The effects of plasmid copy number and sequence context upon transfection efficiency

Self-documenting plasmids

Plasmids are the workhorse of biotechnology. These small DNA molecules are used to produce recombinant proteins and to engineer living organisms. They can be regarded as the blueprints of many biotechnology products. Therefore, it is critical to ensure that the sequences of these DNA molecules match their intended designs. Yet, plasmid verification remains challenging. To secure the exchange of plasmids in research and development workflows, we have developed self-documenting plasmids that encode information about themselves in their own DNA molecules. Users of self-documenting plasmids can retrieve critical information about the plasmid without prior knowledge of the plasmid identity. The insertion of documentation in the plasmid sequence does not preclude their propagation in bacteria or functional fluorescent protein expression in mammalian cells. This technology simplifies plasmid verification, hardens supply chains, and has the potential to transform the protection of intellectual property (IP) in the life sciences.

Self-Documenting Plasmids

Plasmids are the workhorse of biotechnology. These small DNA molecules are used to produce recombinant proteins and to engineer living organisms. They can be regarded as the blueprints of many biotechnology products. It is, therefore, critical to ensure that the sequences of these DNA molecules match their intended designs. Yet, plasmid verification remains challenging. To secure the exchange of plasmids in research and development workflows, we have developed self-documenting plasmids that encode information about themselves in their own DNA molecules. Users of self-documenting plasmids can retrieve critical information about the plasmid without prior knowledge of the plasmid identity. The insertion of documentation in the plasmid sequence does not adversely affect their propagation in bacteria and does not compromise protein expression in mammalian cells. This technology simplifies plasmid verification, hardens supply chains, and has the potential to transform the protection of intellectual property in the life sciences.

Enhanced Proliferation of Endothelial Progenitor Cells Post-Ultrasonic Microbubble Transfection Is Plasmid DNA Size Dependent and Contributed by Interleukin-6 Generation

We investigated whether ultrasonic microbubble transfection (UMT) would enhance the transfection of large-sized luciferase plasmids (5.6, 9.2 and 33 kb) and biological impacts. Porcine venous blood endothelial progenitor cells (EPCs) were cultured in a medium containing plasmid DNA (pDNA) of different sizes followed by UMT and functional assays. Real-time polymerase chain reaction was conducted to investigate the effects of transfection of pDNA on multiple molecules central to endothelial function. The results indicated enhanced luciferase expression after UMT but the enhancement declined with increase in the size of the plasmid. UMT of pDNAs sized 5.6 and 9.2 kb into EPCs led to significant enhancement of proliferation. The interleukin-6 (IL-6) secreted from UMT of EPCs also increased in the 5.6- and 9.2-kb pDNA groups. Treatment of the transfected EPCs with anti-IL-6 antibody neutralized the proliferation. In conclusion, UMT of pDNAs sized 5.6 and 9.2 kb into EPCs increased the secretion of IL-6, which in turn enhanced cell proliferation.

Toward Contactless Biology: Acoustophoretic DNA Transfection

Acoustophoresis revolutionized the field of container-less manipulation of liquids and solids by enabling mixing procedures which avoid contamination and loss of reagents due to the contact with the support. While its applications to chemistry and engineering are straightforward, additional developments are needed to obtain reliable biological protocols in a contactless environment. Here, we provide a first, fundamental step towards biological reactions in air by demonstrating the acoustophoretic DNA transfection of mammalian cells. We developed an original acoustophoretic design capable of levitating, moving and mixing biological suspensions of living mammalians cells and of DNA plasmids. The precise and sequential delivery of the mixed solutions into tissue culture plates is actuated by a novel mechanism based on the controlled actuation of the acoustophoretic force. The viability of the contactless procedure is tested using a cellular model sensitive to small perturbation of neuronal differentiation pathways. Additionally, the efficiency of the transfection procedure is compared to standard, container-based methods for both single and double DNA transfection and for different cell types including adherent growing HeLa cancer cells, and low adhesion neuron-like PC12 cells. In all, this work provides a proof of principle which paves the way to the development of high-throughput acoustophoretic biological reactors.

Delivery of an adenovirus vector plasmid by ultrapure oligochitosan based polyplexes

Ultrapure oligochitosans have been recently reported as efficient non-viral vectors for the delivery of pCMS-EGFP plasmid (5.5kbp) to the cornea and retina. However, the delivery of oncolytic adenoviral plasmids (40kbp) represents a unique challenge. In this work, we elaborated self assembled O15 and O25 UOC/pAdTLRGD polyplexes, and we studied the influence of the N/P ratio, the pH of the transfection medium and the salt concentration on the particle size and zeta potential by an orthogonal experimental design. All polyplexes showed a particle size lower than 200nm and a positive zeta potential. These parameters were influenced by the N/P ratio, salt concentration, and pH of the transfection medium. The selected polyplexes were able to bind, release, and protect the plasmid from DNase degradation. Transfection experiments in HEK293 and A549 cell lines demonstrated that UOC/pAdTLRGD polyplexes were able to deliver the plasmid and transfect both cell lines. These results suggest that O15 and O25 UOC based polyplexes are suitable for future in vivo applications.

Advances in host and vector development for the production of plasmid DNA vaccines

Recent developments in DNA vaccine research provide a new momentum for this rather young and potentially disruptive technology. Gene-based vaccines are capable of eliciting protective immunity in humans to persistent intracellular pathogens, such as HIV, malaria, and tuberculosis, for which the conventional vaccine technologies have failed so far. The recent identification and characterization of genes coding for tumor antigens has stimulated the development of DNA-based antigen-specific cancer vaccines. Although most academic researchers consider the production of reasonable amounts of plasmid DNA (pDNA) for immunological studies relatively easy to solve, problems often arise during this first phase of production. In this chapter we review the current state of the art of pDNA production at small (shake flasks) and mid-scales (lab-scale bioreactor fermentations) and address new trends in vector design and strain engineering. We will guide the reader through the different stages of process design starting from choosing the most appropriate plasmid backbone, choosing the right Escherichia coli (E. coli) strain for production, and cultivation media and scale-up issues. In addition, we will address some points concerning the safety and potency of the produced plasmids, with special focus on producing antibiotic resistance-free plasmids. The main goal of this chapter is to make immunologists aware of the fact that production of the pDNA vaccine has to be performed with as much as attention and care as the rest of their research.

Magnetically guided lentiviral-mediated transduction of airway epithelial cells

BACKGROUND

Lentiviral (LV) vectors are able to only slowly and inefficiently transduce nondividing cells such as those of the airway epithelium. To address this issue, we have exploited the magnetofection technique in in vitro models of airway epithelium.

METHODS

Magnetofectins were formed by noncovalent interaction between LV particles and polycation-coated iron oxide nanoparticles. Efficiency of LV-mediated transduction (as evaluated through green fluorescent protein (GFP) expression by cytofluorimetric analysis) was measured in bronchial epithelial cells in the presence or absence of a magnetic field. Cytotoxicity was evaluated by lactate dehydrogenase (LDH) release; cell monolayer integrity by measurement of transepithelial resistance (TER) and evaluation of correct zonula occludens-1 (ZO-1) localization at tight junctions (TJs) by immunofluorescence and confocal microscopy.

RESULTS

In nonpolarized cells, magnetofectins enhanced LV-mediated transduction at multiplicity of infection (MOI) of 50 up to 3.9-fold upon a 24-h incubation, to levels that approached those achieved at MOI of 200 for LV alone, in the presence or absence of the magnetic field. Magnetofection significantly increased the percentage of transduced cells up to 186-fold already after 15 min of incubation. In polarized cells, magnetofection increased GFP+ cells up to 24-fold compared to LV alone. Magnetofection did not enhance LDH release and slightly altered TER but not ZO-1 localization at the TJs.

CONCLUSIONS

We conclude that magnetofection can facilitate in vitro LV-mediated transduction of airway epithelial cells, in the absence of overt cytotoxicity and maintaining epithelial integrity, by lowering the necessary vector dose and reducing the incubation time required to achieve efficient transduction.

Bioreducible liposomes for gene delivery: from the formulation to the mechanism of action

Background

A promising strategy to create stimuli-responsive gene delivery systems is to exploit the redox gradient between the oxidizing extracellular milieu and the reducing cytoplasm in order to disassemble DNA/cationic lipid complexes (lipoplexes). On these premises, we previously described the synthesis of SS14 redox-sensitive gemini surfactant for gene delivery. Although others have attributed the beneficial effects of intracellular reducing environment to reduced glutathione (GSH), these observations cannot rule out the possible implication of the redox milieu in its whole on transfection efficiency of bioreducible transfectants leaving the determinants of DNA release largely undefined.

Methodology/Principal Findings

With the aim of addressing this issue, SS14 was here formulated into binary and ternary 100 nm-extruded liposomes and the effects of the helper lipid composition and of the SS14/helper lipids molar ratio on chemical-physical and structural parameters defining transfection effectiveness were investigated. Among all formulations tested, DOPC/DOPE/SS14 at 25∶50∶25 molar ratio was the most effective in transfection studies owing to the presence of dioleoyl chains and phosphatidylethanolamine head groups in co-lipids. The increase in SS14 content up to 50% along DOPC/DOPE/SS14 liposome series yielded enhanced transfection, up to 2.7-fold higher than that of the benchmark Lipofectamine 2000, without altering cytotoxicity of the corresponding lipoplexes at charge ratio 5. Secondly, we specifically investigated the redox-dependent mechanisms of gene delivery into cells through tailored protocols of transfection in GSH-depleted and repleted vs. increased oxidative stress conditions. Importantly, GSH specifically induced DNA release in batch and in vitro.

Conclusions/Significance

The presence of helper lipids carrying unsaturated dioleoyl chains and phosphatidylethanolamine head groups significantly improved transfection efficiencies of DOPC/DOPE/SS14 lipoplexes. Most importantly, this study shows that intracellular GSH levels linearly correlated with transfection efficiency while oxidative stress levels did not, highlighting for the first time the pivotal role of GSH rather than oxidative stress in its whole in transfection of bioreducible vectors.

Regulated expression of a transgene introduced on an oriP/EBNA-1 PAC shuttle vector into human cells

BACKGROUND

Sequencing of the human genome has led to most genes being available in BAC or PAC vectors. However, limited functional information has been assigned to most of these genes. Techniques for the manipulation and transfer of complete functional units on large DNA fragments into human cells are crucial for the analysis of complete genes in their natural genomic context. One limitation of the functional studies using these vectors is the low transfection frequency.

RESULTS

We have constructed a shuttle vector, pPAC7, which contains both the EBNA-1 gene and oriP from the Epstein-Barr virus allowing stable maintenance of PAC clones in the nucleus of human cells. The pPAC7 vector also contains the EGFP reporter gene, which allows direct monitoring of the presence of PAC constructs in transfected cells, and the Bsr-cassette that allows highly efficient and rapid selection in mammalian cells by use of blasticidin. Positive selection for recombinant PAC clones is obtained in pPAC7 because the cloning sites are located within the SacBII gene. We show regulated expression of the CDH3 gene carried as a 132 kb genomic insert cloned into pPAC7, demonstrating that the pPAC7 vector can be used for functional studies of genes in their natural genomic context. Furthermore, the results from the transfection of a range of pPAC7 based constructs into two human cell lines suggest that the transfection efficiencies are not only dependent on construct size.

CONCLUSION

The shuttle vector pPAC7 can be used to transfer large genomic constructs into human cells. The genes transferred could potentially contain all long-range regulatory elements, including their endogenous regulatory promoters. Introduction of complete genes in PACs into human cells would potentially allow complementation assays to identify or verify the function of genes affecting cellular phenotypes.

Polyethylenimine-mediated gene delivery to the lung and therapeutic applications

Nonviral gene delivery is now considered a promising alternative to viral vectors. Among nonviral gene delivery agents, polyethylenimine (PEI) has emerged as a potent candidate for gene delivery to the lung. PEI has some advantages over other polycations in that it combines strong DNA compaction capacity with an intrinsic endosomolytic activity. However, intracellular (mainly the nuclear membrane) and extracellular obstacles still hamper its efficiency in vitro and in vivo, depending on the route of administration and the type of PEI. Nuclear delivery has been increased by adding nuclear localization signals. To overcome nonspecific interactions with biological fluids, extracellular matrix components and nontarget cells, strategies have been developed to protect polyplexes from these interactions and to increase target specificity and gene expression. When gene delivery into airway epithelial cells of the conducting airways is necessary, aerosolization of complexes seems to be better suited to guarantee higher transgene expression in the airway epithelial cells with lower toxicity than observed with either intratracheal or intravenous administration. Aerosolization, indeed, is useful to target the alveolar epithelium and pulmonary endothelium. Proof-of-principle that PEI-mediated gene delivery has therapeutic application to some genetic and acquired lung disease is presented, using as genetic material either plasmidic DNA or small-interfering RNA, although optimization of formulation and delivery protocols and limitation of toxicity need further studies.

Involvement of glycosaminoglycans in vesicular stomatitis virus G glycoprotein pseudotyped lentiviral vector-mediated gene transfer into airway epithelial cells

BACKGROUND

The involvement of surface molecules in HIV-1-derived lentivirus (LV)-mediated transduction of airway epithelial cells has not been studied so far. The present study aimed to evaluate the role of glycosaminoglycans (GAGs) in gene transfer mediated by a third generation vesicular stomatitis virus G glycoprotein (VSV-G) pseudotyped LV vector in an in vitro model of polarized airway epithelial cells.

METHODS

Human bronchial (16HBE-S1) and tracheal (CFT1-C2) epithelial cells were grown either on plastic or on filters and transduced with the LV vector polypurine tract (PPT)-green fluoresecent protein (GFP). Zonula Occludens (ZO)-1, a marker of tight junction, and GAG localization were assessed by cytofluorimetry and confocal microscopy. Soluble GAGs and removal of cell surface GAGs were used to affect LV-mediated transduction.

RESULTS

Extensive optimization of experimental parameters (presence of polybrene during the infection, the incubation time in the presence of LV particles, period of time intercurring between infection and gene expression analysis) was carried out in plastic-adherent cells. Polybrene resulted to be cytotoxic and was not further used. In CFT1-C2 polarized cells, EGTA treatment determined a 20% decrease in transepithelial resistance, a diminished ZO-1 localization at the tight junction location and a 31% increase in GFP positive cells. Heparane sulfate was distributed evenly on the cell surface. Heparin and soluble chondroitin sulfate A and B inhibited LV-mediated transduction in a dose-dependent fashion. These results were confirmed upon enzymatic removal of GAGs from the cell surface.

CONCLUSIONS

Taken together, these results show that GAGs are involved in VSV-G LV transduction of airway epithelial cells.

Rational vector design for efficient non-viral gene delivery: challenges facing the use of plasmid DNA

Although non-viral gene delivery is a very straightforward technology, there are currently no FDA-approved gene medicinal products available. Therefore, improving potency, safety, and efficiency of current plasmid DNA vectors will be a major task for the near future. This article will provide an overview on factors influencing production yield and quality as well as safety issues that emerge from the vector design itself. Special focus will be on generating bacterial pDNA vectors by circumventing the use of antibiotic resistance genes, to generate safer gene medicinal products as well as smaller, more efficient DNA vectors.

Chimeric constructs endow the human CFTR Cl- channel with the gating behavior of murine CFTR

The cystic fibrosis transmembrane conductance regulator (CFTR) is a Cl(-) channel gated by ATP-driven nucleotide-binding domain (NBD) dimerization. Here we exploit species differences between human and murine CFTR to investigate CFTR channel gating. Using homologous recombination, we constructed human-murine CFTR (hmCFTR) chimeras with sequences from NBD1, NBD2, or the regulatory domain (RD) of human CFTR replaced by the equivalent regions of murine CFTR. The gating behavior of hmRD and human CFTR were indistinguishable, whereas hmNBD1 and hmNBD2 had subtle effects on channel gating, prolonging both burst duration and interburst interval. By contrast, hmNBD1+2, containing both NBDs of murine CFTR, reproduced the gating behavior of the subconductance state of murine CFTR, which has dramatically prolonged channel openings. The CFTR potentiator pyrophosphate (PP(i)) enhanced human, hmRD, and hmNBD1 CFTR Cl(-) currents, but not those of hmNBD2, hmNBD1+2, and murine CFTR. By analyzing the rate-equilibrium free-energy relationships of chimeric channels, we obtained snapshots of the conformation of the NBDs during ATP-driven dimerization. Our data demonstrate that the conformation of NBD1 changes before that of NBD2 during channel opening. This finding suggests that NBD dimerization does not proceed by a symmetric tweezer-like motion, but instead in an asymmetric fashion led by NBD1. We conclude that the NBDs of murine CFTR determine the unique gating behavior of its subconductance state, whereas NBD2 controls channel potentiation by PP(i).

Investigations of the effect of DNA size in transient transfection assay using dual luciferase system

In transient transfection assays deletions, insertions, or truncations are broadly used to define cis regulatory elements, such as promoters, enhancers, and silencers. This application is based on the assumption that size changes of a test fragment have little or no effect on the apparent activity of the reporter genes. While it is known that unusually large size of a construct, such as PAC DNA, substantially reduces transfection efficiency, the size effect of a DNA fragment ranging from a couple of hundred basepairs to a few thousand basepairs, within which most transient transfection assays are performed, has not been rigorously investigated. Here we report a systematic study on the effect of plasmid size on the measurement of promoter/enhancer activity in transient transfection assay based on the dual luciferase reporter system. By inserting various lengths of stuffer DNA into the luciferase parental plasmids, we found an inverse correlation between the relative luciferase activity and the construct size. Furthermore, this size effect can be only partially corrected by inserting the same size of stuffer DNA into both experimental and control plasmids. The results suggest that the effect of DNA size should be taken into consideration for evaluation of transcriptional elements using transient transfection analysis.

Polyethylenimine-based non-viral gene delivery systems

Gene therapy has become a promising strategy for the treatment of many inheritable or acquired diseases that are currently considered incurable. Non-viral vectors have attracted great interest, as they are simple to prepare, rather stable, easy to modify and relatively safe, compared to viral vectors. Unfortunately, they also suffer from a lower transfection efficiency, requiring additional effort for their optimization. The cationic polymer polyethylenimine (PEI) has been widely used for non-viral transfection in vitro and in vivo and has an advantage over other polycations in that it combines strong DNA compaction capacity with an intrinsic endosomolytic activity. Here, we give some insight into strategies developed for PEI-based non-viral vectors to overcome intracellular obstacles, including the improvement of methods for polyplex preparation and the incorporation of endosomolytic agents or nuclear localization signals. In recent years, PEI-based non-viral vectors have been locally or systemically delivered, mostly to target gene delivery to tumor tissue, the lung or liver. This requires strategies to efficiently shield transfection polyplexes against non-specific interaction with blood components, extracellular matrix and untargeted cells and the attachment of targeting moieties, which allow for the directed gene delivery to the desired cell or tissue. In this context, materials, facilitating the design of novel PEI-based non-viral vectors are described.

Potent stimulation of gene expression by histone deacetylase inhibitors on transiently transfected DNA

Transcription activity of chromatin is associated with histone acetylation which is regulated by recruitment of histone acetyltransferases and deacetylases (HDAC) to specific chromatin regions. We have tested how expression of a transfected or stably introduced gene correlates with histone acetylation. Our results demonstrate that expression of transiently transfected green fluorescence protein (GFP) genes is significantly enhanced by HDAC inhibitors. Although HDAC treatment did not induce noticeable changes in the chromatin structure of genomic DNA, chromatin immunoprecipitation showed that more transiently transfected DNA is assembled into chromatin containing acetylated histones in HDAC inhibitor treated cells when compared to untreated cells. For stably integrated GFP, the expression response to HDAC inhibitors varies between independent stable cell lines. However, there was no difference in histone acetylation associated with the integrated transgene between HDAC inhibitor responsive and non-responsive cells. Furthermore, the overall enhancement of transgene expression by HDAC inhibitors was not as pronounced as in transiently transfected cells.

KLN-5: a safe monocationic lipophosphoramide to transfect efficiently haematopoietic cell lines and human CD34+ cells

The safe and efficient delivery of nucleic acids into haematopoietic stem cells (HSCs) has a wide range of therapeutic applications. Although viruses are being used in most clinical trials owing to their high transfection efficacy, recent results highlight many concerns about their use. Synthetic transfection reagents, in contrast, have the advantage of being safe and easy to manage while their low transfection efficiency remains a hurdle that needs to be addressed before they can be widely used. Using information on transfection mechanisms, a new family of monocationic lipids called lipophosphoramides was synthesized. Their efficiency to transfer genes into haematopoietic cell lines (K562, Jurkat and Daudi) and CD34+ cells was assessed. In this study, we report that one of these new compounds, KLN-5, leads to more efficient transfection activity than one of our previously most efficient reagents (EG-308) and the commercially available monocationic lipids (DC-CHOL and DOTAP/DOPE) (P<0.05). In addition, only a slight toxicity related to the chemical structure of the new compounds is observed. Moreover, we show that KLN-5 can successfully carry the transgene into haematopoietic progenitor cells (CD34+). These results demonstrate that synthetic transfection reagents represent a viable alternative to viruses and could have potential practical utility in a number of applications.

HIV-1 Tat protein transduction domain peptide facilitates gene transfer in combination with cationic liposomes

The protein transduction domain (PTD) of the HIV-1 Tat protein can facilitate the cellular and nuclear uptake of macromolecular particles. Here, we demonstrate that incorporation without covalent linkage of a 17-amino acid PTD peptide into gene delivery lipoplexes improves gene transfer. Tat/Liposome/DNA (TLD) transfection, as evaluated by Fluorescence Activated Cell Scan analysis of a Green Fluorescence Protein expression plasmid, enabled transfection of highly recalcitrant primary cells in the form of air/liquid interface cultures of sheep tracheal epithelium. Treatment with chloroquine increased, and incubation at low temperature decreased, TLD transfection, suggesting that the endocytosis uptake pathway is involved.