Fed-batch operation of an industrial cell culture process in shaken microwells

A deep-well plate enabled automated high-throughput cell line development platform

Cell line development (CLD) plays a crucial role in the manufacturing process development of therapeutic biologics. Most biologics are produced in Chinese hamster ovary (CHO) cell. Because of the nature of random transgene integration in CHO genome and CHO's inherent plasticity, stable CHO transfectants usually have a vast diversity in productivity, growth, and product quality. Thus, we often must resort to screening a large number of cell pools and clones to increase the probability of identifying the ideal production cell line, which is a very laborious and resource-demanding process. Here we have developed a deep-well plate (DWP) enabled high throughput (DEHT) CLD platform using 24-well DWP (24DWP), liquid handler, and other automation components. This platform has capabilities covering the key steps of CLD including cell passaging, clone imaging and expansion, and fed-batch production. We are the first to demonstrate the suitability of 24DWP for CLD by confirming minimal well-to-well and plate-to-plate variability and the absence of well-to-well cross contamination. We also demonstrated that growth, production, and product quality of 24DWP cultures were comparable to those of conventional shake flask cultures. The DEHT platform enables scientists to screen five times more cultures than the conventional CLD platform, thus significantly decreases the resources needed to identify an ideal production cell line for biologics manufacturing.

The Need for Research on the Comparison of Sensory Characteristics between Cultured Meat Produced Using Scaffolds and Meat

Cultured meat is one of the research areas currently in the spotlight in the agricultural and livestock industry, and refers to cells obtained from livestock that are proliferated and differentiated and processed into edible meat. These cell-cultured meats are mainly studied at the lab-scale by culturing them in flasks, and for commercial use, they are produced using scaffolds that mimic cell supports. Scaffolds are broadly divided into fiber scaffolds, hydrogels, and micro-carrier beads, and these are classified according to processing methods and materials. In particular, a scaffold is essential for mass production, which allows it to have appearance, texture, and flavor characteristics similar to meat. Because cultured meat is cultured in a state where oxygen is blocked, it may be lighter in color or produce less flavor substances than edible meat, but these can be compensated for by adding natural substances to the scaffolds or improving fat adhesion. In addition, it has the advantage of being able to express the texture characteristics of the scaffolds that make up the meat in various ways depending on the materials and manufacturing methods of the scaffolds. As a result, to increase consumers' preference for cultured meat and its similarity to edible meat, it is believed that manufacturing scaffolds taking into account the characteristics of edible meat will serve as an important factor. Therefore, continued research and interest in scaffolds is believed to be necessary.

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.

Drug Evaluation Based on a Multi-Channel Cell Chip with a Horizontal Co-Culture

We developed a multi-channel cell chip containing a three-dimensional (3D) scaffold for horizontal co-culture and drug toxicity screening in multi-organ culture (human glioblastoma, cervical cancer, normal liver cells, and normal lung cells). The polydimethylsiloxane (PDMS) multi-channel cell chip (PMCCC) was based on fused deposition modeling (FDM) technology. The architecture of the PMCCC was an open-type cell chip and did not require a pump or syringe. We investigated cell proliferation and cytotoxicity by conducting 3-(4,5-dimethylthiazol-2-yl)-2,5-dphenyltetrazolium bromide (MTT) and lactate dehydrogenase (LDH) assays and analysis of oleanolic acid (OA)-treated multi-channel cell chips. The results of the MTT and LDH assays showed that OA treatment in the multi-channel cell chip of four cell lines enhanced chemoresistance of cells compared with that in the 2D culture. Furthermore, we demonstrated the feasibility of the application of our multi-channel cell chip in various analysis methods through Annexin V-fluorescein isothiocyanate/propidium iodide staining, which is not used for conventional cell chips. Taken together, the results demonstrated that the PMCCC may be used as a new 3D platform because it enables simultaneous drug screening in multiple cells by single point injection and allows analysis of various biological processes.

Model-based workflow for scale-up of process strategies developed in miniaturized bioreactor systems

Miniaturized bioreactor (MBR) systems are routinely used in the development of mammalian cell culture processes. However, scale-up of process strategies obtained in MBR- to larger scale is challenging due to mainly non-holistic scale-up approaches. In this study, a model-based workflow is introduced to quantify differences in the process dynamics between bioreactor scales and thus enable a more knowledge-driven scale-up. The workflow is applied to two case studies with antibody-producing Chinese hamster ovary cell lines. With the workflow, model parameter distributions are estimated first under consideration of experimental variability for different scales. Second, the obtained individual model parameter distributions are tested for statistical differences. In case of significant differences, model parametric distributions are transferred between the scales. In case study I, a fed-batch process in a microtiter plate (4 ml working volume) and lab-scale bioreactor (3750 ml working volume) was mathematically modeled and evaluated. No significant differences were identified for model parameter distributions reflecting process dynamics. Therefore, the microtiter plate can be applied as scale-down tool for the lab-scale bioreactor. In case study II, a fed-batch process in a 24-Deep-Well-Plate (2 ml working volume) and shake flask (40 ml working volume) with two feed media was investigated. Model parameter distributions showed significant differences. Thus, process strategies were mathematically transferred, and model predictions were simulated for a new shake flask culture setup and confirmed in validation experiments. Overall, the workflow enables a knowledge-driven evaluation of scale-up for a more efficient bioprocess design and optimization.

High-throughput screening for high-efficiency small-molecule biosynthesis

Systems metabolic engineering faces the formidable task of rewiring microbial metabolism to cost-effectively generate high-value molecules from a variety of inexpensive feedstocks for many different applications. Because these cellular systems are still too complex to model accurately, vast collections of engineered organism variants must be systematically created and evaluated through an enormous trial-and-error process in order to identify a manufacturing-ready strain. The high-throughput screening of strains to optimize their scalable manufacturing potential requires execution of many carefully controlled, parallel, miniature fermentations, followed by high-precision analysis of the resulting complex mixtures. This review discusses strategies for the design of high-throughput, small-scale fermentation models to predict improved strain performance at large commercial scale. Established and promising approaches from industrial and academic groups are presented for both cell culture and analysis, with primary focus on microplate- and microfluidics-based screening systems.

Microbioreactors for Process Development and Cell-Based Screening Studies

Microbioreactors (MBRs) have emerged as potent cultivation devices enabling automated small-scale experiments in parallel while enhancing their cost efficiency. The widespread use of MBRs has contributed to recent advances in industrial and pharmaceutical biotechnology, and they have proved to be indispensable tools in the development of many modern bioprocesses. Being predominantly applied in early stage process development, they open up new fields of research and enhance the efficacy of biotechnological product development. Their reduced reaction volume is associated with numerous inherent advantages - particularly the possibility for enabling parallel screening operations that facilitate high-throughput cultivations with reduced sample consumption (or the use of rare and expensive educts). As a result, multiple variables can be examined in a shorter time and with a lower expense. This leads to a simultaneous acceleration of research and process development along with decreased costs.MBRs range from simple miniaturized cultivations vessels (i.e., in the milliliter scale with limited possibilities for process control) to highly complex and automated small-scale microreactors with integrated sensors that allow for comprehensive screenings in very short time or a precise reflection of large-scale cultivation conditions. Progressive developments and improvements in manufacturing and automation techniques are already helping researchers to make use of the advantages that MBRs offer. This overview of current MBR systems surveys the diverse application for microbial and mammalian cell cultivations that have been developed in recent years.

Towards the development of automated fed-batch cell culture processes at microscale

Aim: To investigate the impact of various feeding strategies on the growth and productivity of a GS-CHO cell line. Methods: Feed additions were conducted at fixed volumes or linked to a marker such as cell growth or metabolism and added as bolus or near-continuously using the automated feeding module of the micro-Matrix (Applikon). Results: The selected feeding regimens supported maximum viable cell densities of up to 1.9 × 107 cells ml−1 and final titers of up to 1.13 g l−1. Differences in growth and titer between feeding strategies were insignificant, with the exception of one feeding strategy. Conclusion: As the more complex feeding strategies did not create an advantage, the selection of a simple feeding strategy such as bolus or continuous addition of feed medium is preferred.

New Mammalian Expression Systems

There are an increasing number of recombinant antibodies and proteins in preclinical and clinical development for therapeutic applications. Mammalian expression systems are key to enabling the production of these molecules, and Chinese hamster ovary (CHO) cell platforms continue to be central to delivery of the stable cell lines required for large-scale production. Increasing pressure on timelines and efficiency, further innovation of molecular formats and the shift to new production systems are driving developments of these CHO cell line platforms. The availability of genome and transcriptome data coupled with advancing gene editing tools are increasing the ability to design and engineer CHO cell lines to meet these challenges. This chapter aims to give an overview of the developments in CHO expression systems and some of the associated technologies over the past few years.

High-throughput screening of antibody-expressing CHO clones using an automated shaken deep-well system

Biopharmaceutical protein manufacturing requires the highest producing cell lines to satisfy current multiple grams per liter requirements. Screening more clones increases the probability of identifying the high producers within the pool of available transfectant candidate cell lines. For the predominant industry mammalian host cell line, Chinese hamster ovary (CHO), traditional static‐batch culture screening does not correlate with the suspension fed‐batch culture used in manufacturing, and thus has little predictive utility. Small scale fed‐batch screens in suspension culture correlate better with bioreactor processes but a limited number of clones can be screened manually. Scaled‐down systems, such as shaken deep well plates, combined with automated liquid handling, offer a way for a limited number of scientists to screen many clones. A statistical analysis determined that 384 is the optimal number of clones to screen, with a 99% probability that six clones in the 95th percentile for productivity are included in the screen. To screen 384 clones efficiently by the predictive method of suspension fed‐batch, the authors developed a shaken deep‐well plate culturing platform, with an automated liquid handling system integrating cell counting and protein titering instruments. Critical factors allowing deep‐well suspension culture to correlate with shake flask culture were agitation speed and culture volume. Using our automated system, one scientist can screen five times more clones than by manual fed‐batch shake‐flask or shaken culture tube screens and can identify cell lines for some therapeutic protein projects with production levels greater than 6 g/L. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:1460–1471, 2018

A simple method to determine evaporation and compensate for liquid losses in small-scale cell culture systems

Objectives

Establish a method to indirectly measure evaporation in microwell-based cell culture systems and show that the proposed method allows compensating for liquid losses in fed-batch processes.

Results

A correlation between evaporation and the concentration of Na⁺ was found (R² = 0.95) when using the 24-well-based miniature bioreactor system (micro-Matrix) for a batch culture with GS-CHO. Based on these results, a method was developed to counteract evaporation with periodic water additions based on measurements of the Na⁺ concentration. Implementation of this method resulted in a reduction of the relative liquid loss after 15 days of a fed-batch cultivation from 36.7 ± 6.7% without volume corrections to 6.9 ± 6.5% with volume corrections.

Conclusion

A procedure was established to indirectly measure evaporation through a correlation with the level of Na⁺ ions in solution and deriving a simple formula to account for liquid losses.

Assessment of the scalability of a microtiter plate system for screening of oleaginous microorganisms

Recent developments in molecular biology and metabolic engineering have resulted in a large increase in the number of strains that need to be tested, positioning high-throughput screening of microorganisms as an important step in bioprocess development. Scalability is crucial for performing reliable screening of microorganisms. Most of the scalability studies from microplate screening systems to controlled stirred-tank bioreactors have been performed so far with unicellular microorganisms. We have compared cultivation of industrially relevant oleaginous filamentous fungi and microalga in a Duetz-microtiter plate system to benchtop and pre-pilot bioreactors. Maximal glucose consumption rate, biomass concentration, lipid content of the biomass, biomass, and lipid yield values showed good scalability for Mucor circinelloides (less than 20% differences) and Mortierella alpina (less than 30% differences) filamentous fungi. Maximal glucose consumption and biomass production rates were identical for Crypthecodinium cohnii in microtiter plate and benchtop bioreactor. Most likely due to shear stress sensitivity of this microalga in stirred bioreactor, biomass concentration and lipid content of biomass were significantly higher in the microtiter plate system than in the benchtop bioreactor. Still, fermentation results obtained in the Duetz-microtiter plate system for Crypthecodinium cohnii are encouraging compared to what has been reported in literature. Good reproducibility (coefficient of variation less than 15% for biomass growth, glucose consumption, lipid content, and pH) were achieved in the Duetz-microtiter plate system for Mucor circinelloides and Crypthecodinium cohnii. Mortierella alpina cultivation reproducibility might be improved with inoculation optimization. In conclusion, we have presented suitability of the Duetz-microtiter plate system for the reproducible, scalable, and cost-efficient high-throughput screening of oleaginous microorganisms.

Early retinal differentiation of human pluripotent stem cells in microwell suspension cultures

Objective

To develop a microwell suspension platform for the adaption of attached stem cell differentiation protocols into mixed suspension culture.

Results

We adapted an adherent protocol for the retinal differentiation of human induced pluripotent stem cells (hiPSCs) using a two-step protocol. Establishing the optimum embryoid body (EB) starting size and shaking speed resulted in the translation of the original adherent process into suspension culture. Embryoid bodies expanded in size as the culture progressed resulting in the expression of characteristic markers of early (Rx, Six and Otx2) and late (Crx, Nrl and Rhodopsin) retinal differentiation. The new process also eliminated the use of matrigel, an animal-derived extracellular matrix coating.

Conclusions

Shaking microwells offer a fast and cost-effective method for proof-of-concept studies to establish whether pluripotent stem cell differentiation processes can be translated into mixed suspension culture.

Electronic supplementary material

The online version of this article (doi:10.1007/s10529-016-2244-7) contains supplementary material, which is available to authorized users.

Screening and optimization of chemically defined media and feeds with integrated and statistical approaches

The majority of therapeutic proteins are expressed in mammalian cells, predominantly in Chinese Hamster Ovary cells. While cell culture media and feed supplements are crucial to protein productivity, medium optimization can be labor intensive and time-consuming. In this chapter, we describe some basic concepts in medium development and introduce a rational and rapid workflow to screen and optimize media and feeds. The major goal of medium screening is to select a base formulation as the foundation for further optimization, but ironically, the most conventional screening method may actually rule out ideal chemically defined medium candidates. Appropriate cell adaptation is the key to identifying an optimal base medium, particularly when cells were originally cultured in serum-free medium containing recombinant proteins and/or undefined hydrolysates. The efficient workflow described herein integrates the optimization of both medium and feed simultaneously using a Design-of-Experiment (DOE) approach. The feasibility of the workflow is then demonstrated with a case study, in which chemically defined medium and feed were optimized in a single fed-batch study using a high-throughput microbioreactor system (SimCell™), which resulted in improving protein titers three- to sixfold.

Comparison of the behavior of CHO cells during cultivation in 24-square deep well microplates and conventional shake flask systems

In biopharmaceutical production, the optimization of cell culture media and supplementation is a vital element of process development. Optimization is usually achieved through the screening of multiple media, feed and feeding strategies. However, most screening is performed in shake flasks, which makes the screening process very time consuming and inefficient. The use of small scale culture systems for the screening process can aid in the ability to screen multiple formulations during process development. In order to assess the suitability of 24 deep well (24DW) plates with the Duetz sandwich-covers as a small scale culture system for process development, we have tested growth and production performance of CHO cells in 24DW plates and conventional shake flask cultures. Multiple studies were performed to assess well-to-well and plate-to-plate variability in 24DW plates. Additional studies were performed to determine the applicability of 24DW plates for cell culture medium and supplement screening in batch and fed batch processes. Cultures in 24DW plates exhibited similar kinetics in growth, viability and protein production to those cultured in shake flasks, suggesting that 24DW plates with Duetz sandwich-covers can be effectively used for high throughput cell culture screening.

Characterization of lentiviral vector production using microwell suspension cultures of HEK293T-derived producer cells

ProSavin(®) is a lentiviral vector (LV)-based gene therapy for Parkinson's disease. ProSavin(®) is currently in a Phase I/II clinical trial using material that was generated by transient transfection of adherent human embryonic kidney (HEK)293T cells. For future large-scale productions of ProSavin(®), we have previously reported the development and characterization of two inducible producer cell lines, termed PS5.8 and PS46.2. PS46.2 has been successfully adapted to grow in suspension cultures. The present study describes the creation of a small-scale (<2 ml) microwell-based experimental platform for the parallel investigation of ProSavin(®) production using suspension-adapted PS46.2. This is combined with statistical design of experiments (DoE) techniques to enable rapid characterization of the process conditions that impact cell growth and LV production. The effects of postinduction period, microwell liquid fill volume, and concentration of inducer (doxycycline) on ProSavin(®) titer and the particle:infectivity (P:I) ratio was investigated using three rounds of DoE, in order to identify appropriate factor ranges and optimize production conditions. We identified an optimal "harvest window" between approximately 26-46 hr within which maximal titers of around 6×10(4) transducing units (TU)/ml were obtained (an approximately 30-fold improvement compared to starting microwell conditions), providing that the fill volume was maintained at or below 1 ml and the doxycycline concentration was at least 1.0 μg/ml. Insights from the microwell studies were subsequently used to rapidly establish operating conditions for ProSavin(®) production in a 0.5-L wave bioreactor culture. The information presented herein thus aids the design and evaluation of scalable production processes for LVs.

Conference scene: recent advancements in microscale bioprocess development

Advances in genetics, as well as molecular and cellular biology, are continually fueling innovations in the biopharmaceutical sector. Increasingly specialized therapies are emerging that offer exciting prospects for the treatment of human diseases. Defining a suitable manufacturing route for each therapeutic product, however, can often present a significant challenge. There is a growing trend in the biopharmaceutical sector to use microscale models (that mimic key manufacturing steps) during the early stages of process development, as such technologies enable key process information to be accrued rapidly and at relatively low costs. The 2nd Annual Miniaturisation conference, organized by Euroscicon, brought together 34 delegates from industry and academia for a lively discussion of the current state-of-the-art in microscale bioprocess technologies.