litter' in gene and cell therapy

Gene delivery to human somatic cells is a well-established therapeutic strategy to treat a variety of diseases. In addition, gene transfer to human cells is required to generate human induced pluripotent cells and also to eliminate tumorigenic undifferentiated cells in many types of stem-cell derived transplantation material. The expression of transgenes in these medical technologies is often required only in some of the recipient cells and only in specific limited time-windows, with inappropriately located or untimely expressed transgenes presenting a risk of undesired collateral effects. Unfortunately, current gene transfer procedures commonly result in a number of cells in the patient's body containing fragments of transferred genetic material which are either not therapeutically necessary at all, are no longer necessary or are necessary but in some other cells. Such transgenic material in the patient, created as a by-product of the chosen therapeutic procedure, constitutes, in fact, 'genetic litter', that is, persisting potentially-hazardous foreign genetic material which is neither required therapeutically nor explicitly chosen by an informed and free-willing person as an artificial body element. Wider use and more frequent administration of gene and cell therapy in the future are likely to give greater prominence to the issue of misdelivered genetic medicines and of their unwanted remainders accumulating in human bodies. Thus, novel DNA templates, which, on the one hand, are capable of providing transgene expression over broad time-windows, and, on the other hand, do not leave unwanted permanent 'genetic traces', are required. I propose that the problem of 'genetic litter' in patients' bodies can be addressed through the employment of a new type of gene vectors delivering DNA-based transgenic modules with pre-programmed self-destruction. Such vectors could deliver therapeutic DNA cargo and then execute self-liquidation through pre-scheduled activation of co-delivered genome editing tools, such as CRISPR/Cas9 nucleases, specific for the DNA to be eliminated. In this model, all unnecessary transgenic DNA is edited away precisely at a desired time point. Activity of the gene correction apparatus for the specific and effective destruction of transgenic DNA could be turned on by well-timed external signals or could be triggered through intracellular sensors of particular epigenetic signatures. It is expected that the employment of the proposed DNA-based gene vectors equipped with a transgene self-destruct mechanism can extend the safe and ethical application of gene and cell therapy to a broader range of curative and lifestyle-choice medical treatments, e.g., full body prophylactic gene therapy of cancer.

Knock-in/Knock-out (KIKO) vectors for rapid integration of large DNA sequences, including whole metabolic pathways, onto the Escherichia coli chromosome at well-characterised loci

Background

Metabolic engineering projects often require integration of multiple genes in order to control the desired phenotype. However, this often requires iterative rounds of engineering because many current insertion approaches are limited by the size of the DNA that can be transferred onto the chromosome. Consequently, construction of highly engineered strains is very time-consuming. A lack of well-characterised insertion loci is also problematic.

Results

A series of knock-in/knock-out (KIKO) vectors was constructed for integration of large DNA sequences onto the E. coli chromosome at well-defined loci. The KIKO plasmids target three nonessential genes/operons as insertion sites: arsB (an arsenite transporter); lacZ (β-galactosidase); and rbsA-rbsR (a ribose metabolism operon). Two homologous ‘arms’ target each insertion locus; insertion is mediated by λ Red recombinase through these arms. Between the arms is a multiple cloning site for the introduction of exogenous sequences and an antibiotic resistance marker (either chloramphenicol or kanamycin) for selection of positive recombinants. The resistance marker can subsequently be removed by flippase-mediated recombination. The insertion cassette is flanked by hairpin loops to isolate it from the effects of external transcription at the integration locus. To characterize each target locus, a xylanase reporter gene (xynA) was integrated onto the chromosomes of E. coli strains W and K-12 using the KIKO vectors. Expression levels varied between loci, with the arsB locus consistently showing the highest level of expression. To demonstrate the simultaneous use of all three loci in one strain, xynA, green fluorescent protein (gfp) and a sucrose catabolic operon (cscAKB) were introduced into lacZ, arsB and rbsAR respectively, and shown to be functional.

Conclusions

The KIKO plasmids are a useful tool for efficient integration of large DNA fragments (including multiple genes and pathways) into E. coli. Chromosomal insertion provides stable expression without the need for continuous antibiotic selection. Three non-essential loci have been characterised as insertion loci; combinatorial insertion at all three loci can be performed in one strain. The largest insertion at a single site described here was 5.4 kb; we have used this method in other studies to insert a total of 7.3 kb at one locus and 11.3 kb across two loci. These vectors are particularly useful for integration of multigene cassettes for metabolic engineering applications.

Mc-hES, a novel plasmid carrying human endostatin gene, inhibits nasopharyngeal carcinoma growth

Conventional plasmids for gene therapy produce low-level and short-term gene expression. Here, we first created minicircle carrying endostatin (mc-hES) for measurement of transfection efficiency. Compared with pcDNA-hES, MC-mediated endostatin gene transfer in vitro resulted in seven-fold greater endostatin expression levels in transfected cells and inhibited the growth of Human umbilical vein endothelial cells (HUVEC) more efficiently. HUVEC cell migration and tube-formation assays suggested that MC-mediated endostatin gene has significant anti-migration and anti-tube-formation capacity than that in pcDNA-hES. In vivo experiments showed that after transfection, mc-hES inhibited the growth of nasopharyngeal carcinoma xenografts. The tumor inhibition rates of mc-hES and pcDNA-hES were 60.8% and 26.9%, respectively (P<0.05). MC-mediated intratumoral endostatin expression in vivo was 2.2-17.9 times higher than pcDNA-hES in xenografted mice and lasted for 20 days. Our results suggest that minicircle DNA vectors might be a promising vector for biotherapy and should be further investigated.

Designing plasmid vectors

Nonviral gene therapy vectors are commonly based on recombinant bacterial plasmids or their derivatives. The plasmids are propagated in bacteria, so, in addition to their therapeutic cargo, they necessarily contain a bacterial replication origin and a selection marker, usually a gene conferring antibiotic resistance. Structural and maintenance plasmid stability in bacteria is required for the plasmid DNA production and can be achieved by carefully choosing a combination of the therapeutic DNA sequences, replication origin, selection marker, and bacterial strain. The use of appropriate promoters, other regulatory elements, and mammalian maintenance devices ensures that the therapeutic gene or genes are adequately expressed in target human cells. Optimal immune response to the plasmid vectors can be modulated via inclusion or exclusion of DNA sequences containing immunostimulatory CpG sequence motifs. DNA fragments facilitating construction of plasmid vectors should also be considered for inclusion in the design of plasmid vectors. Techniques relying on site-specific or homologous recombination are preferred for construction of large plasmids (>15 kb), while digestion of DNA by restriction enzymes with subsequent ligation of the resulting DNA fragments continues to be the mainstream approach for generation of small- and medium-size plasmids. Rapid selection of a desired recombinant plasmid against a background of other plasmids continues to be a challenge. In this chapter, the emphasis is placed on efficient and flexible versions of DNA cloning protocols using selection of recombinant plasmids by restriction endonucleases directly in the ligation mixture.

Gene doping: the hype and the reality

Some spectacular results from genetic manipulation of laboratory rodents and increasing developments in human gene therapy raise the spectre of genetic modification or 'gene doping' in sports. Candidate targets include the induction of muscle hypertrophy through overexpression of specific splice variants of insulin-like growth factor-1 or blockade of the action of myostatin, increasing oxygen delivery by raising the hematocrit through the use of erythropoietin, induction of angiogenesis with vascular endothelial growth factors or related molecules and changes in muscle phenotype through expression of peroxisome-proliferator-activated receptor- delta and associated molecules. Some of these potential genetic enhancements, particularly where the genetic modification and its action are confined to the muscles, may be undetectable using current tests. This had lead to exaggerated predictions that gene doping in athletics will be common within the next few years. However, a review of the methods of gene transfer and the current 'state of the art' in development of genetic treatments for human disease show that the prospects for gene doping remain essentially theoretical at present. Despite this conclusion, it will be important to continue to monitor improvements in the technology and to develop methods of detection, particularly those based on identifying patterns of changes in response to doping as opposed to the detection of specific agents.

Design of PCR-amplified DNA fragments for in vivo gene delivery: size-dependency on stability and transgene expression

PCR-amplified DNA fragments can be more efficient and safer vectors than conventional plasmid DNA because of their smaller size and fewer numbers of immunostimulatory cytosine-phosphate-guanine (CpG) motifs. In the present study, the expression unit of plasmid DNA encoding farnesylated enhanced green fluorescent protein (EGFPF; pEGFP-F) or firefly luciferase (pLuc) was amplified by polymerase chain reaction (PCR) to obtain DNA fragments (EGFPF-mini, Luc-mini). EGFPF-mini was as effective as pEGFP-F on the basis of the number of EGFPF-expressing cells after intravenous injection into mice by the hydrodynamics-based procedure. Then, the effects of the length of DNA fragments on transgene expression were examined using luciferase-expressing DNA preparations. Luc-mini preparations showed high levels of luciferase activity in cultured cells as well as in mouse liver, even although the levels did not exceed that of pLuc. An elongation of the DNA fragment on either side of the minimal expression unit was effective in increasing the transgene expression and the stability against nucleases. PCR-amplified DNA fragments showed a sustained luciferase activity in mouse liver compared with pLuc, indicating that they are effective in achieving a prolonged expression. Their stabilization against nucleases will further increase the potential of such short, structure-controlled and synthetic DNA fragments for in vivo gene delivery.