DNA-mediated Gene Transfer Research Articles

Both Conifer II and Gnetales are characterized by a high frequency of ancient mitochondrial gene transfer to the nuclear genome

BackgroundMitochondrial gene transfer/loss is common in land plants, and therefore the fate of missing mitochondrial genes has attracted more and more attention. The gene content of gymnosperm mitochondria varies greatly, supplying a system for studying the evolutionary fate of missing mitochondrial genes.ResultsHere, we studied the tempo and pattern of mitochondrial gene transfer/loss in gymnosperms represented by all 13 families, using high-throughput sequencing of both DNA and cDNA. All 41 mitochondrial protein-coding genes were found in cycads, Ginkgo and Pinaceae, whereas multiple mitochondrial genes were absent in Conifer II and Gnetales. In Conifer II, gene transfer from mitochondria to the nucleus followed by loss of the mitochondrial copy was common, but complete loss of a gene in both mitochondrial and nuclear genomes was rare. In contrast, both gene transfer and loss were commonly found in Gnetales. Notably, in Conifer II and Gnetales, the same five mitochondrial genes were transferred to the nuclear genome, and these gene transfer events occurred, respectively, in ancestors of the two lineages. A two-step transfer mechanism (retroprocessing and subsequent DNA-mediated gene transfer) may be responsible for mitochondrial gene transfer in Conifer II and Gnetales. Moreover, the mitochondrial gene content variation is correlated with gene length, GC content, hydrophobicity, and nucleotide substitution rates in land plants.ConclusionsThis study reveals a complete evolutionary scenario for variations of mitochondrial gene transferring in gymnosperms, and the factors responsible for mitochondrial gene content variation in land plants.

Anti-OspA DNA-Encoded Monoclonal Antibody Prevents Transmission of Spirochetes in Tick Challenge Providing Sterilizing Immunity in Mice

We recently developed anti-OspA human immunoglobulin G1 monoclonal antibodies (HuMAbs) that are effective in preventing Borrelia transmission from ticks in a murine model. Here, we investigated a novel approach of DNA-mediated gene transfer of HuMAbs that provide protection against Lyme disease. Plasmid DNA-encoded anti-OspA HuMAbs inoculated in mice achieved a serum antibody concentration of >6 μg/mL. Among mice injected with DNA-encoded monoclonal antibodies, 75%-77% were protected against an acute challenge by Borrelia-infected ticks. Our results represent the first demonstration of employing DNA transfer as a delivery system for antibodies that block transmission of Borrelia in animal models.

Horizontal Gene Transfer in Five Parasite Plant Species in Orobanchaceae.

We sequenced genomes of five parasite species in family Orobanchaceae to explore the evolutionary role of horizontal gene transfer in plants. Orobanche minor and Aeginetia indica are obligate parasites with no photosynthetic activity, whereas the other three (Pedicularis keiskei, Phtheirospermum japonicum, and Melampyrum roseum) are facultative parasites. By using reference genome sequences and/or transcriptomes of 14 species from Fabaceae and Poaceae, their major host families, we detected 106 horizontally transferred genes (HGT genes), only in the genomes of the two obligate parasites (22 and 84 for Oro. minor and Ae. indica, respectively), whereas none in the three facultative parasites. The HGT genes, respectively, account for roughly 0.1% and 0.2% of the coding genes in the two species. We found that almost all HGT genes retained introns at the same locations as their homologs in potential host species, indicating a crucial role of DNA-mediated gene transfer, rather than mRNA mediated retro transfer. Furthermore, some of the HGT genes might have transferred simultaneously because they located very closely in the host reference genome, indicating that the length of transferred DNA could exceed 100 kb. We confirmed that almost all introns are spliced in the current genome of the parasite species, and that about half HGT genes do not have any missense mutations or frameshift-causing indels, suggesting that some HGT genes may be still functional. Evolutionary analyses revealed that the nonsynonymous–synonymous substitution ratio is on average elevated on the lineage leading to HGT genes, due to either relaxation of selection or positive selection.

Autophagy Induced by Calcium Phosphate Precipitates Targets Damaged Endosomes

Calcium phosphate precipitates (CPPs) form complexes with DNA, which enter cells via endocytosis. Under this condition CPPs induce autophagy via the canonic autophagy machinery. Here we showed that CPP-induced autophagy was also dependent on endocytosis as the process was significantly inhibited by methyl-β-cyclodextrin and dynasore, which suppress clathrin-dependent endocytosis. Consistently, CPP treatment triggered the formation of filipin-positive intracellular vesicles whose membranes are rich in cholesterol. Unexpectedly, these vesicles were also positive for galectin 3, suggesting that they were damaged and the membrane glycans became accessible to galectins to bind. Endosome damage was caused by endocytosis of CPPs and was reversed by calcium chelators or by endocytosis inhibitors. Notably, CPP-induced LC3-positive autophagosomes were colocalized with galectin 3, ubiquitin, and p62/SQSTM1. Inhibition of galectin 3 reduced p62 puncta and autophagosome formation. Knockdown of p62 additionally inhibited the colocalization of autophagosomes with galectins. Furthermore, most of the galectin 3-positive vesicles were colocalized with Rab7 or LAMP1. Agents that affect endosome/lysosome maturation and function, such as bafilomycin A1, also significantly affected CPP-induced tubulovesicular autophagosome formation. These findings thus indicate that endocytosed CPPs caused endosome damage and recruitment of galectins, particularly at the later endosome stage, which led to the interaction of the autophagosomal membranes with the damaged endosome in the presence of p62.

Development of a Liver-specific Tet-On Inducible System for AAV Vectors and Its Application in the Treatment of Liver Cancer

Recombinant adeno-associated virus (rAAV) are effective gene delivery vehicles that can mediate long-lasting transgene expression. However, tight regulation and tissue-specific transgene expression is required for certain therapeutic applications. For regulatable expression from the liver we designed a hepatospecific bidirectional and autoregulatory tetracycline (Tet)-On system (Tet(bidir)Alb) flanked by AAV inverted terminal repeats (ITRs). We characterized the inducible hepatospecific system in comparison with an inducible ubiquitous expression system (Tet(bidir)CMV) using luciferase (luc). Although the ubiquitous system led to luc expression throughout the mouse, luc expression derived from the hepatospecific system was restricted to the liver. Interestingly, the induction rate of the Tet(bidir)Alb was significantly higher than that of Tet(bidir)CMV, whereas leakage of Tet(bidir)Alb was significantly lower. To evaluate the therapeutic potential of this vector, an AAV-Tet(bidir)-Alb-expressing interleukin-12 (IL-12) was tested in a murine model for hepatic colorectal metastasis. The vector induced dose-dependent levels of IL-12 and interferon-γ (IFN-γ), showing no significant toxicity. AAV-Tet(bidir)-Alb-IL-12 was highly efficient in preventing establishment of metastasis in the liver and induced an efficient T-cell memory response to tumor cells. Thus, we have demonstrated persistent, and inducible in vivo expression of a gene from a liver-specific Tet-On inducible construct delivered via an AAV vector and proved to be an efficient tool for treating liver cancer.

Various carrier system(s)- mediated genetic vaccination strategies against malaria - Retracted

The introduction of vaccine technology has facilitated an unprecedented multiantigen approach to develop an effective vaccine against complex pathogens, such as Plasmodium spp., that cause severe malaria. The capacity of multisubunit DNA vaccines encoding different stage Plasmodium antigens to induce CD8(+) cytotoxic T lymphocytes and IFN-gamma responses in mice, monkeys and humans has been observed. Moreover, genetic vaccination may be multi-immune (i.e., capable of eliciting more than one type of immune response, including cell-mediated and humoral). In the case of malaria parasites, a cytotoxic T-lymphocyte response is categorically needed against the intracellular hepatocyte stage while a humoral response, with antibodies targeted against antigens from all stages of the life cycle, is also needed. Therefore, the key to success for any DNA-based therapy is to design a vector able to serve as a safe and efficient delivery system. This has encouraged the development of nonviral DNA-mediated gene-transfer techniques, such as liposomes, virosomes, microspheres and nanoparticles. Efficient and relatively safe DNA transfection using lipoplexes makes them an appealing alternative to be explored for gene delivery. In addition, liposome-entrapped DNA has been shown to enhance the potency of DNA vaccines, possibly by facilitating uptake of the plasmid by antigen-presenting cells. Another recent technology using cationic lipids has been deployed and has generated substantial interest in this approach to gene transfer. This review comprises various aspects that could be decisive in the formulation of efficient and stable carrier system(s) for the development of malaria vaccines.

Preferential delivery of the Sleeping Beauty transposon system to livers of mice by hydrodynamic injection.

Nonviral, DNA-mediated gene transfer is an alternative to viral delivery systems for expressing new genes in cells and tissues. The Sleeping Beauty (SB) transposon system combines the advantages of viruses and naked DNA molecules for gene therapy purposes; however, efficacious delivery of DNA molecules to animal tissues can still be problematic. Here we describe the hydrodynamic delivery procedure for the SB transposon system that allows efficient delivery to the liver in the mouse. The procedure involves rapid, high-pressure injection of a DNA solution into the tail vein. The overall procedure takes <1 h although the delivery into one mouse requires only a few seconds. Successful injections result in expression of the transgene in 5-40% of hepatocytes 1 d after injection. Several weeks after injection, transgene expression stabilizes at approximately 1% of the level at 24 h, presumably owing to integration of the transposons into chromosomes.

Experimental Reconstruction of Functional Gene Transfer from the Tobacco Plastid Genome to the Nucleus

Eukaryotic cells arose through the uptake of free-living bacteria by endosymbiosis and their gradual conversion into organelles (plastids and mitochondria). Capture of the endosymbionts was followed by massive translocation of their genes to the genome of the host cell. How genes were transferred from the (prokaryotic) organellar genome to the (eukaryotic) nuclear genome and how the genes became functional in their new eukaryotic genetic environment is largely unknown. Here, we report the successful experimental reconstruction of functional gene transfer between an organelle and the nucleus, a process that normally occurs only on large evolutionary timescales. In consecutive genetic screens, we first transferred a chloroplast genome segment to the nucleus and then selected for gene activation in the nuclear genome. We show that DNA-mediated gene transfer can give rise to functional nuclear genes if followed by suitable rearrangements in the nuclear genome. Acquisition of gene function involves (1) transcriptional activation by capture of the promoter of an upstream nuclear gene and (2) utilization of AT-rich noncoding sequences downstream of the plastid gene as RNA cleavage and polyadenylation sites. Our results reveal the molecular mechanisms of how organellar DNA transferred to the nucleus gives rise to functional genes and reproduce in the laboratory a key process in the evolution of eukaryotic cells.

Sleeping Beauty-Mediated Transposition and Long-Term Expression in Vivo: Use of the LoxP/Cre Recombinase System to Distinguish Transposition-Specific Expression

The Sleeping Beauty transposon system (SB) has been shown to mediate nonviral integration of expression constructs resulting in long-term gene expression in several mammalian targets. Often, however, it is difficult to discern long-term expression resulting from transposition vs nonhomologous chromosomal recombination or maintenance of plasmid DNA in an extrachromosomal form. We have designed a system to silence expression from nontransposed sequences, making it possible to determine more specifically the amount of expression resulting from transposition. A transposon plasmid, pT2F/Cage (carrying a murine erythropoietin (Epo) gene transcriptionally regulated by the ubiquitously expressed CAGS promoter), was engineered to contain LoxP sites positioned so as to interrupt expression upon Cre-mediated recombination. Upon transposition these sites become segregated, thus protecting the expression construct from Cre-mediated recombination and subsequent silencing. Interferon-inducible Mx1Cre mice were administered pT2F/Cage with or without transposase-encoding plasmid. At 2 to 4 weeks postinjection, in the absence of SB transposase, Cre induction reduced Epo expression to about 1% of that seen in the group that was administered transposase-encoding plasmid, which maintained Epo levels near those of the uninduced groups. Southern hybridization analysis and plasmid rescue of transfected tissue supported the efficient Cre-mediated silencing of nontransposed sequences. These results indicate a substantial level of DNA-mediated expression not associated with transposition, but which can be quantitatively distinguished from transposition by its sensitivity to Cre recombinase. The results also provide additional evidence for the effectiveness of the Sleeping Beauty transposon system as an in vivo DNA-mediated gene transfer strategy for achieving long-term expression.

Expression of foreign genes in chicks by hydrodynamics-based naked plasmid transfer in vivo

The study of gene function in vivo is considered one of the top achievements of modern biology, inasmuch as it provides tools to study gene function in the context of the whole animal. In chickens, techniques of DNA-mediated gene transfer are less advanced than in other animal or livestock models, and remain a significant challenge. The study presented here is the first to show that a hydrodynamics-based gene-transfer technique, originally developed for naked DNA transfer in mice, can be applied to chickens. Rapid injection of naked plasmids containing expression cassettes into the jugular vein of 6- to 10-day-old chicks resulted in specific expression of the transgenes. A CMV promoter-driven luciferase reporter gene was expressed at significant levels in the liver during the first 3 days post-injection with lower levels also detected in the kidney. Significantly, all injected birds showed detectable levels of luciferase expression. Similarly, injection of a plasmid containing the secreted human coagulation factor IX (hFIX) gene under the control of human alpha-1-anti-trypsin promoter resulted in detectable levels of the hFIX in the plasma during the first 2 days post-injection. The method described herein has the potential for a quick and simple route for gain and loss-of function experiments in chicken liver and kidney, as well as for studying systemic effects of secreted proteins and hormones.

851. Development of Brain Tumor Organ Cultures for Characterizing Polymer/Plasmid DNA Mediated Gene Transfer

Development of effective gene therapy requires an expeditious and reproducible test system. The syngenic RG2 rat brain tumor model satisfies the criteria for a clinically relevant animal model. Pluronic block copolymer L44 was formulated with a green fluorescent protein (GFP) expression plasmid, and sterotacticly injected into rat brain tumors. GFP positive cells were observed in the tumor. Yet, the numbers of transfected cells were insufficient for a therapeutic effect. Hence, the formulation requires other components to increase gene transfer efficiency. The turn around time for obtaining results from this animal model was not amendable to screening formulations for tumor gene transfer. Cell culture using rat glioma cell lines has proven to be advantageous in screening gene transfer vectors. Conversely, due to the two-dimensional single cell layer and volume of growth media necessary for tissue culture, it is not applicable for evaluating local administration of plasmid DNA. For this reason, an organ culture was developed to optimize screening. Rat brains tumors were sliced into 300-micron sections and cultured for 7days. Tumors were observed to grow over the 7-day period ultimately taking over the brain slice. Local injection of Poloxamer formulated GFP expression plasmid was shown to transfect tumor cells in the organ culture model. Presently, the brain organ cultures are being characterized for expression of normal and brain tumor cell markers. Comparison of staining patterns for biomarkers in the organ culture and in vivo brain tumors are being used to validate the organ culture. Concomitantly, formulation conditions are being tested to optimize gene transfer to the brain tumor.

DNA-mediated gene transfer.

DNA-mediated gene transfer.

Controlled plasmid gene transfer to murine renal carcinoma by hexadecylphosphocholine

We report here that the anticancer drug hexadecylphosphocholine (HPC) can control plasmid DNA-mediated gene transfer to renal carcinoma following intratumoral administration. Significant improvement of gene expression levels could be achieved depending on HPC dose administered. Optimal concentration of HPC co-injected with plasmid DNA was found to be 0.2% (w/v) showing up to a 10-fold increase in reporter gene expression levels when compared to DNA administered alone. In vivo gene transfer activity of HPC was not affected by the nature of the diluent used, i.e. glucose-based or saline-based isotonic solutions. Although in vitro transfection activity of HPC formulations could not be evidenced, a liposome leakage assay revealed that HPC could significantly destabilize stable lipid membranes suggesting that a possible membrane permeation enhancer activity of HPC combined to the physical stress induced by the intratumor injection may facilitate plasmid DNA entry inside the cells resulting in increased gene expression. HPC/plasmid formulations represent new and attractive non-viral gene delivery systems with potential in cancer gene therapy and vaccination.

Gene insertion and long-term expression in lung mediated by the sleeping beauty transposon system

Gene transfer to the lung could provide important new treatments for chronic and acquired lung diseases such as cystic fibrosis, α1-antitrypsin deficiency, emphysema, and cancer. DNA-mediated gene transfer to the lung has been previously demonstrated, but anticipated effectiveness has been limited by low gene transfer efficiencies and by transient expression of the transgene. Here, we combine plasmid-based gene transfer with the integrating capacity of the nonviral Sleeping Beauty (SB) transposon vector system to mediate gene insertion and long-term gene expression in mouse lung. We observed transgene expression after 24 h in lungs of all animals injected with the luciferase transposon (pT/L), but expression for up to 3 months required codelivery of a plasmid encoding the Sleeping Beauty transposase. We also observed long-term expression in pT/L-injected animals transgenic for SB transposase. Transgene expression was localized to the alveolar region of the lung, with transfection including mainly type II pneumocytes. We used a linker-mediated PCR technique to recover transposon flanking sequences, demonstrating transposition of pT/L into mouse chromosomal DNA of the lung.

981. Naked DNA-Mediated Insulin Gene Transfer to the Liver. Inclusion of a Long Genomic Sequence Prolongs Insulin Expression

981. Naked DNA-Mediated Insulin Gene Transfer to the Liver. Inclusion of a Long Genomic Sequence Prolongs Insulin Expression

Production of retroviral vectors in primary human keratinocytes after DNA-mediated gene transfer leads to prolonged gene expression.

Prolonged stability and controlled expression of gene constructs transferred directly to human skin improve the possibility of using this tissue in somatic gene therapy. We aim to develop a simple transfection method resulting in retroviral mediated gene transfer to keratinocyte stem cells in situ. We here show that after DNA-mediated gene transfer into primary human keratinocytes it is possible to achieve production of retroviral vectors, leading to the transduction of co-cultured keratinocytes and prolonged reporter gene expression. The method is a first step in a strategy to generate retroviral producer cells in situ in the skin furthermore the method can be used for rapid analysis of the possible effects of transgenes in cultured human keratinocytes without preparatory retroviral vector production in packaging cell lines.

Efficient non-viral DNA-mediated gene transfer to human primary myoblasts using electroporation

Gene transfer of human primary myoblasts with various non-viral methods has been hampered by low yield of transfection. We report here an efficient, simple and reproducible non-viral DNA-mediated gene transfer procedure for transfecting human myoblasts. We found that electroporation promotes a highly efficient DNA uptake by human primary cultures of myogenic cells. Under optimal conditions, 60-70% of human myoblasts transfected with the enhanced green fluorescent gene expressed the enhanced green fluorescent protein. Electroporated myoblasts behaved normally as judged by their ability to synthesize and express developmentally regulated proteins and to undergo terminal differentiation, i.e. to fuse and form myotubes. We showed, in addition, that a subpopulation of cultured human myoblasts with self-renewing properties and equivalent to native muscle satellite cells were as efficiently transfected by electroporation as proliferating myoblasts. Thus, the development of gene therapies based on the engineering and transplantation of human myoblasts may greatly benefit from gene transfer by electroporation.

Efficient site-directed dna integration into es and hematopoietic cells

DNA mediated gene transfer to hematopoietic cells has been hindered by low gene transfer efficiency. In an attempt to achieve efficient, stable integration of potentially large DNA vectors at a site which confers expression in a defined and a predictable manner, we are exploiting a Cre/lox based recombination strategy. As an initial test in hematopoietic cells, murine BaF3 cells were used to introduce a hygromycin resistant gene flanked by 34 bp lox sites (floxed) using a retrovirus. Subsequently, co-electroporation of a floxed green flourescent protein (GFP) construct and the cre recombinase plasmid should mediate integration through the lox sites replacing hygromycin with GFP. Site directed, stable integration as confirmed by FACS and Southern blot analysis occurred at a high frequency ranging from 1–7% in 5 different BaF3 clones, or some 100 fold higher than the efficiency for a control GFP vector lacking lox sites. To assess if the expression characteristics of an initial integration site can be reutilized to express a transgene in a defined and predictable manner, floxed GFP expressing BaF3 clones were chosen that had clonally distinct levels of GFP expression that spanned over 300 fold. This differential expression was maintained following cre mediated replacement with a floxed cDNA human Thy-1 construct. Analogous findings were also obtained in the human K562 cell line. As an initial effort to extend this approach to primitive primary cells, we introduced lox sites into murine embryonic stem cells (ES) cells either by a retrovirus or by a plasmid. Subsequent cre mediated integration again occurred with high efficiency—up to 22% and clones retained in vitro differentiation capacity and germline competency. Site directed DNA integration should provide a powerful new approach for studying gene function and regulatory mechanisms in hematopoietic cells.

Dependence of Elevated Human Leukocyte Antigen Class I Molecule Expression on Increased Heavy Chain, Light Chain (β2-Microglobulin), Transporter Associated with Antigen Processing, Tapasin, and Peptide

Human leukocyte antigen (HLA) class I molecule expression was investigated by DNA-mediated gene transfer. Cell surface expression was increased up to 75% by transfection of HLA-A2 or HLA-B8 heavy chain genes but not genes encoding light chains (beta(2)-microglobulin (beta(2)m)), transporter associated with antigen processing (TAP), or tapasin. Interferon (IFN) treatment further increased expression of transfected heavy chains, suggesting that IFN inducible molecules support heavy chain expression. IFN induces beta(2)m, TAP, and tapasin mRNAs. Transfected heavy chain expression increased upon cotransfection with genes encoding TAP1 and TAP2 but not individual TAP subunits, beta(2)m, or tapasin. Tetracycline inducible heavy chain gene expression was also increased by IFN treatment or TAP cotransfection, suggesting that IFN-induced TAP supports heavy chain maturation. Expression of a mutant that does not interact strongly with TAP, HLA-A2-T134K, was also increased by IFN. Inhibition of TAP-dependent peptide transport by ICP47 reduced heavy chain expression. Expression of HLA-A2, but not HLA-B8, was restored in ICP47 cells by HLA-A2-binding (IP-30) signal peptides. However, these peptides did not further increase transfected HLA-A2 expression, suggesting that peptide availability does not limit heavy chain expression in the absence of ICP47. These results suggest that cytokine-induced TAP supports maturation of HLA class I molecules through combined chaperone and peptide supply functions.

In vivo gene delivery to the lung using polyethylenimine and fractured polyamidoamine dendrimers

Gene transfer into the airways could be of importance for the treatment of chronic lung diseases such as cystic fibrosis. In the past few years several attempts have been made to effectively deliver DNA to the lung using different viral and non-viral vector systems. Viral vectors and cationic lipids have been tested intensively but the properties of cationic polymers such as polyethylenimine (PEI) 25 kDa and fractured polyamidoamine dendrimers to deliver DNA to the airways have not been studied. Surfactant preparations have been shown to influence pulmonary adenoviral and naked plasmid DNA mediated gene transfer in vivo. We investigated the gene delivery efficiency of branched PEI 25 kDa and fractured dendrimers to the murine lung in vivo and also examined the effect of surfactant on PEI 25 kDa mediated gene transfer to the lung. Cationic polymer/DNA complexes were prepared in 25 mM HEPES buffer (pH = 7.4) or double distilled water and administered to the lungs of BALB/c mice via cannula intubation. The trachea, left and right lung, heart, liver and esophagus were examined for luciferase activity. Inflammation was assessed by performing standard histology. PEI/DNA complexes showed a high level of luciferase gene expression in the lung. Complexes formed in double distilled water exhibited higher gene expression than complexes formed in 25 mM HEPES buffer (pH 7.4). The optimal N/P ratio was found to be N/P = 10 in double distilled water. Luciferase activity was only detected in the lung and decreased rapidly in a time-dependent manner. The addition of a natural surfactant preparation, Alveofact, slightly reduced gene transfer of branched PEI 25 kDa. Luciferase gene expression obtained by using fractured dendrimers was very low. The present study demonstrates that PEI 25 kDa, but not polyamidoamine dendrimers, effectively mediates transient gene transfer to the murine lung after intratracheal intubation. In conclusion, branched PEI 25 kDa was found to be an effective vector for pulmonary gene delivery in vivo, being superior to fractured dendrimers.