Characterization of replication-competent adenovirus isolates from large-scale production of a recombinant adenoviral vector

Current Status of Poultry Recombinant Virus Vector Vaccine Development

Inactivated and live attenuated vaccines are the mainstays of preventing viral poultry diseases. However, the development of recombinant DNA technology in recent years has enabled the generation of recombinant virus vector vaccines, which have the advantages of preventing multiple diseases simultaneously and simplifying the vaccination schedule. More importantly, some can induce a protective immune response in the presence of maternal antibodies and offer long-term immune protection. These advantages compensate for the shortcomings of traditional vaccines. This review describes the construction and characterization of primarily poultry vaccine vectors, including fowl poxvirus (FPV), fowl adenovirus (FAdV), Newcastle disease virus (NDV), Marek's disease virus (MDV), and herpesvirus of turkey (HVT). In addition, the pathogens targeted and the immunoprotective effect of different poultry recombinant virus vector vaccines are also presented. Finally, this review discusses the challenges in developing vector vaccines and proposes strategies for improving immune efficacy.

Adenoviral Gene Therapy Vectors in Clinical Use-Basic Aspects with a Special Reference to Replication-Competent Adenovirus Formation and Its Impact on Clinical Safety

Adenoviral vectors are commonly used in clinical gene therapy. Apart from oncolytic adenoviruses, vector replication is highly undesired as it may pose a safety risk for the treated patient. Thus, careful monitoring for the formation of replication-competent adenoviruses (RCA) during vector manufacturing is required. To render adenoviruses replication deficient, their genomic E1 region is deleted. However, it has been known for a long time that during their propagation, some viruses will regain their replication capability by recombination in production cells, most commonly HEK293. Recently developed RCA assays have revealed that many clinical batches contain more RCA than previously assumed and allowed by regulatory authorities. The clinical significance of the higher RCA content has yet to be thoroughly evaluated. In this review, we summarize the biology of adenovirus vectors, their manufacturing methods, and the origins of RCA formed during HEK293-based vector production. Lastly, we share our experience using minimally RCA-positive serotype 5 adenoviral vectors based on observations from our clinical cardiovascular gene therapy studies.

A Method to Generate and Rescue Recombinant Adenovirus Devoid of Replication-Competent Particles in Animal-Origin-Free Culture Medium

Adenoviruses are promising vectors for vaccine production and gene therapy. Despite all the efforts in removing animal-derived components such as fetal bovine serum (FBS) during the production of adenovirus vector (AdV), FBS is still frequently employed in the early stages of production. Conventionally, first-generation AdVs (E1 deleted) are generated in different variants of adherent HEK293 cells, and plaque purification (if needed) is performed in adherent cell lines in the presence of FBS. In this study, we generated an AdV stock in SF-BMAdR (A549 cells adapted to suspension culture in serum-free medium). We also developed a limiting dilution method using the same cell line to replace the plaque purification assay. By combining these two technologies, we were able to completely remove the need for FBS from the process of generating and producing AdVs. In addition, we demonstrated that the purified AdV stock is free of any replication-competent adenovirus (RCA). Furthermore, we demonstrated that our limiting dilution method could effectively rescue an AdV from a stock that is highly contaminated with RCA.

Contextualizing Wastewater-Based surveillance in the COVID-19 vaccination era

SARS-CoV-2 wastewater-based surveillance (WBS) offers a tool for cost-effective oversight of a population's infections. In the past two years, WBS has proven to be crucial for managing the pandemic across different geographical regions. However, the changing context of the pandemic due to high levels of COVID-19 vaccination warrants a closer examination of its implication towards SARS-CoV-2 WBS. Two main questions were raised: 1) Does vaccination cause shedding of viral signatures without infection? 2) Does vaccination affect the relationship between wastewater and clinical data? To answer, we review historical reports of shedding from viral vaccines in use prior to the COVID-19 pandemic including for polio, rotavirus, influenza and measles infection and provide a perspective on the implications of different COVID-19 vaccination strategies with regard to the potential shedding of viral signatures into the sewershed. Additionally, we reviewed studies that looked into the relationship between wastewater and clinical data and how vaccination campaigns could have affected the relationship. Finally, analyzing wastewater and clinical data from the Netherlands, we observed changes in the relationship concomitant with increasing vaccination coverage and switches in dominant variants of concern. First, that no vaccine-derived shedding is expected from the current commercial pipeline of COVID-19 vaccines that may confound interpretation of WBS data. Secondly, that breakthrough infections from vaccinated individuals contribute significantly to wastewater signals and must be interpreted in light of the changing dynamics of shedding from new variants of concern.

A qPCR-Based Method for Quantification of RCA Contaminants in Oncolytic Adenovirus Products

Oncolytic adenovirus is one of the most promising treatments against cancer and is widely evaluated clinically. During high titer production, “Wild-type-” like replication-competent adenovirus (RCA) contaminants can be generated through recombination events due to the DNA sequence similarity between oncolytic virus and host cells. These RCA contaminants raise various safety concerns in clinics. Cell culture-based methods have been developed to detect RCA contaminants in replication-deficient adenovirus vectors. These methods were based on that only RCA contaminants, but not the vectors, are able to grow in and lyse the test cell line. However, these methods are not suitable for distinguishing RCA contaminants from the oncolytic adenovirus products because both can replicate in test cell lines. Herein, we reported a qPCR-based method to quantify RCA contaminants quickly and reliably in E1B-deleted oncolytic adenovirus products. This method is based on specific detection of the E1B gene, which can be acquired during production via recombination events between viral and host cell DNA. The assay is sensitive with the limit of detection at 10 VP of the RCA contaminants and the limit of quantification at 75 VP of the RCA contaminants in each 40 µL qPCR reaction. We have also validated the method on virus batches produced in the non-GMP and GMP conditions. Our results showed that this qPCR-based method was reliable and robust for detecting and quantifying RCA contaminants in oncolytic adenovirus products. The method may also be adapted for other oncolytic adenoviruses products by switching primer sets.

A qPCR-Based Method for Quantification of Replication Competent Adenovirus (RCA) in Conditionally Replicating Oncolytic Adenoviruses

Production of conditionally replicating adenoviruses may unfortunately generate undesired replication-competent adenovirus (RCA) which raises safety concerns in clinical usage. Cell-based assays can detect RCA in batches of nonreplicating adenoviral vectors but cannot distinguish RCA from conditionally replicating oncolytic adenoviruses. Considering the great potential in using oncolytic viruses for cancer treatment, there is a need for comprehensive RCA-detection and -quantification methods. Here, we present a quantitative polymerase chain reaction (qPCR)-based assay that can be used to detect RCA particles in batches of conditionally replicating oncolytic adenoviruses. The assay is quantifying RCA by detection of the specific DNA sequence generated after a recombination event. Results showed that the method can successfully detect low levels of RCA, with a low limit of detection of ten viral particles.

Current status of virus-vectored vaccines against pathogens that affect poultry

The most effective strategies for the control of disease in poultry are vaccination and biosecurity. Vaccines useful against pathogens affecting poultry must be safe, effective with a single dose, inexpensive, applicable by mass vaccination methods, and able to induce a protective immune response in the presence of maternal antibodies. Viral vector meet some of these characteristics and if the attenuated virus used as vector infects birds, the vaccine will have the advantage of being bivalent. Thus, viral vectors are currently a tool of choice for the development of new poultry vaccines. This review describes the main viruses used as vectors for the delivery and in vivo expression of antigens of poultry pathogens. It also presents the methodologies most frequently used to obtain recombinant viral vectors and summarizes the state-of-the-art related to vectored vaccines in poultry (some of them currently licensed), the pathogens targeted and their antigens, and the ability of these vaccines to induce an effective immune response. Finally, the review discusses the results of a few studies comparing recombinant viral vector vaccines and live-attenuated vaccines in vaccine matching challenges, and mentions strategies and future researches that can help to improve the efficacy of vectored vaccines in poultry birds.

Peroxiredoxin I participates in the protection of reactive oxygen species-mediated cellular senescence

Peroxiredoxin I (Prx I) plays an important role as a reactive oxygen species (ROS) scavenger in protecting and maintaining cellular homeostasis; however, the underlying mechanisms are not well understood. Here, we identified a critical role of Prx I in protecting cells against ROS-mediated cellular senescence by suppression of p16^INK4a expression. Compared to wild-type mouse embryonic fibroblasts (WT-MEFs), Prx I^−/− MEFs exhibited senescence-associated phenotypes. Moreover, the aged Prx I^−/− mice showed an increased number of cells with senescence associated-β-galactosidase (SA-β-gal) activity in a variety of tissues. Increased ROS levels and SA-β-gal activity, and reduction of chemical antioxidant in Prx I^−/− MEF further supported an essential role of Prx I peroxidase activity in cellular senescence that is mediated by oxidative stress. The up-regulation of p16^INK4a expression in Prx I^−/− and suppression by overexpression of Prx I indicate that Prx I possibly modulate cellular senescence through ROS/p16^INK4a pathway.

Advancements in the design and scalable production of viral gene transfer vectors

The last 10 years have seen a rapid expansion in the use of viral gene transfer vectors, with approved therapies and late stage clinical trials underway for the treatment of genetic disorders, and multiple forms of cancer, as well as prevention of infectious diseases through vaccination. With this increased interest and widespread adoption of viral vectors by clinicians and biopharmaceutical industries, there is an imperative to engineer safer and more efficacious vectors, and develop robust, scalable and cost-effective production platforms for industrialization. This review will focus on major innovations in viral vector design and production systems for three of the most widely used viral vectors: Adenovirus, Adeno-Associated Virus, and Lentivirus.

Progress on adenovirus-vectored universal influenza vaccines

Influenza virus (IFV) infection causes serious health problems and heavy financial burdens each year worldwide. The classical inactivated influenza virus vaccine (IIVV) and live attenuated influenza vaccine (LAIV) must be updated regularly to match the new strains that evolve due to antigenic drift and antigenic shift. However, with the discovery of broadly neutralizing antibodies that recognize conserved antigens, and the CD8(+) T cell responses targeting viral internal proteins nucleoprotein (NP), matrix protein 1 (M1) and polymerase basic 1 (PB1), it is possible to develop a universal influenza vaccine based on the conserved hemagglutinin (HA) stem, NP, and matrix proteins. Recombinant adenovirus (rAd) is an ideal influenza vaccine vector because it has an ideal stability and safety profile, induces balanced humoral and cell-mediated immune responses due to activation of innate immunity, provides 'self-adjuvanting' activity, can mimic natural IFV infection, and confers seamless protection against mucosal pathogens. Moreover, this vector can be developed as a low-cost, rapid-response vaccine that can be quickly manufactured. Therefore, an adenovirus vector encoding conserved influenza antigens holds promise in the development of a universal influenza vaccine. This review will summarize the progress in adenovirus-vectored universal flu vaccines and discuss future novel approaches.

Adenoviral Vector Vaccines Antigen Transgene

In the past decade adenovirus-based vaccines have progressed from preclinical studies, which universally showed the vectors’ high immunogenicity, to testing in humans. Clinical trials showed that adenovirus vectors are well tolerated by humans. They induce robust immune responses that can be expanded by booster immunization. The effect of preexisting neutralizing antibodies on vectors’ immunogenicity appears to be less severe than was observed in experimental animals and can readily be circumvented by using vectors to which most humans lack neutralizing antibodies. Additional clinical studies are needed to firmly establish the efficacy of adenoviral vector vaccines.

Detection of replication competent adenovirus upon serial passaging of recombinant adenovirus expressing FMDV capsid proteins

Replication deficient human adenovirus type 5 (hAd5) is an important gene delivery vehicle and has been used in various fields of biomedical sciences such as gene therapy, cancer therapy and vaccination. Inspite of its various useful features, emergence of replication competent adenovirus (RCA) in recombinant virus stocks is a great concern. In the present study, recombinant adenovirus expressing foot-and-mouth disease virus serotype-O capsid proteins was propagated in HEK-293 cells and purified by CsCl density gradient ultracentrifugation. The virus was serially passaged in HEK-293 cells and at passage level (P) 2-4, 6, 8 and 12, tested for the presence of RCA. A vector dose of 2 × 10(8) and 1 × 10(10) TCID50 of the virus was used in cell line bioassay and PCR, respectively. Our results demonstrated that the PCR is more sensitive and rapid technique for the detection of RCA in recombinant adenovirus stocks as early as at P3, whereas the bioassay detected the RCA at P8.

Development of a platform process for adenovirus purification that removes human SET and nucleolin and provides high purity vector for gene delivery

The manufacturing of virus occurs at a modest scale in comparison to many therapeutic proteins mainly because a gene therapy dose is typically only µg of vector. Although modest in scale the generation of high purity virus is challenging due to low viral expression levels and the difficulties in adequately characterizing such a large and complex molecule. A 100 L bioreactor might produce only 100 mg of virus that must be separated from host and process impurities that are typically greater by several orders of magnitude. Furthermore, in the later purification stages the main milieu component is often virus at low concentration (µg/mL) which may non-specifically adsorb to purification surfaces resulting in a lowered virus recovery. This study describes our approach to develop a scalable, manufacturable robust process for an Adenovirus (Ad) gene therapy vector. A number of analytical tools were developed to guide the purification design. During process development, two human proteins, SET and nucleolin, were identified in viral preparations. To our knowledge, this is the first time that SET and nucleolin have been described in Ad. In this report we detail a process for their removal and the robust removal of all process, product and host cell impurities.

Advances and future challenges in recombinant adenoviral vectored H5N1 influenza vaccines

The emergence of a highly pathogenic avian influenza virus H5N1 has increased the potential for a new pandemic to occur. This event highlights the necessity for developing a new generation of influenza vaccines to counteract influenza disease. These vaccines must be manufactured for mass immunization of humans in a timely manner. Poultry should be included in this policy, since persistent infected flocks are the major source of avian influenza for human infections. Recombinant adenoviral vectored H5N1 vaccines are an attractive alternative to the currently licensed influenza vaccines. This class of vaccines induces a broadly protective immunity against antigenically distinct H5N1, can be manufactured rapidly, and may allow mass immunization of human and poultry. Recombinant adenoviral vectors derived from both human and non-human adenoviruses are currently being investigated and appear promising both in nonclinical and clinical studies. This review will highlight the current status of various adenoviral vectored H5N1 vaccines and will outline novel approaches for the future.

Development of a recombinant adenovirus vector production system free of replication-competent adenovirus by utilizing a packaging size limit of the viral genome

In a conventional adenovirus (Ad) vector production method using 293 cells, homologous recombination between Ad vector DNA and 293 cell-derived Ad E1 DNA occurs with low efficiency, resulting in the generation of replication-competent adenovirus (RCA). RCA can induce the spread of replication-incompetent Ad vectors, leading to unexpected tissue damage. In order to overcome this problem, we developed an Ad vector production system free of RCA generation by utilizing the Ad packaging size limit of the viral genome. It is well known that up to approximately 105% (37.7 kb) of the wild-type genome (35.9 kb) can be packaged in the Ad virion. We designed the Ad vector genome by insertion of a transgene expression cassette into the E3 region, such that homologous recombination between the Ad vector DNA and 293 cell-derived Ad E1 DNA would produce an Ad vector genome that exceeds in the size of the packaging limit. In accord with our strategy, no RCA generation was observed during the passages when we used the E1 (3.2kb)-deleted Ad vectors containing a more than 3.0-kb transgene expression cassette in the E3 region. In contrast, the E1 (3.2kb)-deleted Ad vectors, which retain 37.7 kb of the viral genome and have an insertion of a 2.1-kb transgene expression cassette in the E3 region, generated RCA, although RCA derived from this Ad vector exceeded the packaging size limit (105.0%). These results suggest that RCA generation can be avoided when the genome size of RCA is more than 108.3% (38.9 kb) of the wild-type Ad genome. This Ad vector production system generates safe, easy, and efficient Ad vector stock for both basic study as well as clinical research.

Adenoviral producer cells

Adenovirus (Ad) vectors, in particular those of the serotype 5, are highly attractive for a wide range of gene therapy, vaccine and virotherapy applications (as discussed in further detail in this issue). Wild type Ad5 virus can replicate in numerous tissue types but to use Ad vectors for therapeutic purposes the viral genome requires modification. In particular, if the viral genome is modified in such a way that the viral life cycle is interfered with, a specific producer cell line is required to provide trans-complementation to overcome the modification and allow viral production. This can occur in two ways; use of a producer cell line that contains specific adenoviral sequences incorporated into the cell genome to trans-complement, or use of a producer cell line that naturally complements for the modified Ad vector genome. This review concentrates on producer cell lines that complement non-replicating adenoviral vectors, starting with the historical HEK293 cell line developed in 1977 for first generation Ad vectors. In addition the problem of replication-competent adenovirus (RCA) contamination in viral preparations from HEK293 cells is addressed leading to the development of alternate cell lines. Furthermore novel cell lines for more complex Ad vectors and alternate serotype Ad vectors are discussed.

Avian influenza vaccination in chickens and pigs with replication-competent adenovirus-free human recombinant adenovirus 5

Protective immunity to avian influenza (AI) virus can be elicited in chickens by in ovo or intramuscular vaccination with replication-competent adenovirus (RCA)-free human recombinant adenovirus serotype 5 (Ad5) encoding AI virus H5 (AdTW68.H5) or H7 (AdCN94.H7) hemagglutinins. We evaluated bivalent in ovo vaccination with AdTW68.H5 and AdCN94.H7 and determined that vaccinated chickens developed robust hemagglutination inhibition (HI) antibody levels to both H5 and H7 AI strains. Additionally, we evaluated immune responses of 1-day-old chickens vaccinated via spray with AdCN94.H7. These birds showed increased immunoglobulin A responses in lachrymal fluids and increased interleukin-6 expression in Harderian gland-derived lymphocytes. However, specific HI antibodies were not detected in the sera of these birds. Because pigs might play a role as a "mixing vessel" for the generation of pandemic influenza viruses we explored the use of RCA-free adenovirus technology to immunize pigs against AI virus. Weanling piglets vaccinated intramuscularly with a single dose of RCA-free AdTW68.H5 developed strong systemic antibody responses 3 wk postvaccination. Intranasal application of AdTW68.H5 in piglets resulted in reduced vaccine coverage, i.e., 33% of pigs (2/6) developed an antibody response, but serum antibody levels in those successfully immunized animals were similar to intramuscularly vaccinated animals.

Generation of antioxidant adenovirus gene transfer vectors encoding CuZnSOD, MnSOD, and catalase

Replication-deficient adenovirus gene transfer vectors are very useful for the experimental delivery of genes into cells and are widely used both in vitro and in vivo to determine the effects of transgene expression. Having a broad cell tropism, these vectors allow efficient transduction of many cell types and permit transfer of large amounts of DNA with resulting high expression levels within the target cell. Manganese superoxide dismutase (MnSOD), copper zinc superoxide dismutase (CuZnSOD) and catalase are all known antioxidants whose over-expression can result in amelioration of pathology brought about by an excess of reactive oxygen species within a cell. Their use has been suggested as therapies for many conditions, including cardiovascular disease, arthritis, diabetes, cancer, and damage to central nervous system cells. This chapter describes the methodology commonly used for production of replication-deficient adenovirus vectors encoding MnSOD, CuZnSOD, and catalase.

Protection of chickens against avian influenza with nonreplicating adenovirus-vectored vaccine

Protective immunity against avian influenza (AI) virus has been elicited in chickens by single-dose in ovo or i.m. vaccination with a replication-competent adenovirus (Ad)-free human Ad vector encoding the AI virus A/Turkey/Wisconsin/68 H5 (AdTW68. H5) or the A/Chicken/New York/94 H7 (AdChNY94. H7) hemagglutinin (HA). The AdTW68.H5-vaccinated chickens were protected against both H5N1 and H5N2 highly pathogenic AI virus challenges. The AdChNY94. H7-vaccinated chickens were protected against an H7N3 highly pathogenic avian influenza virus challenge. Chickens vaccinated in ovo with AdTW68.H5 followed by posthatch i.m. vaccination with AdChNY94.H7 responded to both vaccinations, with robust antibody titers against both the H5 and H7 AI proteins. The use of a synthetic AI H5 HA gene codon optimized to match the tRNA pool found in chicken cells is more potent than the cognate H5 HA gene. Mass administration of this AI vaccine can be streamlined with available robotic in ovo injectors. In addition, Ad5-vectored vaccines can be produced rapidly and the safety margin of the nonreplicating vector is superior to that of a replicating counterpart. Furthermore, this mode of vaccination will not interfere with epidemiological surveys of natural AI infections. Finally, the demonstration that Ad-vectored vaccines can be administered repeatedly without appreciably losing potency highlights the commercial potential of this new class of vaccine in poultry.

Adenovirus as a carrier for the development of influenza virus-free avian influenza vaccines

A long-sought goal during the battle against avian influenza is to develop a new generation of vaccines capable of mass immunizing humans as well as poultry (the major source of avian influenza for human infections) in a timely manner. Although administration of the currently licensed influenza vaccine is effective in eliciting protective immunity against seasonal influenza, this approach is associated with a number of insurmountable problems for preventing an avian influenza pandemic. Many of the hurdles may be eliminated by developing new avian influenza vaccines that do not require the propagation of an influenza virus during vaccine production. Replication-competent adenovirus-free adenovirus vectors hold promise as a carrier for influenza virus-free avian influenza vaccines owing to their safety profile and rapid manufacture using cultured suspension cells in a serum-free medium. Simple and efficient mass-immunization protocols, including nasal spray for people and automated in ovo vaccination for poultry, convey another advantage for this class of vaccines. In contrast to parenteral injection of adenovirus vector, the potency of adenovirus-vectored nasal vaccine is not appreciably interfered by pre-existing immunity to adenovirus.

From the first to the third generation adenoviral vector: what parameters are governing the production yield?

Human adenoviral viral vector serotype 5 (AdV) is presently the primary viral vector used in gene therapy trials. Advancements in AdV process development directly contribute to the clinical application and commercialization of the AdV gene delivery technology. Notably, the development of AdV production in suspension culture has driven the increase in AdV volumetric and specific productivity, therefore providing large quantities of AdV required for clinical studies. This review focuses on detailing the viral, cell and cell culture parameters governing the productivity of the three generations of AdV vectors.

Determination of Particle Heterogeneity and Stability of Recombinant Adenovirus by Analytical Ultracentrifugation in CsCl Gradients

Recombinant adenoviruses (rAd), widely used as vectors for gene therapy, are generally purified by column chromatography and frequently contain empty capsids and other aberrant forms of virus particles. To determine particle heterogeneity we utilized analytical ultracentrifugation (AUC) in CsCl density gradients. Preparations of three different rAd vectors were assessed. AUC was able to resolve multiple density forms including two empty capsid types in various virus preparations. One unusual density form (form V), was noninfectious and lacked protein VI. AUC was able to quantify empty capsids and monitor their removal during process development. Their relative concentrations were reduced by either addition of an immobilized zinc affinity chromatography (IZAC) step or by extension of the infection time. The Adenovirus Reference Material (ARM), a wild-type Ad5, had 2.2% empty capsids and no other detectable minor particle forms. Finally, AUC was utilized to monitor the thermal instability of the three rAd vectors via the transformations of different density forms. The vector and empty capsids containing protein IX were more stable than those without IX. Together, these results exemplify AUC in CsCl density gradients as a valuable technique for evaluating product particle heterogeneity and stability.

A rapid and sensitive assay for detection of replication-competent adenoviruses by a combination of microcarrier cell culture and quantitative PCR

The development of a rapid and sensitive assay for detection of replication-competent adenoviruses (RCAs) is described. This RCA assay consists of an incubation step of 4 days of adenoviral vectors on A549 cells in a microcarrier cell culture system followed by detection of amplified RCAs by E1-specific quantitative PCR. The detection limit of this assay is 3 RCAs in 1 x 10(10) vector particles per 70 ml of microcarrier cell culture. The main advantage of the combination of cell culture and PCR detection is that replicated virus can be detected long before cytopathic effects become visible and therefore, it is much faster than conventional cell culture-based assays. This assay was validated by spiking replication-incompetent adenoviral vectors with wild-type adenovirus serotype 5 (wt Ad5) as a positive control for RCA. It was found that the replication of wt Ad5 is hampered above a vector particle per cell ratio of 50. However, if microcarrier beads are used, many cells can be grown in a small suspension culture and consequently a large number of vector particles can be tested for contamination with RCA.

Automated mass immunization of poultry: the prospect for nonreplicating human adenovirus-vectored in ovo vaccines

Automated in ovo vaccination is an efficient method for mass immunization of poultry. Although in ovo vaccination has been used to mass immunize chickens against several infectious diseases, there are common poultry diseases for which in ovo-compatible vaccines are not commercially available. It was recently demonstrated that in ovo administration of a nonreplicating human adenovirus vector encoding an avian influenza virus hemagglutinin induced protective immunity against highly pathogenic avian influenza. The advantages of this new class of poultry vaccine include in ovo delivery of a wide variety of pathogen-derived antigens, high potency in a single-dose regimen, rapid production in response to increased demand, no replication of the vector, no pre-existing immunity to human adenovirus in chickens, compatibility with automated in ovo administration and no interference with epidemiological surveys of natural infections.

Recommendations for the design, optimization, and qualification of cell-based assays used for the detection of neutralizing antibody responses elicited to biological therapeutics

The administration of biological therapeutics can evoke some level of immune response to the drug product in the receiving subjects. An immune response comprised of neutralizing antibodies can lead to loss of efficacy or potentially more serious clinical sequelae. Therefore, it is important to monitor the immunogenicity of biological therapeutics throughout the drug product development cycle. Immunoassays are typically used to screen for the presence and development of anti-drug product antibodies. However, in-vitro cell-based assays prove extremely useful for the characterization of immunoassay-positive samples to determine if the detected antibodies have neutralizing properties. This document provides scientific recommendations based on the experience of the authors for the development of cell-based assays for the detection of neutralizing antibodies in non-clinical and clinical studies.

Investigations of PEGylated Recombinant Adenovirus, Using Fluorescein-Labeled Polyethylene Glycol

As with certain successful protein drug treatments, the attachment of polyethylene glycol (PEG) molecules to recombinant adenovirus (rAd) can augment their therapeutic potential. Unlike these proteins, the rAd particle has thousands of target sites for PEG conjugation. The reliable measurement of the average number of PEG molecules attached to the virion, or the degree of PEGylation (DP), is crucial not only for the characterization of PEGylated virus but also for optimization of the PEGylation reaction. Using a fluorescein-labeled PEG-SPA linker (SPA, succinimidyl ester of PEG propionic acid) with a 5-kDa linear PEG moiety, multiple preparations of fluoro-PEG-rAds were produced under various reaction conditions, purified, and analyzed by size-exclusion high-performance liquid chromatography (HPLC) with fluorescence quantification of the virus peak. The DP was strongly dependent on the percent linker concentration in the reaction. For example, under one set of conditions, fluoro-PEG-rAd samples prepared at 1.3, 2.5, 5.0, 7.4, and 10.0% linker concentration had DPs of approximately 540, 1,000, 1,590, 1,990, and 2,170, respectively. The fluoro-PEG-rAds were compared with a set of nonfluorescent PEG-rAds. Analytical ultracentrifugation in CsCl density gradients showed distinct peaks at decreased buoyant density corresponding to the increased DP of the rAd samples; sodium dodecyl sulfate-polyacrylamide gel electrophoresis/scanning densitometry showed decreased hexon monomer and penton base. Both techniques were used to estimate the DP of nonfluorescent PEG-rAds versus fluoro-PEG-rAds, and anion-exchange HPLC revealed the different surface chemistries of the two vector types. In summary, these studies should provide investigators with the ability to reproducibly prepare and characterize PEGylated rAds or other large viral or nonviral particles for further in vivo studies.

A replication-competent adenovirus assay for E1-deleted Ad35 vectors produced in PER.C6 cells

The presence of replication-competent adenovirus (RCA) is a safety concern for biologics based on recombinant adenoviruses and RCA testing is therefore mandatory for release of clinical material. RCA, which arises from homologous recombination between Ad5 vectors and HEK-293 cells, can be eliminated by the use of PER.C6 cells in combination with a matched vector. However, little is known on RCA formation with vectors based on adenovirus serotypes other than Ad5 and reliable RCA assays to test them are generally lacking. Here we report on the development and qualification of a sensitive RCA assay for Ad35, a promising alternative to Ad5 vectors. The assay is able to detect 1 RCA in 3x10(10) vector particles with 95% confidence, thus meeting current FDA requirements, and can discriminate between RCA and other rare CPE-causing entities, including helper dependent E1 positive particles (HDEP). Using this assay, the first batches of Ad35 vectors produced in PER.C6 cells were analysed and found to be free of RCA and HDEP. Based on the statistical model used, we anticipate that our approach to RCA assay development can be broadly applicable to other adenoviral vectors.

A new complementing cell line for replication-incompetent E1-deleted adenovirus propagation

Recombinant adenoviruses (Ad) are being explored as promising delivery systems for gene therapy and vaccination. However, there is a concern about the possibility of generating replication-competent adenoviruses (RCA) using the human embryonic kidney 293 cell line. We have constructed a new cell line named the UR cell line which can be used to produce Ad vectors free of RCA. This cell line is based on the human embryonic lung HEL 299 cell. We first constructed a shuttle plasmid which encodes the E1A/E1B sequence that is necessary for adenovirus replication. The shuttle plasmid was then transfected into HEL 299 cells. The presence of the E1A/E1B sequence and protein expression in the stably transformed UR cells was confirmed. Viruses produced in UR cells were still RCA-free after ten test passages, while adenovirus produced in 293 cells had generated RCA during the fourth passage. We conclude that the UR cell line is sufficiently stable, can effectively produce a virus yield comparable with 293 cells, and does not generate RCA formation during Ad propagation.

Protective avian influenza in ovo vaccination with non-replicating human adenovirus vector

Protective immunity against avian influenza virus was elicited in chickens by single-dose in ovo vaccination with a non-replicating human adenovirus vector encoding an H5N9 avian influenza virus hemagglutinin. Vaccinated chickens were protected against both H5N1 (89% hemagglutinin homology; 68% protection) and H5N2 (94% hemagglutinin homology; 100% protection) highly pathogenic avian influenza virus challenges. This vaccine can be mass-administered using available robotic in ovo injectors which provide a major advantage over current vaccination regimens. In addition, this class of adenovirus-vectored vaccines can be produced rapidly with improved safety since they do not contain any replication-competent adenoviruses. Furthermore, this mode of vaccination is compatible with epidemiological surveys of natural avian influenza virus infections.

Purification of adenovirus and adeno-associated virus: comparison of novel membrane-based technology to conventional techniques

Adenovirus (Ad) and Adeno-associated virus (AAV) are efficient gene delivery systems; manipulation of the wild-type genome allows their use as vectors for the overexpression of desirable transgenes. Generation and purification of such viral vectors can be labour intensive, costly and require specialized equipment, but a new generation of membrane-mediated ion exchange kits for purification of recombinant virus may facilitate this process. Here, we examine the yields, transgene expression and purity of preparations of Ad and AAV purified using commercially available kits in comparison to other established techniques for purification of recombinant viral vectors. We demonstrate comparable results for Ad and AAV respectively in all parameters investigated, with a substantial reduction in purification time for the kit-based technology. Such approaches are attractive methods for small-scale purification of recombinant Ad and AAV viral vectors.

Matching complementing functions of transformed cells with stable expression of selected viral genes for production of E1-deleted adenovirus vectors

Production of E1-deleted adenovirus (rAd) vectors requires complementation by E1A and E1B functions provided by the production cell line. The two cell lines most commonly used for production of rAd vectors, 293 and Per.C6, were derived from human primary cells and contain contiguous E1A and E1B sequences from the Ad genome. As an alternative system, we tested complementation of rAd vectors using sequential transfection of individual E1A and E1B expression cassettes into A549 human lung tumor cells, which support highly efficient replication of wild type adenovirus. We found that E1A function could be complemented in A549 cells by the mutant E1Adl01/07, and that E1B function could be provided in such cells using only the 55K E1B gene. Production yields in the resulting producer cell line, designated SL0003, were similar to those obtained from 293 cells without generation of detectable recombinant replication competent adenovirus.

Characterization of changes in PER.C6™ cellular metabolism during growth and propagation of a replication-deficient adenovirus vector

PER.C6 cells were cultivated for propagation of a replication-defective adenovirus vector in serum-free suspension bioreactors. Cellular metabolism during cell growth and adenovirus propagation was fully characterized using on-line and off-line methods. The energy metabolism was found to accelerate transiently after adenovirus infection with increases in glucose and oxygen consumption rates. Similar to other mammalian cells, glucose utilization was highly inefficient and a high lactate:glucose yield was observed, both before and after virus infection. A higher consumption of most of the essential amino acids was observed transiently after the infection, likely due to increased protein synthesis requirements for virus propagation. To improve virus propagation, a medium exchange strategy was implemented to increase PER.C6 cell concentration for infection. During cell growth, a 50% increase in glucose consumption and lactate production rates was observed after initiation of the medium exchange in comparison to the batch phase. This decrease in medium capacity only affected the central carbon metabolism and no increase in amino acid consumption was observed. In addition, even though cell concentrations of up to 10 x 10(6) cells/mL were reproducibly obtained by medium exchange, infections at cell concentrations higher than 1 x 10(6) cells/mL did not proportionally improve volumetric adenovirus productivities. No measured nutrient limitation was observed at those high cell concentrations, indicating that adenovirus cell-specific productivity at higher cell concentrations is highly dependent on cell physiology. These results provide a better understanding of PER.C6 cellular metabolism and a basis for intensifying PER.C6 growth and adenovirus propagation.

Adenovirus protein IX: a new look at an old protein

The success of gene therapy depends in part on our understanding of the biology of gene therapy vectors. This knowledge must be used to improve the function, safety, and versatility of the vector system. For decades, we have known which viral proteins are involved in formation of the adenovirus (Ad) capsid, but we are still learning how these proteins can be altered or manipulated to improve vector function. The Ad protein IX (pIX) was originally identified as a minor component of the Ad capsid, but was not essential for virion formation. However, more recent studies have suggested that pIX may have multiple roles in the Ad life cycle, including acting as a transcriptional activator and reorganizing nuclear proteins to provide an environment more conducive to virus replication. In gene therapy studies, removal of pIX from the Ad vector backbone was used to increase the cloning capacity of E1-deleted Ad vectors and to develop a new method for preparing helper-dependent Ad vectors. pIX has also been at the center of numerous attempts to eliminate the problem of replication-competent Ad in Ad vector preparations. Finally, pIX represents a versatile platform for the presentation of polypeptides on the surface of the viral capsid, including ligands for virus retargeting and fluorescent proteins for visualizing the virus in vitro and in vivo. Thus, the importance and uses of this "minor" capsid protein have changed significantly over the past few years.

Sampling strategies for detecting rare impurities: an application in gene therapy products

Detection of rare impurities in drug products presents special challenges. Replication competent adenovirus (RCA) is a rare impurity found in adenovirus-based gene therapy products. Various methods are used for detection of RCAs. We primarily focus on qualitative assays. Acceptance sampling plans for detecting RCAs in batches of gene therapy products are discussed. Assuming that the number of RCA units per patient dose follows a Poisson distribution, operating characteristics (OC) of these sampling plans can be studied. The OC curves display the acceptance probabilities for batches with specific true but unknown level of RCA and can be used to assess the specificity and sensitivity of the test strategies. Application of Bayesian methodologies in the assessment of RCA levels in drug batches is also discussed. Using observed data and prior belief, a 95% credible region for the number of RCA units per patient dose can be constructed. Both classical and Bayesian calculations display the impact of sample size, sampling fraction, and assay quality on the detection of RCA. For better sensitivity, the largest possible sampling fraction that does not interfere with the logistics and the performance of the assay should be used. The choice of sample size will depend on the upper limit of the biologically safe level of RCA, the testing strategy, the desired level of sensitivity and specificity, and also on practical issues.

Integration and long-term expression in xenografted human glioblastoma cells using a plasmid-based transposon system

Gene therapy has the potential to become an effective component of cancer treatment by transferring genes that cause immunomodulation or tumor cell death or that inhibit angiogenesis into tumor cells or tumor-associated stroma. Viral vectors have been the primary gene transfer vehicles used for intratumoral gene transfer to date. Plasmid-based vectors may be safer and more scalable than viral vectors. However, attempts at plasmid-based intratumoral gene transfer have been met with transient expression and poor gene transfer efficiency. Here we report integration and long-term expression of reporter genes in human glial tumors, growing in nude mice, using the Sleeping Beauty (SB) transposon system. A two-plasmid system was used, in which linear polyethylenimine was complexed with a GFP, NEO, or luciferase transposon plasmid and a SB transposase-expressing plasmid. SB-mediated transposition led to chromosomal integration of the NEO transgene in roughly 8% of tumor cells. SB-mediated insertions were cloned from the genomes of glial tumor cells to provide molecular proof of transposase-mediated integration. Luciferase studies showed that SB facilitated long-term expression of the transgene in glial tumors. SB-mediated intratumoral gene transfer is a novel, nonviral technique that could be used to augment conventional therapy for glioblastoma or other cancers.

Anex vivo human model system to evaluate specificity of replicating and non-replicating gene therapy agents

BACKGROUND

Inefficiency, aspecificity and toxicity of gene transfer vectors hamper gene therapy from showing its full potential. On this basis significant research currently focuses on developing vectors with improved infection and/or expression profiles. Screening assays with validity to the clinical context to determine improved characteristics of such agents are not readily available since this requires a close relationship to the human situation. We present a clinically relevant tissue slice technology to preclinically test improved vector characteristics.

METHODS

Slices were prepared from rat, mouse and human liver samples and from tumor tissue. Specificity of gene expression and replication was determined by infecting target and non-target tissue slices with transcriptionally retargeted adenoviruses and oncolytic viruses.

RESULTS

Using rat liver slices, we demonstrate efficient knob-mediated adenoviral infectivity. A favorable tumor-on/liver-off profile, resembling in vitro and mouse in vivo data, was shown for a tumor-specific transcriptionally retargeted adenovirus by infecting slices prepared from tumor or liver tissue. Similar liver-off data were found for mouse, rat and human samples (over 3-log lower activity of the tumor-specific promoter compared to cytomegalovirus (CMV)). More importantly, we show that this technology when applied to human livers is a powerful tool to determine aspecific replication of oncolytic viruses in liver tissue. A 2- to 6-log reduction in viral replication was observed for a tumor-specific oncolytic virus compared to the wild-type adenovirus.

CONCLUSIONS

The precision-cut tissue slice technology is a powerful method to test specificity and efficiency of gene transfer as well as of viral replication using human tissue.

Sleeping Beauty Transposon‐Mediated Gene Therapy for Prolonged Expression

The Sleeping Beauty (SB) transposon system represents a new vector for non-viral gene transfer that melds advantages of viruses and other forms of naked DNA transfer. The transposon itself is comprised of two inverted terminal repeats of about 340 base pairs each. The SB system directs precise transfer of specific constructs from a donor plasmid into a mammalian chromosome. The excision of the transposon from a donor plasmid and integration into a chromosomal site is mediated by Sleeping Beauty transposase, which can be delivered to cells vita its gene or its mRNA. As a result of its integration in chromosomes, and its lack of viral sequences that are often detected by poorly understood cellular defense mechanisms, a gene in a chromosomally integrated transposon can be expressed over the lifetime of a cell. SB transposons integrate nearly randomly into chromosomes at TA-dinucleotide base pairs although the sequences flanking the TAs can influence the probability of integration at a given site. Although random integration of vectors into human genomes is often thought to raise significant safety issues, evidence to date does not indicate that random insertions of SB transposons represent risks that are equal to those of viral vectors. Here we review the activities of the SB system in mice used as a model for human gene therapy, methods of delivery of the SB system, and its efficacy in ameliorating disorders that model human disease.

Adenoviral-mediated expression of porphobilinogen deaminase in liver restores the metabolic defect in a mouse model of acute intermittent porphyria

The aim of this study was to investigate the potential of gene therapy in the treatment of acute intermittent porphyria (AIP), a disorder caused by a partial deficiency of porphobilinogen deaminase (PBGD), the third enzyme in heme synthesis. The condition is biochemically characterized by accumulation of the porphyrin precursors 5-aminolevulinic acid (ALA) and porphobilinogen (PBG). Here we present the first experiments in vivo using adenoviral vectors to replace the deficient enzyme in the liver of an AIP mouse model. The use of adenoviral vector carrying the cDNA of luciferase in wild-type mice confirmed that transgene expression after intravenous administration was found mainly in liver. When PBGD-deficient mice were administered with adenoviral vector carrying the cDNA of mouse PBGD, the hepatic PBGD activity increased in a dose- and time-dependent manner. The highest activity was found 7 days after injection and remained high after 29 days. The expressed enzyme was shown to correct the metabolic defect in the PBGD-deficient mice as no accumulation of ALA or PBG occurred in plasma, liver, or kidney after induction of heme synthesis by phenobarbital. The study demonstrates that hepatic PBGD expression prevents the accumulation of porphyrin precursors, suggesting a future potential for gene therapy in AIP.

Common structure of rare replication-deficient E1-positive particles in adenoviral vector batches

The use of the PER.C6 adenovirus packaging cell line in combination with a designated vector plasmid system, whereby the cell line and vector with E1 deleted have no sequence overlap, eliminates the generation of replication-competent adenovirus during vector production. However, we have found cytopathic effect (CPE)-inducing particles in 2 out of more than 40 large-scale manufacturing lots produced in PER.C6 cells. The CPE inducer was detected at a frequency of 1 event in 7.5 x 10(12) vector particles. Despite amplification, it was not readily purified, indicating that the agent itself is replication deficient and requires the parental recombinant adenovirus serotype 5 (rAd5) vector for replication and packaging. Therefore, we designated the agent as a helper-dependent E1-positive region containing viral particle (HDEP). Here, we report the molecular structure of the HDEP genome, revealing an Ad comprised of E1 sequences derived from PER.C6 cells flanked by inverted terminal repeat, packaging signal, and transgene sequences. These sequences form a palindromic structure devoid of E2, E3, E4, and late genes. Since only 5 bp were shared between E1 sequences in the PER.C6 genome and viral vector sequences, the data strongly suggested that insertion of genomic DNA into an adenoviral genome had occurred essentially via nonhomologous recombination. HDEPs have been found in unrelated virus batches and appear to share a common structure that may explain their mechanism of generation. This finding allowed development of an HDEP assay to screen batches of rAd5 produced on the PER.C6 cell line and resulted in detection of seven HDEP agents from four different transgene-virus vector constructs in separate batches of Ad.

Liver-Directed Adenoviral Gene Transfer in Murine Succinate Semialdehyde Dehydrogenase Deficiency

Murine succinate semialdehyde dehydrogenase (SSADH) deficiency (OMIM 271980; EC 1.2.1.24), a model of the corresponding human disorder, displays 100% mortality at weeks 3-4 of life, associated with lethal tonic-clonic seizures. The biochemical hallmark, gamma-hydroxybutyrate (GHB), accumulates in both human and murine disorders. In the current study we evaluated rescue of the murine model with liver-directed gene therapy using the E1-deleted adenoviral vector AD:pAD-RSV-humanSSADH. Our working hypotheses were: (1) liver expresses considerable SSADH activity and therefore represents a major source of GHB output, (2) correction of liver enzyme deficiency will reduce GHB load both peripherally and in the central nervous system, and (3) SSADH expression will improve survival. SSADH(-/-) and SSADH(+/+) mice were treated under two protocols: (A) intraperitoneal injection of 10(8)-10(11) viral particles by day 10 of life or (B) retro-orbital injection of 10(11) viral particles at day 13 of life. Intravenous administration was prohibited by the small size and fragility of the mice. Maximal survival (39%; P<0.001) was achieved with intraperitoneal administration (10(8) particles) at day 10; intraperitoneal (10(10) and 10(11) particles) and retro-orbital administration (10(11) particles) yielded lower survival of 11-25% (P<0.02). Under both protocols, the maximal hepatic SSADH enzyme activity was approximately 20% of SSADH(+/+) liver activity (retro-orbital > ip). At various time points postinjection, ip-treated animals (10(8) viral particles) demonstrated upward of 80% reduction in liver GHB concentrations, with little impact on brain or serum GHB levels except at 48-72 h posttreatment (approximately 50% reduction for both tissues). Accordingly, we harvested retro-orbitally treated animals at 72 h and observed significant reductions of 60-70% for GHB in liver, kidney, serum, and brain extracts. Histochemical analysis of liver from retro-orbitally treated mutants demonstrated substantial SSADH staining, but with variability both within tissues and between animals. Our studies provide proof-of-principle that liver-mediated gene therapy has efficacy in treating SSADH deficiency and that hepatic tissue contributes significantly to the pool of GHB within the CNS.

Perfusion cultures of human tumor cells: a scalable production platform for oncolytic adenoviral vectors

This study demonstrates the novel use of the HeLaS3 human tumor cell line for propagating ONYX-411, a recombinant oncolytic adenoviral vector. HeLaS3 cells enabled high levels of vector production without the risk of generating vector recombinants, which is possible with HEK293 cells. The development of a high-cell-density perfusion process using ATF technology yielded production levels as high as 6 x 10(11) vp/mL, which was approximately sevenfold greater than the titers achieved in fed-batch bioreactors. Several experiments were performed at the bench (15 L) and pilot (70 L) scales to demonstrate the robust and scalable nature of this industrially relevant technology.

Detection of replication-competent adenoviruses spiked into recombinant adenovirus vector products by infectivity PCR

The presence of replication-competent adenovirus (RCA) in clinical lots of adenovirus vectors raises a variety of safety concerns. To detect RCA in adenovirus vector products, the cell culture/cytopathic effect (CPE) method has generally been preferred. However, it is difficult to evaluate the amount of RCA clearly and quantitatively by this method. In addition, the cell culture/CPE method requires large-scale cell culturing and a substantial amount of time. For the purpose of establishing a method to detect RCA more sensitively and rapidly, we developed the infectivity PCR, a hybrid method that combines the infectivity assay and quantitative PCR. This method allows RCA to be quantified by real-time quantitative PCR using primers and a probe designed for E1 DNA. By infectivity PCR, 1 pfu of RCA spiked into 10(9) particles of adenovirus vectors could be detected. In contrast, CPE was observed in the cells infected with 10(4) pfu of RCA spiked into 10(9) particles of adenovirus vectors. The glass-beads method was suitable for extracting DNA rapidly from the RCA-infected cells. These results showed that infectivity PCR combined with the glass-beads-based DNA extraction method was useful for the detection of RCA in adenovirus vector products.

Optimization of the generation and propagation of gutless adenoviral vectors

Adenoviral vectors devoid of all viral coding regions are referred to by many names, including gutless vectors. Gutless vectors display reduced toxicity and immunogenicity, increased duration of transgene expression, and increased coding capacity compared to early generation vectors, which contain the majority of the viral backbone genes. However, the production of gutless vectors at a scale and purity suitable for clinical use has limited the utility of this technology. In this work we describe the optimization of the production of gutless vectors. We constructed an improved helper virus and generated an alternative gutless vector producer cell line, PERC6-Cre. We demonstrated increased gutless vector yields, minimal helper virus contamination, and no replication-competent adenovirus contamination using the optimized system. Furthermore, the PERC6-Cre cells were adapted to serum-free suspension culture and high-titer gutless vector preparations were produced using bioreactor technology, suggesting the feasibility of gutless vector scale-up for clinical use. Finally, we observed that helper virus lacking a packaging signal could be packaged at a low frequency, revealing an inherent limitation to the differential packaging strategy for gutless vector propagation.