Metabolic Control in Mammalian Fed-Batch Cell Cultures for Reduced Lactic Acid Accumulation and Improved Process Robustness

Intensified Influenza Virus Production in Suspension HEK293SF Cell Cultures Operated in Fed-Batch or Perfusion with Continuous Harvest

Major efforts in the intensification of cell culture-based viral vaccine manufacturing focus on the development of high-cell-density (HCD) processes, often operated in perfusion. While perfusion operations allow for higher viable cell densities and volumetric productivities, the high perfusion rates (PR) normally adopted-typically between 2 and 4 vessel volumes per day (VVD)-dramatically increase media consumption, resulting in a higher burden on the cell retention device and raising challenges for the handling and disposal of high volumes of media. In this study, we explore high inoculum fed-batch (HIFB) and low-PR perfusion operations to intensify a cell culture-based process for influenza virus production while minimizing media consumption. To reduce product retention time in the bioreactor, produced viral particles were continuously harvested using a tangential flow depth filtration (TFDF) system as a cell retention device and harvest unit. The feeding strategies developed-a hybrid fed-batch with continuous harvest and a low-PR perfusion-allowed for infections in the range of 8-10 × 106 cells/mL while maintaining cell-specific productivity comparable to the batch control, resulting in a global increase in the process productivity. Overall, our work demonstrates that feeding strategies that minimize media consumption are suitable for large-scale influenza vaccine production.

Process engineering of natural killer cell-based immunotherapy

Cell therapy offers the potential for curative treatment of cancers. Although T cells have been the predominantly used cell type, natural killer (NK) cells have attracted great attention owing to their ability to kill cancer cells and because they are naturally suitable for allogeneic applications. Upon stimulation by cytokines or activation by a target cell, NK cells proliferate and expand their population. These cytotoxic NK cells can be cryopreserved and used as an off-the-shelf medicine. The production process for NK cells thus differs from that of autologous cell therapies. We briefly outline key biological features of NK cells, review the manufacturing technologies for protein biologics, and discuss their adaptation for developing robust NK cell biomanufacturing processes.

Next-generation cell line selection methodology leveraging data lakes, natural language generation and advanced data analytics

Cell line development is an essential stage in biopharmaceutical development that often lies on the critical path. Failure to fully characterise the lead clone during initial screening can lead to lengthy project delays during scale-up, which can potentially compromise commercial manufacturing success. In this study, we propose a novel cell line development methodology, referenced as CLD ₄, which involves four steps enabling autonomous data-driven selection of the lead clone. The first step involves the digitalisation of the process and storage of all available information within a structured data lake. The second step calculates a new metric referenced as the cell line manufacturability index (MI _CL) quantifying the performance of each clone by considering the selection criteria relevant to productivity, growth and product quality. The third step implements machine learning (ML) to identify any potential risks associated with process operation and relevant critical quality attributes (CQAs). The final step of CLD ₄ takes into account the available metadata and summaries all relevant statistics generated in steps 1-3 in an automated report utilising a natural language generation (NLG) algorithm. The CLD ₄ methodology was implemented to select the lead clone of a recombinant Chinese hamster ovary (CHO) cell line producing high levels of an antibody-peptide fusion with a known product quality issue related to end-point trisulfide bond (TSB) concentration. CLD ₄ identified sub-optimal process conditions leading to increased levels of trisulfide bond that would not be identified through conventional cell line development methodologies. CLD ₄ embodies the core principles of Industry 4.0 and demonstrates the benefits of increased digitalisation, data lake integration, predictive analytics and autonomous report generation to enable more informed decision making.

Rapid Identification of Chinese Hamster Ovary Cell Apoptosis and Its Potential Role in Process Robustness Assessment

Currently, the assessment of process robustness is often time-consuming, labor-intensive, and material-intensive using process characterization studies. Therefore, a simple and time-saving method is highly needed for the biopharmaceutical industry. Apoptosis is responsible for 80% of Chinese hamster ovary (CHO) cell deaths and affects the robustness of the cell culture process. This study’s results showed that a more robust process can support cells to tolerate apoptosis for a longer time, suggesting that the robustness of the process could be judged by the ability of cells to resist apoptosis. Therefore, it is necessary to establish a rapid method to detect the apoptosis of CHO cells. In trying to establish a new method for detecting apoptosis in large-scale cell cultures, glucose withdrawal was studied, and the results showed that CHO cells began to apoptose after glucose was consumed. Then, the concentration of extracellular potassium increased, and a prolongation of apoptosis time was observed. Further study results showed that the process with poor robustness was associated with a higher proportion of apoptosis and extracellular potassium concentration, so potassium could be used as a biochemical index of apoptosis. The strategy we present may be used to expedite the assessment of process robustness to obtain a robust cell culture process for other biologics.

Enhancing and stabilizing monoclonal antibody production by Chinese hamster ovary (CHO) cells with optimized perfusion culture strategies

The perfusion medium is critical in maintaining high cell concentration in cultures for the production of monoclonal antibody by Chinese hamster ovary cells. In this study, the effects of perfusion culture strategies when using different media on the process stability, product titer, and product quality were investigated in 3-L bioreactor. The results indicated that continuous perfusion could maintain higher levels of cell density, product titer, and quality in comparison with those of the intermittent perfusion culture. Next, the perfusion culture conditions with different perfusion rates and temperature reduction methods were further optimized. When combining the high perfusion rates and delayed reduction of culture temperature at day 6, the product titer reached a higher level of 16.19 g/L with the monomer relative abundant of 97.6%. In this case, the main peak of the product reached 56.3% and the total N-glycans ratio was 95.2%. To verify the effectiveness of the optimized perfusion culture in a larger scale, a 200-L bioreactor was used to perform and the final product titer reached the highest level of 16.79 g/L at day 16. Meanwhile, the product quality (monomer abundant of 97.6%, main peak of 56.3%, and N-glycans ratio of 96.5%) could also be well maintained. This study provided some guidance for the high-efficient production of monoclonal antibody by CHO cells via optimized perfusion culture strategy.

Acetate accumulation and regulation by process parameters control in Chinese hamster ovary cell culture

Chinese hamster ovary (CHO) cells represent a group of predominantly used mammalian hosts for producing recombinant therapeutic proteins. Known for their rapid proliferation rates, CHO cells undergo aerobic glycolysis that is characterized by fast glucose consumption, that ultimately gives rise to a group of small-molecule organic acids. However, only the function of lactate has been extensively studied in CHO cell culture. In this study, we observed the accumulation of acetate from the late exponential phase to harvest day, potentially contributing to the pH decline in late culture stage regardless of lactate consumption. In addition, we evaluated the acidification of the fresh media and the cell culture suspension, and the data revealed that acetate presented a lower acidification capacity compared to lactate and exhibited limited inhibitory effect on cells with less than 20 mM supplemented in the media. This study also explored the ways to control acetate accumulation in CHO cell culture by manipulating the process parameters such as temperature, glucose, and pH control. The positive correlation between the specific glucose consumption rate and acetate generation rate provides evidence of the endogenous acetate generation from overflow metabolism. Reducing these parameters (temperature, glucose consumption) and HCl-controlled low pH ultimately suppress acetate build-up. In addition, the specific acetate generation rate and relevant glucose consumption rate are found to be a metabolic trait associated with specific cell lines. Taken together, the results presented in these experiments provide a means to advance industrial CHO cell culture process control and development.

Progress in fed-batch culture for recombinant protein production in CHO cells

Nearly 80% of the approved human therapeutic antibodies are produced by Chinese Hamster Ovary (CHO) cells. To achieve better cell growth and high-yield recombinant protein, fed-batch culture is typically used for recombinant protein production in CHO cells. According to the demand of nutrients consumption, feed medium containing multiple components in cell culture can affect the characteristics of cell growth and improve the yield and quality of recombinant protein. Fed-batch optimization should have a connection with comprehensive factors such as culture environmental parameters, feed composition, and feeding strategy. At present, process intensification (PI) is explored to maintain production flexible and meet forthcoming demands of biotherapeutics process. Here, CHO cell culture, feed composition in fed-batch culture, fed-batch culture environmental parameters, feeding strategies, metabolic byproducts in fed-batch culture, chemostat cultivation, and the intensified fed-batch are reviewed. KEY POINTS: • Fed-batch culture in CHO cells is reviewed. • Fed-batch has become a common technology for recombinant protein production. • Fed batch culture promotes recombinant protein production in CHO cells.

Modern Sensor Tools and Techniques for Monitoring, Controlling, and Improving Cell Culture Processes

The growing biopharmaceutical industry has reached a level of maturity that allows for the monitoring of numerous key variables for both process characterization and outcome predictions. Sensors were historically used in order to maintain an optimal environment within the reactor to optimize process performance. However, technological innovation has pushed towards on-line in situ continuous monitoring of quality attributes that could previously only be estimated off-line. These new sensing technologies when coupled with software models have shown promise for unique fingerprinting, smart process control, outcome improvement, and prediction. All this can be done without requiring invasive sampling or intervention on the system. In this paper, the state-of-the-art sensing technologies and their applications in the context of cell culture monitoring are reviewed with emphasis on the coming push towards industry 4.0 and smart manufacturing within the biopharmaceutical sector. Additionally, perspectives as to how this can be leveraged to improve both understanding and outcomes of cell culture processes are discussed.

Continuous Feeding Reduces the Generation of Metabolic Byproducts and Increases Antibodies Expression in Chinese Hamster Ovary-K1 Cells

Chinese hamster ovary (CHO) cells are the most important host system used for monoclonal antibody (mAb) expression. Moreover, the fed-batch culture mode is the most widely used method to increase mAb expression in CHO cells by increasing the amount of feed. However, a high amount of culture feed results in the production of metabolic byproducts. In this work, we used a continuous feeding strategy to reduce metabolic byproducts and improve mouse–human chimeric anti-epidermal growth factor receptor vIII (EGFRvIII) antibody C12 expression in Chinese hamster ovary-K1 cells. Moreover, the effects of the feeding strategy on the cell culture and monoclonal antibody production were evaluated in chemically defined suspension cultures of recombinant CHO-K1 cells. Compared with bolus feeding methods, the continuous feeding method did not have any advantages when the feeding amount was low, but with a high feeding amount, the continuous feeding method significantly reduced the concentrations of lactate and NH₄⁺ in the later culture stage. At the end of the culture stage, compared with bolus feeding methods, the lactate and NH₄⁺ concentrations under the continuous feeding mode were reduced by approximately 45% and 80%, respectively. In addition, the antibody C12 expression level was also increased by almost 10%. Compared to the bolus feeding method, the antibody C12 produced by the continuous feeding method had a lower content of high-mannose glycoforms. Further analysis found that the osmolality of the continuous feeding method was lower than that of the typical fed-batch bolus feeding method. Conclusively, these results indicate that the continuous feeding method is very useful for reducing metabolic byproducts and achieving higher levels of mAb production.

Designing a Strategy for pH Control to Improve CHO Cell Productivity in Bioreactor

BACKGROUND

Drastic pH drop is a common consequence of scaling up a mammalian cell culture process, where it may affect the final performance of cell culture. Although CO2 sparging and base addition are used as common approaches for pH control, these strategies are not necessarily successful in large scale bioreactors due to their effect on osmolality and cell viability. Accordingly, a series of experiments were conducted using an IgG1 producing Chinese Hamster Ovary (CHO-S) cell culture in 30 L bioreactor to assess the efficiency of an alternative strategy in controlling culture pH.

METHODS

Factors inducing partial pressure of CO2 and lactate accumulation (as the main factors altering culture pH) were assessed by Plackett-Burman design to identify the significant ones. As culture pH directly influences process productivity, protein titer was measured as the response variable. Subsequently, Central Composite Design (CCD) was employed to obtain a model for product titer prediction as a function of individual and interaction effects of significant variables.

RESULTS

The results indicated that the major factor affecting pH is non-efficient CO2 removal. CO2 accumulation was found to be affected by an interaction between agitation speed and overlay air flow rate. Accordingly, after increasing the agitation speed and headspace aeration, the culture pH was successfully maintained in the range of 6.95-7.1, resulting in 51% increase in final product titer. Similar results were obtained during 250 L scale bioreactor culture, indicating the scalability of the approach.

CONCLUSION

The obtained results showed that pH fluctuations could be effectively controlled by optimizing CO2 stripping.

Enzyme capacity-based genome scale modelling of CHO cells

Chinese hamster ovary (CHO) cells are most prevalently used for producing recombinant therapeutics in biomanufacturing. Recently, more rational and systems approaches have been increasingly exploited to identify key metabolic bottlenecks and engineering targets for cell line engineering and process development based on the CHO genome-scale metabolic model which mechanistically characterizes cell culture behaviours. However, it is still challenging to quantify plausible intracellular fluxes and discern metabolic pathway usages considering various clonal traits and bioprocessing conditions. Thus, we newly incorporated enzyme kinetic information into the updated CHO genome-scale model (iCHO2291) and added enzyme capacity constraints within the flux balance analysis framework (ecFBA) to significantly reduce the flux variability in biologically meaningful manner, as such improving the accuracy of intracellular flux prediction. Interestingly, ecFBA could capture the overflow metabolism under the glucose excess condition where the usage of oxidative phosphorylation is limited by the enzyme capacity. In addition, its applicability was successfully demonstrated via a case study where the clone- and media-specific lactate metabolism was deciphered, suggesting that the lactate-pyruvate cycling could be beneficial for CHO cells to efficiently utilize the mitochondrial redox capacity. In summary, iCHO2296 with ecFBA can be used to confidently elucidate cell cultures and effectively identify key engineering targets, thus guiding bioprocess optimization and cell engineering efforts as a part of digital twin model for advanced biomanufacturing in future.

Consequences of trace metal variability and supplementation on Chinese hamster ovary (CHO) cell culture performance: A review of key mechanisms and considerations

Trace metals are supplied to chemically-defined media (CDM) for optimal Chinese hamster ovary (CHO) cell culture performance during the production of monoclonal antibodies and other therapeutic proteins. However, lot-to-lot and vendor-to-vendor variability in raw materials consequently leads to an imbalance of trace metals that are supplied to CDM. This imbalance can yield detrimental effects rooted in several primary mechanisms and pathways including oxidative stress, apoptosis, lactate accumulation, and unfavorable glycan synthesis. Recent research endeavors involve supplying zinc, copper, and manganese to CDM in excess to further maximize culture productivity and product quality. These treatments significantly impact critical quality attributes and furthermore highlight the degree to which trace metal availability can affect CHO cell culture performance. This review highlights the role of trace metal variability, supplementation, and interplay on key cellular mechanisms responsible for overall culture performance and the production and quality of therapeutic proteins.

Decision Tree-PLS (DT-PLS) algorithm for the development of process: Specific local prediction models

This work presents a novel multivariate statistical algorithm, Decision Tree-PLS (DT-PLS), to improve the prediction and understanding of dynamic processes based on local partial least square regression (PLSR) models for characteristic process groups defined based on Decision Tree (DT) analysis. The DT-PLS algorithm is successfully applied to two different cell culture data sets, one obtained from bioreactors of 3.5 L lab scale and the other obtained from the 15 ml ambr microbioreactor system. Substantial improvement in the predictive capabilities of the model can be achieved based on the localization compared to the classical PLSR approach, which is implemented in the commercially available packages. Additionally, the differences in the model parameters of the local models suggest that the governing process variables vary for the different process regimes indicating the different states of the cell under different process conditions.

The Less the Better: How Suppressed Base Addition Boosts Production of Monoclonal Antibodies With Chinese Hamster Ovary Cells

Biopharmaceutical production processes strive for the optimization of economic efficiency. Among others, the maximization of volumetric productivity is a key criterion. Typical parameters such as partial pressure of CO2 (pCO2) and pH are known to influence the performance although reasons are not yet fully elucidated. In this study the effects of pCO2 and pH shifts on the phenotypic performance were linked to metabolic and energetic changes. Short peak performance of qmAb (23 pg/cell/day) was achieved by early pCO2 shifts up to 200 mbar but followed by declining intracellular ATP levels to 2.5 fmol/cell and 80% increase of qLac. On the contrary, steadily rising qmAb could be installed by slight pH down-shifts ensuring constant cell specific ATP production (qATP) of 27 pmol/cell/day and high intracellular ATP levels of about 4 fmol/cell. As a result, maximum productivity was achieved combining highest qmAb (20 pg/cell/day) with maximum cell density and no lactate formation. Our results indicate that the energy availability in form of intracellular ATP is crucial for maintaining antibody synthesis and reacts sensitive to pCO2 and pH-process parameters typically responsible for inhomogeneities after scaling up.

Effective bioreactor pH control using only sparging gases

pH control is critical in bioreactor operations, typically realized through a two-sided control loop, where CO₂ sparging and base addition are used in bicarbonate-buffered media. Though a common approach, base addition could compromise culture performance due to the potential impact from pH excursions and osmolality increase in large-scale bioreactors. In this study, the feasibility of utilizing control of sparge gas composition as part of the pH control loop was assessed in Chinese hamster ovary (CHO) fed-batch cultures. Fine pH control was evaluated in multiple processes at different setpoints in small-scale ambr®250 bioreactors. Desired culture pH setpoints were successfully maintained via air sparge feedback control. As part of the pH control loop, air sparging was increased to improve CO₂ removal automatically, hence increase culture pH, and vice versa. The effectiveness of this pH control strategy was seamlessly transferred from ambr®250 to 200 L scale, demonstrating scalability of the proposed methodology. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2743, 2019.

Development of Capacitance Tools: At-Line Method for Assessing Biomass of Mammalian Cell Culture and Fixed Cell Calibration Standard

Capacitance is used to monitor "biomass" in cell culture and fermentation processes. The present work explores various ways to support good manufacturing practices (GMP) use and create robust methods that can assure proper performance of capacitance equipment. An at-line capacitance measurement method is particularly valuable as it can be used to correct or confirm online measurements from bioreactors. To obtain consistent predictions of online capacitance, the at-line method requires appropriate control of culture temperature, vessel geometry, mixing, and timing. The at-line method yields values that differ systematically from online values, but the variation is ≤11% for two cell lines tested. A cell line-specific conversion factor addresses the difference and enables accurate predictions of online capacitance values. In addition to the at-line method, verification of equipment performance is further enabled by using formaldehyde-treated cell standards. The cell-derived standards create a stabilized system for studying capacitance and recapitulate the performance of metabolically active cell culture. The formaldehyde-treated cells, however, require a much greater conversion factor to predict online outputs. The stabilized system proves useful for evaluation and calibration of capacitance measuring systems. The at-line method and stabilized cell-derived suspensions support use of capacitance for process control in large scale mammalian cell culture.

Process Analytical Technology for Advanced Process Control in Biologics Manufacturing with the Aid of Macroscopic Kinetic Modeling

Productivity improvements of mammalian cell culture in the production of recombinant proteins have been made by optimizing cell lines, media, and process operation. This led to enhanced titers and process robustness without increasing the cost of the upstream processing (USP); however, a downstream bottleneck remains. In terms of process control improvement, the process analytical technology (PAT) initiative, initiated by the American Food and Drug Administration (FDA), aims to measure, analyze, monitor, and ultimately control all important attributes of a bioprocess. Especially, spectroscopic methods such as Raman or near-infrared spectroscopy enable one to meet these analytical requirements, preferably in-situ. In combination with chemometric techniques like partial least square (PLS) or principal component analysis (PCA), it is possible to generate soft sensors, which estimate process variables based on process and measurement models for the enhanced control of bioprocesses. Macroscopic kinetic models can be used to simulate cell metabolism. These models are able to enhance the process understanding by predicting the dynamic of cells during cultivation. In this article, in-situ turbidity (transmission, 880 nm) and ex-situ Raman spectroscopy (785 nm) measurements are combined with an offline macroscopic Monod kinetic model in order to predict substrate concentrations. Experimental data of Chinese hamster ovary cultivations in bioreactors show a sufficiently linear correlation (R² ≥ 0.97) between turbidity and total cell concentration. PLS regression of Raman spectra generates a prediction model, which was validated via offline viable cell concentration measurement (RMSE ≤ 13.82, R² ≥ 0.92). Based on these measurements, the macroscopic Monod model can be used to determine different process attributes, e.g., glucose concentration. In consequence, it is possible to approximately calculate (R² ≥ 0.96) glucose concentration based on online cell concentration measurements using turbidity or Raman spectroscopy. Future approaches will use these online substrate concentration measurements with turbidity and Raman measurements, in combination with the kinetic model, in order to control the bioprocess in terms of feeding strategies, by employing an open platform communication (OPC) network—either in fed-batch or perfusion mode, integrated into a continuous operation of upstream and downstream.

Process System Engineering Methodologies Applied to Tissue Development and Regenerative Medicine

Tissue engineering and the manufacturing of regenerative medicine products demand strict control over the production process and product quality monitoring. In this chapter, the application of process systems engineering (PSE) approaches in the production of cell-based products has been discussed. Mechanistic, empirical, continuum and discrete models are compared and their use in describing cellular phenomena is reviewed. In addition, model-based optimization strategies employed in the field of tissue engineering and regenerative medicine are discussed. An introduction to process control theory is given and the main applications of classical and advanced methods in cellular production processes are described. Finally, new nondestructive and noninvasive monitoring techniques have been reviewed, focusing on large-scale manufacturing systems for cell-based constructs and therapeutic products. The application of the PSE methodologies presented here offers a promising alternative to overcome the main challenges in manufacturing engineered tissue and regeneration products.

Elevated pCO2 affects the lactate metabolic shift in CHO cell culture processes

The shift from lactate production to consumption in CHO cell metabolism is a key event during cell culture cultivations and is connected to increased culture longevity and final product titers. However, the mechanisms controlling this metabolic shift are not yet fully understood. Variations in lactate metabolism have been mainly reported to be induced by process pH and availability of substrates like glucose and glutamine. The aim of this study was to investigate the effects of elevated pCO₂ concentrations on the lactate metabolic shift phenomena in CHO cell culture processes. In this publication, we show that at elevated pCO₂ in batch and fed-batch cultures, the lactate metabolic shift was absent in comparison to control cultures at lower pCO₂ values. Furthermore, through metabolic flux analysis we found a link between the lactate metabolic shift and the ratio of NADH producing and regenerating intracellular pathways. This ratio was mainly affected by a reduced oxidative capacity of cultures at elevated pCO₂. The presented results are especially interesting for large-scale and perfusion processes where increased pCO₂ concentrations are likely to occur. Our results suggest, that so far unexplained metabolic changes may be connected to increased pCO₂ accumulation in larger scale fermentations. Finally, we propose several mechanisms through which increased pCO₂ might affect the cell metabolism and briefly discuss methods to enable the lactate metabolic shift during cell cultivations.

Advanced multivariate data analysis to determine the root cause of trisulfide bond formation in a novel antibody-peptide fusion

Product quality heterogeneities, such as a trisulfide bond (TSB) formation, can be influenced by multiple interacting process parameters. Identifying their root cause is a major challenge in biopharmaceutical production. To address this issue, this paper describes the novel application of advanced multivariate data analysis (MVDA) techniques to identify the process parameters influencing TSB formation in a novel recombinant antibody-peptide fusion expressed in mammalian cell culture. The screening dataset was generated with a high-throughput (HT) micro-bioreactor system (AmbrTM 15) using a design of experiments (DoE) approach. The complex dataset was firstly analyzed through the development of a multiple linear regression model focusing solely on the DoE inputs and identified the temperature, pH and initial nutrient feed day as important process parameters influencing this quality attribute. To further scrutinize the dataset, a partial least squares model was subsequently built incorporating both on-line and off-line process parameters and enabled accurate predictions of the TSB concentration at harvest. Process parameters identified by the models to promote and suppress TSB formation were implemented on five 7 L bioreactors and the resultant TSB concentrations were comparable to the model predictions. This study demonstrates the ability of MVDA to enable predictions of the key performance drivers influencing TSB formation that are valid also upon scale-up. Biotechnol. Bioeng. 2017;114: 2222-2234. © 2017 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.