Impact of intrinsic DNA structure on processing of plasmids for gene therapy and DNA vaccines

A machine learning-based approach for improving plasmid DNA production in Escherichia coli fed-batch fermentations

Artificial Intelligence (AI) technology is spearheading a new industrial revolution, which provides ample opportunities for the transformational development of traditional fermentation processes. During plasmid fermentation, traditional subjective process control leads to highly unstable plasmid yields. In this study, a multi-parameter correlation analysis was first performed to discover a dynamic metabolic balance among the oxygen uptake rate, temperature, and plasmid yield, whilst revealing the heating rate and timing as the most important optimization factor for balanced cell growth and plasmid production. Then, based on the acquired on-line parameters as well as outputs of kinetic models constructed for describing process dynamics of biomass concentration, plasmid yield, and substrate concentration, a machine learning (ML) model with Random Forest (RF) as the best machine learning algorithm was established to predict the optimal heating strategy. Finally, the highest plasmid yield and specific productivity of 1167.74 mg L-1 and 8.87 mg L-1/OD600 were achieved with the optimal heating strategy predicted by the RF model in the 50 L bioreactor, respectively, which was 71% and 21% higher than those obtained in the control cultures where a traditional one-step temperature upshift strategy was applied. In addition, this study transformed empirical fermentation process optimization into a more efficient and rational self-optimization method. The methodology employed in this study is equally applicable to predict the regulation of process dynamics for other products, thereby facilitating the potential for furthering the intelligent automation of fermentation processes.

Enabling mRNA Therapeutics: Current Landscape and Challenges in Manufacturing

Recent advances and discoveries in the structure and role of mRNA as well as novel lipid-based delivery modalities have enabled the advancement of mRNA therapeutics into the clinical trial space. The manufacturing of these products is relatively simple and eliminates many of the challenges associated with cell culture production of viral delivery systems for gene and cell therapy applications, allowing rapid production of mRNA for personalized treatments, cancer therapies, protein replacement and gene editing. The success of mRNA vaccines during the COVID-19 pandemic highlighted the immense potential of this technology as a vaccination platform, but there are still particular challenges to establish mRNA as a widespread therapeutic tool. Immunostimulatory byproducts can pose a barrier for chronic treatments and different production scales may need to be considered for these applications. Moreover, long-term storage of mRNA products is notoriously difficult. This review provides a detailed overview of the manufacturing steps for mRNA therapeutics, including sequence design, DNA template preparation, mRNA production and formulation, while identifying the challenges remaining in the dose requirements, long-term storage and immunotolerance of the product.

Development and application of a real-time PCR assay for the sensitive detection of diarrheic toxin producer Prorocentrum lima

Prorocentrum lima (P. lima) is a widely spread dinoflagellate in the Mediterranean Sea and it has become increasingly involved in harmful algal blooms. The purpose of this study is to develop a probe-based real-time polymerase chain reaction (PCR) targeting the ITS1-5.8S-ITS2 region for the detection and absolute quantification of P. lima based on linear and circular DNA standards. The results have shown that the quantitative PCR (q-PCR), using circular plasmid as a template, gave a threshold cycle number 1.79-5.6 greater than equimolar linear standards. When microalgae, commonly found in aquatic samples were tested, no cross-amplification was observed. The q-PCR brought about a good intra and inter-run reproducibility and a detection limit of 5 copies of linear plasmid per reaction. A quantitative relationship between the cell numbers and their corresponding plasmid copy numbers was attained. Afterwards, the effectiveness of the developed protocol was tested with 130 aquatic samples taken from 19 Tunisian sampling sites. The developed q-PCR had a detection sensitivity of up to 1 cell. All the positive samples were taken from three sampling sites of Medenine Governorate with cell abundances that ranged from 22 to 156,000 cells L-1 of seawater. The q-PCR assay revealed a high sensitivity in monitoring the aquatic samples in which the low concentrations of P. lima were not accurately detected by light microscopy. Indeed, this approach is at the same time rapid, specific and sensitive than the traditional microscopy techniques and it represents a great potential for the monitoring of P. lima blooms.

DNA Quadruple Helices in Nanotechnology

DNA has played an early and powerful role in the development of bottom-up nanotechnologies, not least because of DNA's precise, predictable, and controllable properties of assembly on the nanometer scale. Watson-Crick complementarity has been used to build complex 2D and 3D architectures and design a number of nanometer-scale systems for molecular computing, transport, motors, and biosensing applications. Most of such devices are built with classical B-DNA helices and involve classical A-T/U and G-C base pairs. However, in addition to the above components underlying the iconic double helix, a number of alternative pairing schemes of nucleobases are known. This review focuses on two of these noncanonical classes of DNA helices: G-quadruplexes and the i-motif. The unique properties of these two classes of DNA helix have been utilized toward some remarkable constructions and applications: G-wires; nanostructures such as DNA origami; reconfigurable structures and nanodevices; the formation and utilization of hemin-utilizing DNAzymes, capable of generating varied outputs from biosensing nanostructures; composite nanostructures made up of DNA as well as inorganic materials; and the construction of nanocarriers that show promise for the therapeutics of diseases.

The Five Immune Forces Impacting DNA-Based Cancer Immunotherapeutic Strategy

DNA-based vaccine strategy is increasingly realized as a viable cancer treatment approach. Strategies to enhance immunogenicity utilizing tumor associated antigens have been investigated in several pre-clinical and clinical studies. The promising outcomes of these studies have suggested that DNA-based vaccines induce potent T-cell effector responses and at the same time cause only minimal side-effects to cancer patients. However, the immune evasive tumor microenvironment is still an important hindrance to a long-term vaccine success. Several options are currently under various stages of study to overcome immune inhibitory effect in tumor microenvironment. Some of these approaches include, but are not limited to, identification of neoantigens, mutanome studies, designing fusion plasmids, vaccine adjuvant modifications, and co-treatment with immune-checkpoint inhibitors. In this review, we follow a Porter’s analysis analogy, otherwise commonly used in business models, to analyze various immune-forces that determine the potential success and sustainable positive outcomes following DNA vaccination using non-viral tumor associated antigens in treatment against cancer.

Towards effective non-viral gene delivery vector

Despite very good safety records, clinical trials using plasmid DNA failed due to low transfection efficiency and brief transgene expression. Although this failure is both due to poor plasmid design and to inefficient delivery methods, here we will focus on the former. The DNA elements like CpG motifs, selection markers, origins of replication, cryptic eukaryotic signals or nuclease-susceptible regions and inverted repeats showed detrimental effects on plasmids' performance as biopharmaceuticals. On the other hand, careful selection of promoter, polyadenylation signal, codon optimization and/or insertion of introns or nuclear-targeting sequences for therapeutic protein expression can enhance the clinical efficacy. Minimal vectors, which are devoid of the bacterial backbone and consist exclusively of the eukaryotic expression cassette, demonstrate better performance in terms of expression levels, bioavailability, transfection rates and increased therapeutic effects. Although the results are promising, minimal vectors have not taken over the conventional plasmids in clinical trials due to challenging manufacturing issues.

Locked nucleic acid probe-based real-time PCR for the diagnosis of Listeria monocytogenes in ruminants

Because of its high fatality rate, listeriosis ranks among the most important infectious diseases worldwide. Although ruminants are known as natural reservoirs for Listeria monocytogenes and a possible source of human listeriosis, studies of the prevalence and risk factors associated with ruminant listeriosis are limited to some developed countries. Therefore, this report describes the development of a real-time PCR targeting the hly gene for the absolute quantification of L. monocytogenes based on circular and linear DNA standards. Results show that the PCR that uses circular plasmid as a template gave a 2.6-7.89 greater threshold cycle number than did equimolar linear standards. No cross-amplification was observed when bacteria commonly found in bovine and ovine diseases were tested. The PCR achieved good intra and inter-run reproducibility and a detection limit of 6.1 copies of linear plasmid per reaction. This PCR was then applied to 1134 samples taken from 378 Tunisian ruminants. Based on the test sensitivity (90%) and specificity (100%), the true individual animal prevalence of listeriosis was 5.7% in cattle and 10.2% in sheep. In addition, the true herd-level prevalence was 50.1% in cattle and 26.7% in sheep. A multivariable logistic regression analysis at the animal-population level indicated that for cattle, the variables strata and mastitis were important risk factors, whereas for sheep, the variables strata, age and abortion were found to be associated with listeriosis. At the herd level, risk factors for Listeria test-positivity they were: abortion, herd composition and silage storage for cattle, whereas for sheep were: management system, cleaning frequency, silage storage and floor type. Animal hygiene, food quality and sanitary practices on the farm should be applied as strategies to control this pathogen in ruminant herds.

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.

Engineering Escherichia coli to increase plasmid DNA production in high cell-density cultivations in batch mode

BACKGROUND

Plasmid DNA (pDNA) is a promising molecule for therapeutic applications. pDNA is produced by Escherichia coli in high cell-density cultivations (HCDC) using fed-batch mode. The typical limitations of such cultivations, including metabolic deviations like aerobic acetate production due to the existence of substrate gradients in large-scale bioreactors, remain as serious challenges for fast and effective pDNA production. We have previously demonstrated that the substitution of the phosphotransferase system by the over-expressed galactose permease for glucose uptake in E. coli (strain VH33) allows efficient growth, while strongly decreases acetate production. In the present work, additional genetic modifications were made to VH33 to further improve pDNA production. Several genes were deleted from strain VH33: the recA, deoR, nupG and endA genes were inactivated independently and in combination. The performance of the mutant strains was evaluated in shake flasks for the production of a 6.1 kb plasmid bearing an antigen gene against mumps. The best producer strain was cultivated in lab-scale bioreactors using 100 g/L of glucose to achieve HCDC in batch mode. For comparison, the widely used commercial strain DH5α, carrying the same plasmid, was also cultivated under the same conditions.

RESULTS

The various mutations tested had different effects on the specific growth rate, glucose uptake rate, and pDNA yields (YP/X). The triple mutant VH33 Δ (recA deoR nupG) accumulated low amounts of acetate and resulted in the best YP/X (4.22 mg/g), whereas YP/X of strain VH33 only reached 1.16 mg/g. When cultivated at high glucose concentrations, the triple mutant strain produced 186 mg/L of pDNA, 40 g/L of biomass and only 2.2 g/L of acetate. In contrast, DH5α produced only 70 mg/L of pDNA and accumulated 9.5 g/L of acetate. Furthermore, the supercoiled fraction of the pDNA produced by the triple mutant was nearly constant throughout the cultivation.

CONCLUSION

The pDNA concentration obtained with the engineered strain VH33 Δ (recA deoR nupG) is, to the best of our knowledge, the highest reported for a batch cultivation, and its supercoiled fraction remained close to 80%. Strain VH33 Δ (recA deoR nupG) and its cultivation using elevated glucose concentrations represent an attractive technology for fast and efficient pDNA production and a valuable alternative to fed-batch cultivations of commercial strains.

Preparation and in vitro characterisation of Ehrlichia ruminantium plasmid DNA and proteins encapsulated into and DNA adsorbed onto biodegradable microparticles

Four E. ruminantium 1H12 open reading frames and their proteins known to protect sheep against heartwater needle challenge were encapsulated into, or adsorbed onto poly(d,l-lactide-co-glycolide) microparticles. Microspheres with smooth surface and smaller than 5 μm diameters were produced, with high adsorption and encapsulation efficiencies. Gel electrophoresis showed that neither encapsulation nor adsorption affected the stability of the DNA or proteins. Cationic microparticles released ∼40% of plasmid DNA on day 1 while PLGA 50:50-COOH microparticles co-encapsulating plasmid DNA and polyvinyl alcohol only started to release from days 12-28. Recombinant proteins were released from PLGA 85:15 and homopolymer R 203 S microparticles in a biphasic manner with a high initial burst release (∼45-80%). In contrast, PLGA 50:50 microparticles had low (15-65%) initial burst release followed by (25-80%) release by days (days 28-42). A cocktail of these microparticles could therefore be used as single-dose auto-booster vaccine.

Vector insert-targeted integrative antisense expression system for plasmid stabilization

Some DNA vaccine and gene therapy vector-encoded transgenes are toxic to the E. coli plasmid production host resulting in poor production yields. For plasmid products undergoing clinical evaluation, sequence modification to eliminate toxicity is undesirable because an altered vector is a new chemical entity. We hypothesized that: (1) insert-encoded toxicity is mediated by unintended expression of a toxic insert-encoded protein from spurious bacterial promoters; and (2) that toxicity could be eliminated with antisense RNA-mediated translation inhibition. We developed the pINT PR PL vector, a chromosomally integrable RNA expression vector, and utilized it to express insert-complementary (anti-insert) RNA from a single defined site in the bacterial chromosome. Anti-insert RNA eliminated leaky fluorescent protein expression from a target plasmid. A toxic retroviral gag pol helper plasmid produced in a gag pol anti-insert strain had fourfold improved plasmid fermentation yields. Plasmid fermentation yields were also fourfold improved when a DNA vaccine plasmid containing a toxic Influenza serotype H1 hemagglutinin transgene was grown in an H1 sense strand anti-insert production strain, suggesting that in this case toxicity was mediated by an antisense alternative reading frame-encoded peptide. This anti-insert chromosomal RNA expression technology is a general approach to improve production yields with plasmid-based vectors that encode toxic transgenes, or toxic alternative frame peptides.

Mutation detection in plasmid-based biopharmaceuticals

As the number of applications involving therapeutic plasmid DNA (pDNA) increases worldwide, there is a growing concern over maintaining rigorous quality control through a panel of high-quality assays. For this reason, efficient, cost-effective and sensitive technologies enabling the identification of genetic variants and unwanted side products are needed to successfully establish the identity and stability of a plasmid-based biopharmaceutical. This review highlights several bioinformatic tools for ab initio detection of potentially unstable DNA regions, as well as techniques used for mutation detection in nucleic acids, with particular emphasis on pDNA.

Serious overestimation in quantitative PCR by circular (supercoiled) plasmid standard: microalgal pcna as the model gene

Quantitative real-time PCR (qPCR) has become a gold standard for the quantification of nucleic acids and microorganism abundances, in which plasmid DNA carrying the target genes are most commonly used as the standard. A recent study showed that supercoiled circular confirmation of DNA appeared to suppress PCR amplification. However, to what extent to which different structural types of DNA (circular versus linear) used as the standard may affect the quantification accuracy has not been evaluated. In this study, we quantitatively compared qPCR accuracies based on circular plasmid (mostly in supercoiled form) and linear DNA standards (linearized plasmid DNA or PCR amplicons), using proliferating cell nuclear gene (pcna), the ubiquitous eukaryotic gene, in five marine microalgae as a model gene. We observed that PCR using circular plasmids as template gave 2.65-4.38 more of the threshold cycle number than did equimolar linear standards. While the documented genome sequence of the diatom Thalassiosira pseudonana shows a single copy of pcna, qPCR using the circular plasmid as standard yielded an estimate of 7.77 copies of pcna per genome whereas that using the linear standard gave 1.02 copies per genome. We conclude that circular plasmid DNA is unsuitable as a standard, and linear DNA should be used instead, in absolute qPCR. The serious overestimation by the circular plasmid standard is likely due to the undetected lower efficiency of its amplification in the early stage of PCR when the supercoiled plasmid is the dominant template.

Generic plasmid DNA production platform incorporating low metabolic burden seed-stock and fed-batch fermentation processes

DNA vaccines have tremendous potential for rapid deployment in pandemic applications, wherein a new antigen is "plugged" into a validated vector, and rapidly produced in a validated, fermentation-purification process. For this application, it is essential that the vector and fermentation process function with a variety of different antigen genes. However, many antigen genes are unpredictably "toxic" or otherwise low yielding in standard fermentation processes. We report cell bank and fermentation process unit operation innovations that reduce plasmid-mediated metabolic burden, enabling successful production of previously known toxic influenza hemagglutinin antigen genes. These processes, combined with vector backbone modifications, doubled fermentation productivity compared to existing high copy vectors, such as pVAX1 and gWiz, resulting in high plasmid yields (up to 2,220 mg/L, 5% of total dry cell weight) even with previously identified toxic or poor producing inserts.

Plasmid DNA vaccine vector design: impact on efficacy, safety and upstream production

Critical molecular and cellular biological factors impacting design of licensable DNA vaccine vectors that combine high yield and integrity during bacterial production with increased expression in mammalian cells are reviewed. Food and Drug Administration (FDA), World Health Organization (WHO) and European Medical Agencies (EMEA) regulatory guidance's are discussed, as they relate to vector design and plasmid fermentation. While all new vectors will require extensive preclinical testing to validate safety and performance prior to clinical use, regulatory testing burden for follow-on products can be reduced by combining carefully designed synthetic genes with existing validated vector backbones. A flowchart for creation of new synthetic genes, combining rationale design with bioinformatics, is presented. The biology of plasmid replication is reviewed, and process engineering strategies that reduce metabolic burden discussed. Utilizing recently developed low metabolic burden seed stock and fermentation strategies, optimized vectors can now be manufactured in high yields exceeding 2 g/L, with specific plasmid yields of 5% total dry cell weight.

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.

Bioprocess engineering issues that would be faced in producing a DNA vaccine at up to 100 m3 fermentation scale for an influenza pandemic

The risk of a pandemic with a virulent form of influenza is acknowledged by the World Health Organization (WHO) and other agencies. Current vaccine production facilities would be unable to meet the global requirement for vaccine. As a possible supplement a DNA vaccine may be appropriate, and bioprocess engineering factors bearing on the use of existing biopharmaceutical and antibiotics plants to produce it are described. This approach addresses the uncertainty of timing of a pandemic that precludes purpose-built facilities. The strengths and weaknesses of alternative downstream processing routes are analyzed, and several gaps in public domain information are addressed. The conclusion is that such processing would be challenging but feasible.

Successful parallel development and integration of a plasmid-based biologic, container/closure system and electrokinetic delivery device

We have developed three major technologies that allow plasmid-based products to be used for large-scale vaccination or therapeutic protein applications. Our team has integrated these components into one complete, cost-effective, easy-to-use system capable of rapid implementation under field conditions. The proprietary manufacturing process uses a lysis method and membrane-based chromatography to rapidly produce large-scale batches of plasmid. Plasmid doses are filled into the Becton-Dickinson Uniject container/closure system. The Uniject adapts to the electrode array of our constant current electrokinetic device, such that the plasmid is delivered in the area of tissue defined by the electrodes. Thus, plasmid uptake and expression levels are dramatically improved. This is the first completely integrated delivery system for plasmid-based products.