Development of a novel, high-throughput screening tool for efficient perfusion-based cell culture process development

Perfusion Process Intensification for Lentivirus Production Using a Novel Scale-Down Model

Process intensification has become an important strategy to lower production costs and increase manufacturing capacities for biopharmaceutical products. In particular for the production of viral vectors like lentiviruses (LVs), the transition from (fed-)batch to perfusion processes is a key strategy to meet the increasing demands for cell and gene therapy applications. However, perfusion processes are associated with higher medium consumption. Therefore, it is necessary to develop appropriate small-scale models to reduce development costs. In this work, we present the use of the acoustic wave separation technology in combination with the Ambr 250 high throughput bioreactor system for intensified perfusion process development using stable LV producer cells. The intensified perfusion process developed in the Ambr 250 model, performed at a harvest rate of 3 vessel volumes per day (VVD) and high cell densities, resulted in a 1.4-fold higher cell-specific functional virus yield and 2.8-fold higher volumetric virus yield compared to the control process at a harvest rate of 1 VVD. The findings were verified at bench scale after optimizing the bioreactor set-up, resulting in a 1.4-fold higher cell-specific functional virus yield and 3.1-fold higher volumetric virus yield.

Cell clone selection-impact of operation modes and medium exchange strategies on clone ranking

Bioprocessing has been transitioning from batch to continuous processes. As a result, a considerable amount of resource was dedicated to optimising strategies for continuous production. However, the focus has been on developing a suitable and scalable perfusion strategy with little attention given to the selection of optimal cell clones. Cell line development and lead clone selection are critical to bioprocess development. The screening and selection process is typically performed in stages. Microwell plates (MWP) are used to narrow down the number of clone candidates, which will undergo further selective screening in progressively larger small-scale bioreactors (12 mL-3 L) to identify the top clone for GMP production. Perfusion mode is typically applied at bench-scale for optimisation purposes, while process development and cell clone screening studies at mL-scale still commonly use fed-batch methods. The change of operation mode from bolus feeding to perfusion with a regular exchange of medium, leads to questions regarding the reliability and fit of initial clone selection. Is the early-stage clone ranking impacted by the discrepancy in the operation mode, and does this potentially result in the exclusion of cell clones suitable for perfusion processes? To address this question, we evaluated various CHO cell clones expressing two antibody products using MWP methodologies in fed-batch and semi-perfusion mode. We assessed growth, metabolic, and productivity performance, and ranked cell clones using two different strategies. The first strategy evaluated clones based on a single parameter: the cell-specific productivity (qP). The second considered a collection of multiple parameters using the metric of the Manufacturability index (MICL). Both ranking strategies showed an impact of operation mode and perfusion rate on the clone ranking. Notably, depending on the chosen operation mode, different sets of candidate clones might have been selected for further, more extensive screening. Additionally, we evaluated the reproducibility of our results demonstrating consistency in cell clone growth performance and ranking.

Realization of digital twin for dynamic control toward sample variation of ion exchange chromatography in antibody separation

Digital twin (DT) is a virtual and digital representation of physical objects or processes. In this paper, this concept is applied to dynamic control of the collection window in the ion exchange chromatography (IEC) toward sample variations. A possible structure of a feedforward model-based control DT system was proposed. Initially, a precise IEC mechanistic model was established through experiments, model fitting, and validation. The average root mean square error (RMSE) of fitting and validation was 8.1% and 7.4%, respectively. Then a model-based gradient optimization was performed, resulting in a 70.0% yield with a remarkable 11.2% increase. Subsequently, the DT was established by systematically integrating the model, chromatography system, online high-performance liquid chromatography, and a server computer. The DT was validated under varying load conditions. The results demonstrated that the DT could offer an accurate control with acidic variants proportion and yield difference of less than 2% compared to the offline analysis. The embedding mechanistic model also showed a positive predictive performance with an average RMSE of 11.7% during the DT test under >10% sample variation. Practical scenario tests indicated that tightening the control target could further enhance the DT robustness, achieving over 98% success rate with an average yield of 72.7%. The results demonstrated that the constructed DT could accurately mimic real-world situations and perform an automated and flexible pooling in IEC. Additionally, a detailed methodology for applying DT was summarized.

Miniaturization of hiPSC-derived 3D neural cultures in stirred-tank bioreactors for parallelized preclinical assessment of rAAV

Introduction: Engineered 3D models employing human induced pluripotent stem cell (hiPSC) derivatives have the potential to recapitulate the cell diversity and structure found in the human central nervous system (CNS). Therefore, these complex cellular systems offer promising human models to address the safety and potency of advanced therapy medicinal products (ATMPs), such as gene therapies. Specifically, recombinant adeno-associated viruses (rAAVs) are currently considered highly attractive for CNS gene therapy due to their broad tropism, low toxicity, and moderate immunogenicity. To accelerate the clinical translation of rAAVs, in-depth preclinical evaluation of efficacy and safety in a human setting is primordial. The integration of hiPSC-derived CNS models in rAAV development will require, amongst other factors, robust, small-scale, high-throughput culture platforms that can feed the preclinical trials. Methods: Herein, we pioneer the miniaturization and parallelization of a 200 mL stirred-tank bioreactor-based 3D brain cell culture derived from hiPSCs. We demonstrate the applicability of the automated miniaturized Ambr® 15 Cell Culture system for the maintenance of hiPSC-derived neurospheroids (iNSpheroids), composed of neuronal and glial cells. Critical process parameters were optimized, namely, cell density and agitation mode. Results: Under optimized conditions, stable iNSpheroid cultures were attained in the microbioreactors for at least 15 days, with high cell viability and astrocytic and neuronal phenotype maintenance. This culture setup allowed the parallelization of different rAAVs, in different multiplicity of infections (MOIs), to address rAAV-host interactions at a preclinical scale. The iNSpheroids were exposed to rAAV2- and rAAV9-eGFP in the microbioreactors. Transgene expression was detected 14 days post-transduction, revealing different astrocyte/neuron tropism of the two serotypes. Discussion: We advocate that the iNSpheroid cultures in miniaturized bioreactors are reliable and reproducible screening tools for addressing rAAV transduction and tropism, compatible with preclinical demands.

A novel hybrid bioprocess strategy addressing key challenges of advanced biomanufacturing

Monoclonal antibodies (mAb) are commonly manufactured by either discontinuous operations like fed-batch (FB) or continuous processes such as steady-state perfusion. Both process types comprise opposing advantages and disadvantages in areas such as plant utilization, feasible cell densities, media consumption and process monitoring effort. In this study, we show feasibility of a promising novel hybrid process strategy that combines beneficial attributes of both process formats. In detail, our strategy comprises a short duration FB, followed by a fast media exchange and cell density readjustment, marking the start of the next FB cycle. Utilizing a small-scale screening tool, we were able to identify beneficial process parameters, including FB interval duration and reinoculation cell density, that allow for multiple cycles of the outlined process in a reproducible manner. In addition, we could demonstrate scalability of the process to a 5L benchtop system, using a fluidized-bed centrifuge as scalable media exchange system. The novel process showed increased productivity (+217%) as well as longer cultivation duration, in comparison to a standard FB with a significantly lower media consumption per produced product (-50%) and a decreased need for process monitoring, in comparison to a perfusion cultivation. Further, the process revealed constant glycosylation pattern in comparison to the perfusion cultivation and has strong potential for further scale-up, due to the use of fully scalable cultivation and media exchange platforms. In summary, we have developed a novel hybrid process strategy that tackles the key challenges of current biomanufacturing of either low productivity or high media consumption, representing a new and innovative approach for future process intensification efforts.

The liquid-liquid extractive fermentation of L-lactic acid in a novel semi-partition bioreactor (SPB)

Fermentation technology is commonly used as a mature process to produce numerous products with the help of micro-organisms. However, these organisms are sometimes inhibited by the accumulation of these products or their by-products. One route to circumvent this is via extractive fermentation, which combines the fermentation process with extraction. To facilitate this, novel bioreactor designs are required, such as the semi-partition bioreactor (SPB) which has been recently proposed for in-situ extractive fermentation. The latter combines a fermentation and an extraction unit into a single vessel using a mixer-settler principle. Where the bioproduct is produced in the mixer and removed continuous in the settler. As the SPB functionality is a subject of interest, this study builds on demonstrating different process conditions in the production of a sample bioprocess (lactic acid (LA)) which is susceptible to product inhibition. The results showed a 34.5 g/L LA concentration was obtained in the pH-controlled condition. While LA production can suffer from product inhibition, neutralizing agents can be easily used to curb inhibitory problems, however, the LA fermentation is a simple (and well-studied) example, which can demonstrate an alternative route to avoiding product inhibition (for systems which cannot be rescued using pH control). Hence, to replicate a scenario of product inhibition, two different process conditions were investigated, no pH control with no extraction (non-integrated), and no pH control with integrated extractive fermentation. Key findings showed higher LA concentration in integrated (25.10 g/L) as compared to the non-integrated (14.94 g/L) case with improved yield (0.75 gg^-1 (integrated) versus 0.60 gg^-1 (non-integrated)) and overall productivity (0.35 gL^-1h^-1(integrated) versus 0.20 gL^-1h^-1(non-integrated)) likewise. This is the first demonstration of an SP bioreactor, and shows how the reactor can be applied to improve productivity. Based on these results, the SPB design can be applied to produce any product liable to product inhibition.

Upstream continuous processing: recent advances in production of biopharmaceuticals and challenges in manufacturing

Upstream continuous processing, or most commonly perfusion processing, for biopharmaceutical production, is emerging as a feasible and viable manufacturing approach. Development in production of recombinant therapeutic proteins as well as viral vectors, vaccines, and cell therapy products, has numerous research publications that came out in previous years. Recent research areas are in perfusion-operation strategies maximizing and controlling bioreactor cell density, adding feed solution designed to supplement basal medium feed stream, combining cell line engineering with bioreactor conditions such as hypoxia, and implementing online process monitoring of cell density by capacitance sensor and metabolites by Raman spectroscopy. Perfusion applications are not limited to production process alone but include other upstream areas where high cell density process is essential such as in cell bank preparation, N-1 seed bioreactor, and combination with intensified fed-batch production process. This review covers recent advances in continuous processing over the last two years for biopharmaceutical production.

Soft-sensors application for automated feeding control in high-throughput mammalian cell cultures

The ever-increasing demand for biopharmaceuticals has created the need for improving the overall productivity of culture processes. One such operational concept that is considered is fed-batch operations as opposed to batch operations. However, optimal fed-batch operations require complete knowledge of the cell culture to optimize the culture conditions and the nutrients feeding. For example, when using high-throughput small-scale bioreactors to test multiple clones that do not behave the same, depletion or overfeeding of some key components can occur if the feeding strategy is not individually optimized. Over the recent years, various solutions for real-time measuring of the main cell culture metabolites have been proposed. Still, the complexity in the implementation of these techniques has limited their use. Soft-sensors present an opportunity to overcome these limitations by indirectly estimate these variables in real-time. This manuscript details the development of a new soft-sensor based fed-batch strategy to maintain substrate concentration (glucose and glutamine) at optimal levels in small-scale multi parallel CHO cultures. Two alternatives to the standard feeding strategy were tested: an OUR soft-sensor-based strategy for glucose and glutamine (Strategy 1) and a dual OUR for glutamine and CO₂ /alkali addition for glucose soft-sensor strategy (Strategy 2). The results demonstrated the applicability of the OUR soft-sensor based strategy to optimize glucose and glutamine feedings, which yielded a 21% increase in final viable cell density (VCD) and a 31% in erythropoietin (EPO) titer compared with the reference one. However, CO2/alkali addition soft-sensor suffered from insufficient data to relate alkali addition with glucose consumption. As a result, the culture was overfed with glucose resulting in a 4% increase on final VCD, but a 9% decrease in final titer compared to the Reference Strategy. This article is protected by copyright. All rights reserved.

Deep Learning in Therapeutic Antibody Development

Deep learning applied to antibody development is in its adolescence. Low data volumes and biological platform differences make it challenging to develop supervised models that can predict antibody behavior in actual commercial development steps. But successes in modeling general protein behaviors and early antibody models give indications of what is possible for antibodies in general, particularly since antibodies share a common fold. Meanwhile, new methods of data collection and the development of unsupervised and self-supervised deep learning methods like generative models and masked language models give the promise of rich and deep data sets and deep learning architectures for better supervised model development. Together, these move the industry toward improved developability , lower costs, and broader access of biotherapeutics .

Perfusion culture of Chinese Hamster Ovary cells for bioprocessing applications

Much of the biopharmaceutical industry's success over the past 30 years has relied on products derived from Chinese Hamster Ovary (CHO) cell lines. During this time, improvements in mammalian cell cultures have come from cell line development and process optimization suited for large-scale fed-batch processes. Originally developed for high cell densities and sensitive products, perfusion processes have a long history. Driven by high volumetric titers and a small footprint, perfusion-based bioprocess research has regained an interest from academia and industry. The recent pandemic has further highlighted the need for such intensified biomanufacturing options. In this review, we outline the technical history of research in this field as it applies to biologics production in CHO cells. We demonstrate a number of emerging trends in the literature and corroborate these with underlying drivers in the commercial space. From these trends, we speculate that the future of perfusion bioprocesses is bright and that the fields of media optimization, continuous processing, and cell line engineering hold the greatest potential. Aligning in its continuous setup with the demands for Industry 4.0, perfusion biomanufacturing is likely to be a hot topic in the years to come.

Miniature auto-perfusion bioreactor system with spiral microfluidic cell retention device

Medium perfusion is critical in maintaining high cell concentration in cultures. The conventional membrane filtration method for medium exchange has been challenged by the fouling and clogging of the membrane filters in long-term cultures. In this study, we present a miniature auto-perfusion system that can be operated inside a common-size laboratory incubator. The system is equipped with a spiral microfluidic chip for cell retention to replace conventional membrane filters, which fundamentally overcomes the clogging and fouling problem. We showed that the system supported continuous perfusion culture of Chinese hamster ovary (CHO) cells in suspension up to 14 days without cell retention chip replacement. Compared to daily manual medium change, 25% higher CHO cell concentration can be maintained at an average auto-perfusion rate of 196 ml/day in spinner flask at 70 ml working volume (2.8 VVD). The auto-perfusion system also resulted in better cell quality at high concentrations, in terms of higher viability, more uniform and regular morphology, and fewer aggregates. We also demonstrated the potential application of the system for culturing mesenchymal stem cells on microcarriers. This miniature auto-perfusion system provides an excellent solution to maintain cell-favorable conditions and high cell concentration in small-scale cultures for research and clinical uses.

Traces matter: Targeted optimization of monoclonal antibody N-glycosylation based on/by implementing automated high-throughput trace element screening

The use of high-throughput systems in cell culture process optimization offers various opportunities in biopharmaceutical process development. Here we describe the potential for acceleration and enhancement of product quality optimization and de novo bioprocess design regarding monoclonal antibody N-glycosylation by using an iterative statistical Design of Experiments (DoE) strategy based on our automated microtiter plate-based system for suspension cell culture. In our example, the combination of an initial screening of trace metal building blocks with a comprehensive DoE-based screening of 13 different trace elemental ions at three concentration levels in one run revealed most effective levers for N-glycan processing and biomass formation. Obtained results served to evaluate optimal concentration ranges and the right supplementation timing of relevant trace elements at shake flask and 2 L bioreactor scale. This setup identified manganese, copper, zinc, and iron as major factors. Manganese and copper acted as inverse key players in N-glycosylation, showing a positive effect of manganese and a negative effect of copper on glycan maturation in a zinc-dependent manner. Zinc and iron similarly improved cell growth and biomass formation. These findings allowed determining optimal concentration ranges for all four trace elements to establish control on desired product quality attributes regarding premature afucosylated and mature galactosylated glycan species. Our results demonstrates the power of combining robotics with DoE screening to enhance product quality optimization and to improve process understanding, thus, enabling targeted product quality control.

Recent Developments in Bioprocessing of Recombinant Proteins: Expression Hosts and Process Development

Infectious diseases, along with cancers, are among the main causes of death among humans worldwide. The production of therapeutic proteins for treating diseases at large scale for millions of individuals is one of the essential needs of mankind. Recent progress in the area of recombinant DNA technologies has paved the way to producing recombinant proteins that can be used as therapeutics, vaccines, and diagnostic reagents. Recombinant proteins for these applications are mainly produced using prokaryotic and eukaryotic expression host systems such as mammalian cells, bacteria, yeast, insect cells, and transgenic plants at laboratory scale as well as in large-scale settings. The development of efficient bioprocessing strategies is crucial for industrial production of recombinant proteins of therapeutic and prophylactic importance. Recently, advances have been made in the various areas of bioprocessing and are being utilized to develop effective processes for producing recombinant proteins. These include the use of high-throughput devices for effective bioprocess optimization and of disposable systems, continuous upstream processing, continuous chromatography, integrated continuous bioprocessing, Quality by Design, and process analytical technologies to achieve quality product with higher yield. This review summarizes recent developments in the bioprocessing of recombinant proteins, including in various expression systems, bioprocess development, and the upstream and downstream processing of recombinant proteins.

Development of a novel, high-throughput screening tool for efficient perfusion-based cell culture process development

Perfusion technology has been successfully used for the commercial production of biotherapeutics, in particular unstable recombinant proteins, for more than a decade. However, there has been a general lack of high‐throughput cell culture tools specifically for perfusion‐based cell culture processes. Here, we have developed a high‐throughput cell retention operation for use with the ambr® 15 bioreactor system. Experiments were run in both 24 and 48 reactor configurations for comparing perfusion mimic models, media development, and clone screening. Employing offline centrifugation for cell retention and a variable volume model developed with MATLAB computational software, the established screening model has demonstrated cell culture performance, productivity, and product quality were comparable to bench scale bioreactors. The automated, single use, high‐throughput perfusion mimic is a powerful tool that enables us to have rapid and efficient process development of perfusion‐based cell culture processes.