Recombinant adeno-associated virus production evaluation in Chinese hamster ovary cells.

The gene therapy field has advanced in recent years with five recombinant adeno-associated virus (rAAV) based products winning Food and Drug Administration (FDA) approval. As the number of therapeutic applications and overall production demands for rAAV increase, it is valuable to evaluate rAAV production in different production cells. Chinese hamster ovary (CHO) cells have been a robust host for biomolecule manufacturing for more than 35 years. However, there is no report to our knowledge describing the use of CHO cells for rAAV production. In this study, we examined the ability of CHO cells to produce rAAV using a transient plasmid transfection approach. Our results demonstrated that CHO is capable of producing rAAV with detectable viral fundamental components including viral RNAs, proteins, and rAAV viral particles. We identified the expression of cap proteins as one of the limiting factors for rAAV production in CHO cells. We therefore added an additional cytomegalovirus (CMV)-Cap plasmid to the CHO transfection. After increasing cap protein expression, we detected rAAV titers as high as 3 × 108 viral genomes for every 2 × 109 capsids in CHO cells using a quintuple transfection method (standard AAV2 Rep/Cap, helper, gene of interest plasmids, plus CMV-E1, and CMV-Cap plasmids) with comparable full particle percent (average 15%) to that of human embryo kidney (HEK)-derived rAAV. Our study provides a foundation for potential rAAV production in CHO cells.

Assessing TCR identity, knock-in efficiency, and potency for individualized TCR-T cell therapy.

Advances in mass spectrometry, genome sequencing techniques, and bioinformatic strategies have accelerated the discovery of cancer-specific neoantigens. Tumors express multiple immunogenic neoantigens, and neoantigen-specific T cell receptors (TCRs) can be identified in peripheral blood's mononuclear cells in cancer patients. Therefore, individualized TCR-based therapies are a promising approach whereby multiple neoantigen-specific TCRs can be selected in each patient, potentially leading to a highly effective treatment for cancer patients. We developed three multiplex analytical assays to determine the quality attributes of the TCR-T cell drug product with a mixture of five engineered TCRs. The identity of each TCR was determined by two NGS-based methods, Illumina MiSeq and PacBio platforms. This approach not only confirms the expected TCR sequences but also differentiates them by their variable regions. The five individual TCR and total TCR knock-in efficiencies were measured by droplet digital PCR using specific reverse primers. A potency assay based on transfection of antigen-encoding-RNA was developed to assess the dose-dependent activation of T cells for each TCR by measuring the surface activation marker CD137 expression and cytokine secretion. This work provides new assays to characterize individualized TCR-T cell products and insights into quality attributes for the control strategy.

Revisiting mouse minute virus inactivation by high temperature short time treatment.

In recent years, high temperature short time (HTST) treatment technology has been increasingly adopted for medium treatment to mitigate the potential risk of viral contamination in mammalian cell culture GMP manufacturing facilities. Mouse minute virus (MMV), also called minute virus of mice (MVM), implicated in multiple viral contamination events is commonly used as a relevant model virus to assess the effectiveness of HTST treatment of cell culture media. However, results from different studies vary broadly in inactivation kinetics as well as log reduction factors (LRFs) achieved under given treatment conditions. To determine whether the reported discrepancies stemmed from differences in MMV strains, laboratory-scale HTST devices, medium matrices, and/or experimental designs, we have taken a collaborative approach to systematically assess the effectiveness of HTST treatment for MMV inactivation. This effort was conceptualized based on a media treatment gap analysis conducted by the Consortium on Adventitious Agent Contamination in Biomanufacturing (CAACB) under the MIT Center for Biomedical Innovation (CBI). Specifically, two different MMV strains were used to evaluate the effectiveness of HTST at various treatment conditions with regard to exposure temperature and hold time duration by two independent laboratories within two different companies. To minimize experimental variations, the two sites used the same batches of MMV stocks, the same commercially purchased medium, and the same model of thermocyclers as the laboratory-scale HTST device. The two independent laboratories yielded similar MMV inactivation kinetics and comparable LRF. No significant differences were observed between the two MMV strains evaluated, suggesting that the variations from prior studies were likely due to differences in equipment, medium matrices, or other factors. The data presented here indicate that MMV inactivation by HTST treatment obeys first-order kinetics and can be mathematically modeled using an Arrhenius equation. The model-based extrapolation provides a quantitative estimate of MMV inactivation by the current industry standard HTST condition (102°C for a hold time of 10 s) used for medium treatment. Finally, based on the data from the current study and the industry experience, it is recommended that any alternative virus barrier technologies adopted for medium treatment should provide a clearance of at least 3.0 LRF based on a worst-case model virus to effectively mitigate potential risks of viral contamination.

Identification and characterization of a Triton X-100 replacement for virus inactivation.

Triton X-100 detergent treatment is a robust enveloped virus inactivation unit operation included in biopharmaceutical manufacturing processes. However, the European Commission officially placed Triton X-100 on the Annex XIV authorization list in 2017 because a degradation product of Triton X-100, 4-(1,1,3,3-tetramethylbutyl) phenol (also known as 4-tert-octylphenol), is considered to have harmful endocrine disrupting activities. As a result, the use of Triton X-100 in the European Economic Area (EEA) would not be allowed unless an ECHA issued authorization was granted after the sunset date of January 4, 2021. This has prompted biopharmaceutical manufacturers to search for novel, environment-friendly alternative detergents for enveloped virus inactivation. In this study, we report the identification of such a novel detergent, Simulsol SL 11W. Simulsol SL 11W is an undecyl glycoside surfactant produced from glucose and C11 fatty alcohol. We report here that Simulsol SL 11W was able to effectively inactive enveloped viruses, such as xenotropic murine leukemia virus (XMuLV) and pseudorabies virus (PRV). By using XMuLV as a representative enveloped virus, the influence of various parameters on the effectiveness of virus inactivation was evaluated. Virus inactivation by Simulsol SL 11W was effective across different clarified bioreactor harvests at broad concentrations, pH, and temperature ranges. Simulsol SL 11W concentration, temperature of inactivation, and treatment time were identified as critical process parameters for virus inactivation. Removal of Simulsol SL 11W was readily achieved by Protein A chromatography and product quality was not affected by detergent treatment. Taken together, these results have shown the potential of Simulsol SL 11W as a desirable alternative to Triton X-100 for enveloped virus inactivation that could be readily implemented into biopharmaceutical manufacturing processes.

Viral contamination in biologic manufacture and implications for emerging therapies.

Recombinant protein therapeutics, vaccines, and plasma products have a long record of safety. However, the use of cell culture to produce recombinant proteins is still susceptible to contamination with viruses. These contaminations cost millions of dollars to recover from, can lead to patients not receiving therapies, and are very rare, which makes learning from past events difficult. A consortium of biotech companies, together with the Massachusetts Institute of Technology, has convened to collect data on these events. This industry-wide study provides insights into the most common viral contaminants, the source of those contaminants, the cell lines affected, corrective actions, as well as the impact of such events. These results have implications for the safe and effective production of not just current products, but also emerging cell and gene therapies which have shown much therapeutic promise.

Insights into virus inactivation by polysorbate 80 in the absence of solvent.

Triton X-100 has long been used either alone or in combination with solvent to inactivate enveloped viruses in biopharmaceutical manufacturing. However, European Chemicals Agency (ECHA) officially placed Triton X-100 on the Annex XIV authorization list in 2017 because 4-(1,1,3,3-tetramethylbutyl) phenol, a degradation product of Triton X-100, is of harmful endocrine disrupting activities. As a result, any use of Triton X-100 in the European Economic Area would require an ECHA issued authorization after the sunset date of January 4, 2021. In search of possible replacements for Triton X-100, we discovered that polysorbate 80 (PS80) in absence of any solvents was able to effectively inactive enveloped viruses such as xenotropic murine leukemia virus and pseudorabies virus with comparable efficacy as measured by log reduction factors. Interestingly, PS80 did not show any virucidal activities in phosphate buffered saline (PBS) while achieving robust virus inactivation in cell-free Chinese hamster ovary (CHO) bioreactor harvests. This intriguing observation led us to speculate that virus inactivation by PS80 involved components in the cell-free CHO bioreactor harvests that were absent in PBS. Specifically, we hypothesized that esterase and/or lipases in the cell-free bioreactor harvests hydrolyzed PS80 to yield oleic acid, a known potent virucidal agent, which in turn inactivated viruses. This theory was confirmed using purified recombinant lysosomal phospholipase A2 isomer (rLPLA2) in PBS. Subsequent characterization work has indicated that virus inactivation by PS80 is effective and robust within temperature and concentration ranges comparable to those of Triton X-100. Similar to Triton X-100, virus inactivation by PS80 is dually dependent on treatment time and temperature. Unlike Triton X-100, PS80 inactivation does not correlate with concentrations in a simple manner. Additionally, we have demonstrated that PS20 exhibits similar virus inactivation activities as PS80. Based on the findings described in the current work, we believe that PS80 is potentially a viable replacement for Triton X-100 and can be used in manufacturing processes for wide spectrum of biopharmaceuticals to achieve desirable virus clearance. Finally, the advantages and disadvantages of using PS80 for virus inactivation are discussed in the contexts of GMP manufacturing.

Understanding lipopolysaccharide aggregation and its influence on activation of Factor C.

The quantification of lipopolysaccharide (LPS) shed by bacteria within aqueous samples is typically performed by binding LPS to a protein called Factor C within a lysate prepared from the blood of horseshoe crabs (Limulus amebocyte lysate (LAL)). How the state of aggregation of LPS impacts Factor C activation, however, is not understood, particularly in the presence of select salts and non-ionic surfactants that are commonly incorporated into pharmaceutical formulations. To address this open question, herein we report on the aggregation status of LPS in aqueous solution, characterized using angle-dependent static and dynamic light scattering with and without chelating salts and polysorbate surfactants, and its correlation with activation of Factor C. Because the aggregation status of LPS is kinetically controlled, care was taken to compare LPS aggregation and activity using identically prepared samples. By plotting LPS activity versus the LPS aggregate size distribution over varied solution conditions, we found a positive correlation between LPS aggregate sizes between 30 and 50 nm and LAL activity. Overall, our results support the hypothesis that activation of Factor C is dependent of LPS aggregate size, and that the modulating effects of salts and surfactants on activation of Factor C is associated with changes in the LPS aggregation.

New insights into the performance characteristics of the Planova-series hollow-fiber parvovirus filters using confocal and electron microscopy.

Virus filtration remains a critical step in the downstream process for the production of monoclonal antibodies and other mammalian cell-derived biotherapeutics. Recent studies have shown large differences in virus capture behavior of different virus filters, although the origin of these differences is still unclear. The objective of this study was to use confocal and scanning electron microscopy to directly evaluate the capture of virus-size nanoparticles in Planova 20N and BioEX hollow-fiber virus filters. Confocal images of fluorescent nanoparticles were quantified using ImageJ image processing software based on the measured fluorescence intensity of the labeled nanoparticles. Nanoparticle capture by the Planova BioEX was independent of transmembrane pressure from 10 to 45 psi. In contrast, the Planova 20N showed significant differences in nanoparticle capture profile at low pressure, consistent with literature data showing virus breakthrough under these conditions. Images obtained after a process interruption show significant migration of previously captured nanoparticles in the Planova 20N filters but not in the BioEX. These results provide important insights into the nature of virus capture in different virus filters and its dependence on the underlying structure of the virus filtration membranes.

Proceedings of the 2017 Viral Clearance Symposium, Session 1.1: Upstream Mitigation, Part 1-Cell Bank and Bulk Harvest Testing.

Monoclonal antibodies (mAbs) are typically produced using mammalian cell lines, which are known to express endogenous retrovirus-like particles (RVLPs) and also have the potential to be infected by viruses. This session focused on the detection and measurement of these viruses and RVLPs. In the first session, it was shown that next-generation sequencing (NGS) can detect, with a similar sensitivity as polymerase chain reaction (PCR), viruses in cells without a priori knowledge of the specific virus and more importantly that a specific NGS approach can decipher whether the signal corresponds to a replicating virus. The second session provided data showing that the PCR assay for detection of ecotropic recombinant virus (ERV) genome is an alternative to quantification by transmission electron microscopy (qTEM) for quantification of RVLP. In addition, the potential use of a harvest filter for RVLP retention in a perfusion process was discussed. In the third session, RVLP data from 67 different Pfizer programs spanning different conditions were presented. No single factor had a significant impact on the level of RVLPs. It was suggested that a "generic" or "worst-case" RVLP value, derived from a well-characterized platform cell culture process, could be used with confidence to determine a conservative retroviral safety margin for platform processes. In the fourth session, the sensitivity of several cell culture- and PCR-based assays for detection of different MMV strains using several production cells was discussed. It was found that molecular assays were generally superior in the breadth of detection with equivalent sensitivity.LAY ABSTRACT: This session focused on the detection and measurement of viruses and virus-like particles in cell lines and manufacturing processes used for production of therapeutic proteins.

Proceedings of the 2017 Viral Clearance Symposium, Session 1.2: Upstream Mitigation, Part 2-Virus Barrier Filter and HTST.

Various mammalian cell lines are used as substrates for drug production without safety issues concerning viral contamination. However, viral contamination events in good manufacturing practice (GMP) cell culture processes, while rare, do sometimes occur. When contamination happens, it can result in serious consequences, including supply risk of life-saving drugs and substantial financial loss. To mitigate the potential risk of viral contamination, one approach taken by the industry is to implement preventative measures upstream. High-temperature short-time (HTST) treatment of culture media, at the point of use, was implemented as a virus barrier following murine minute virus (MMV) contamination. In recent years, nanofiltration, commonly used in downstream purification processes, has been evaluated for potential use as a virus barrier alternative to HTST. Several companies shared their data and experience in evaluating nanofiltration for viral barrier purpose upstream in Session 1, Part 2: Virus Barrier. These presentations are summarized below.LAY ABSTRACT: Viral contamination events in GMP cell culture processes, while rare, do sometimes occur. When contamination happens, it can result in serious consequences, including supply risk of life-saving drugs and substantial financial loss. To mitigate the potential risk of viral contamination, one approach taken by the industry is to implement preventative measures upstream. Several companies shared their data and experience in evaluating virus-retentive filtration for viral barrier purpose upstream.

Endotoxin recovery using limulus amebocyte lysate (LAL) assay.

A phenomenon initially reported by Chen and Vinther in 2013 [1], and now commonly referred to as low endotoxin recovery (LER), has prompted the Food and Drug Administration (FDA) to request specific data demonstrating the capability of the LAL BET method (i.e., USP <85>) to recover endotoxin from spiked samples over time. The results of these spike/hold recovery studies are expected to be included in the Biologics License Applications (BLA) for review by the Center for Drug Evaluation and Research (CDER) Hughes (2014) and Hughes et al. (2015) [2,3]. Such studies involve spiking a known amount of a surrogate endotoxin, such as purified lipopolysaccharide (LPS), into undiluted biological products and then testing at different time points to determine the recovery over time. We report here the experience and learning gained from conducting spike/hold recovery studies for a monoclonal antibody (Mab) product. Results from initial hold studies spiked with purified LPS showed rapid loss of endotoxin activity in the drug substance (DS) and significant batch-to-batch variation in the drug product (DP). After careful review and examination of the experimental details, it was determined that the study design and execution differed from the routine batch release USP <85> BET method with regard to mixing time and sampling scheme. The hold study design was subsequently revised so that the mixing time and sampling were the same as the verified USP <85> BET method used for routine batch release testing. The spike/hold recovery studies were repeated and the results demonstrated that LPS could be consistently recovered over time. These findings highlight the importance of carefully controlling sample preparation procedures in a spike/hold recovery study in order to demonstrate the suitability of using the LAL BET method for endotoxin detection.

Meeting Report: 2015 PDA Virus & TSE Safety Forum.

The report provides a summary of the presentations at the Virus & TSE Safety Forum 2015 organized by the Parenteral Drug Association (PDA) and held in Cascais, Portugal, from 9 to 11 June, 2015. As with previous conferences of this series, the PDA Virus & TSE Safety Forum 2015 provided an excellent forum for the exchange of information and opinions between the industry, research organizations, and regulatory bodies. Regulatory updates on virus and TSE safety aspects illustrating current topics of discussion at regulatory agencies in Europe and the United States were provided; the conference covered emerging viruses and new virus detection systems that may be used for the investigation of human pathogenic viruses as well as the virus safety of cell substrates and of raw material of ovine/caprine or human origin. Progress of development and use of next-generation sequencing methods was shown by several examples. Virus clearance data illustrating the effectiveness of inactivation or removal methods were presented and data provided giving insight into the mechanism of action of these technologies. In the transmissible spongiform encephalopathy (TSE) part of the conference, the epidemiology of variant Creutzfeldt-Jakob disease was reviewed and an overview about diagnostic tests provided; current thinking about the spread and propagation of prions was presented and the inactivation of prions by disinfection (equipment) and in production of bovine-derived reagents (heparin) shown. The current report provides an overview about the outcomes of the 2015 PDA Virus & TSE Safety Forum, a unique event in this field.

Mechanistic evaluation of virus clearance by depth filtration.

Virus clearance by depth filtration has not been well-understood mechanistically due to lack of quantitative data on filter charge characteristics and absence of systematic studies. It is generally believed that both electrostatic interactions and sized based mechanical entrapment contribute to virus clearance by depth filtration. In order to establish whether the effectiveness of virus clearance correlates with the charge characteristics of a given depth filter, a counter-ion displacement technique was employed to determine the ionic capacity for several depth filters. Two depth filters (Millipore B1HC and X0HC) with significant differences in ionic capacities were selected and evaluated for their ability to eliminate viruses. The high ionic capacity X0HC filter showed complete porcine parvovirus (PPV) clearance (eliminating the spiked viruses to below the limit of detection) under low conductivity conditions (≤2.5 mS/cm), achieving a log10 reduction factor (LRF) of > 4.8. On the other hand, the low ionic capacity B1HC filter achieved only ∼2.1-3.0 LRF of PPV clearance under the same conditions. These results indicate that parvovirus clearance by these two depth filters are mainly achieved via electrostatic interactions between the filters and PPV. When much larger xenotropic murine leukemia virus (XMuLV) was used as the model virus, complete retrovirus clearance was obtained under all conditions evaluated for both depth filters, suggesting the involvement of mechanisms other than just electrostatic interactions in XMuLV clearance.

Meeting Report: 2013 PDA Virus & TSE Safety Forum.

The report provides a summary of the presentations and discussions at the Virus & TSE Safety Forum 2013 organized by the Parenteral Drug Association (PDA) and held in Berlin, Germany, from June 4 to 6, 2013. The conference was accompanied by a workshop, "Virus Spike Preparations and Virus Removal by Filtration: New Trends and Developments". The presentations and the discussion at the workshop are summarized in a separate report that will be published in this issue of the journal as well. As with previous conferences of this series, the PDA Virus & TSE Safety Forum 2013 provided again an excellent opportunity to exchange information and opinions between the industry, research organizations, and regulatory bodies. Updates on regulatory considerations related to virus and transmissible spongiform encephalopathy (TSE) safety of biopharmaceuticals were provided by agencies of the European Union (EU), the United States (US), and Singapore. The epidemiology and detection methods of new emerging pathogens like hepatitis E virus and parvovirus (PARV 4) were exemplified, and the risk of contamination of animal-derived raw materials like trypsin was considered in particular. The benefit of using new sequence-based virus detection methods was discussed. Events of bioreactor contaminations in the past drew the attention to root cause investigations and preventive actions, which were illustrated by several examples. Virus clearance data of specific unit operations were provided; the discussion focused on the mechanism of virus clearance and on the strategic concept of viral clearance integration. As in previous years, the virus safety section was followed by a TSE section that covered recent scientific findings that may influence the risk assessment of blood and cell substrates. These included the realization that interspecies transmission of TSE by blood components in sheep is greater than predicted by assays in transgenic mice. Also, the pathogenesis and possibility of productive TSE infection of cell substrates were considered, and cell-based assays that may be suitable for use in TSE clearance studies were discussed. The current report provides an overview about the outcomes of the 2013 PDA Virus & TSE Safety Forum, a unique event in this field.

Meeting report-workshop on spike characterizations and virus removal by filtration: trends and new developments.

This workshop was held on June 3, 2013, in Berlin, Germany, in conjunction with the PDA Virus & TSE Safety Forum 2013. A total of nine speakers presented on key considerations of virus filtration, including a historical overview and emerging trends in evaluating parvovirus filters. Several talks addressed understanding the mechanism of virus capture and breakthrough by filters, as well as addressing this risk by carefully controlling transmembrane pressure. Improvements to validation studies were proposed via the use of highly purified virus preparations, more relevant models such as Chinese Hamster Ovary retrovirus-like particles, as well as new assays for virus quantification. The workshop ended with a panel discussion covering a range of topics including virus breakthrough, up-stream media treatment, virus spike preparation quality control, and regulatory expectations.

Safety assurance for biologics manufactured in mammalian cell cultures: a multitiered strategy.

Contamination by viral and microbial agents is a serious risk for biopharmaceuticals produced by mammalian cell culture processes. In order to effectively mitigate the risk and minimize the occurrence of such contamination events, a multi-tiered approach has been adopted to safeguard the manufacturing processes from A to Z. The multi-tiered approach consists of three separate, yet complementary, elements: (1) control and testing of raw materials in general, and animal sourced materials (ASM) in particular; (2) in-process and release testing for adventitious agents with emphasis on viruses based on risk assessment; and (3) demonstration of an adequate, robust, and consistent viral clearance capability by the downstream purification process. The implementations of these measures will be described in the context of regulatory compliance and GMP manufacturing.

A novel approach to achieving modular retrovirus clearance for a parvovirus filter.

Viral filtration is routinely incorporated into the downstream purification processes for the production of biologics produced in mammalian cell cultures (MCC) to remove potential viral contaminants. In recent years, the use of retentive filters designed for retaining parvovirus (~20 nm) has become an industry standard in a conscious effort to further improve product safety. Since retentive filters remove viruses primarily by the size exclusion mechanism, it is expected that filters designed for parvovirus removal can effectively clear larger viruses such as retroviruses (~100 nm). In an attempt to reduce the number of viral clearance studies, we have taken a novel approach to demonstrate the feasibility of claiming modular retrovirus clearance for Asahi Planova 20N filters. Porcine parvovirus (PPV) and xenotropic murine leukemia virus (XMuLV) were co-spiked into six different feedstreams and then subjected to laboratory scale Planova 20N filtration. Our results indicate that Planova 20N filters consistently retain retroviruses and no retrovirus has ever been detected in the filtrates even when significant PPV breakthrough is observed. Based on the data from multiple in-house viral validation studies and the results from the co-spiking experiments, we have successfully claimed a modular retrovirus clearance of greater than 6 log10 reduction factors (LRF) to support clinical trial applications in both USA and Europe.