Media formulation optimization: current and future opportunities

Leveraging machine learning to dissect role of combinations of amino acids in modulating the effect of zinc on mammalian cell growth

Although the contributions of individual components of cell culture media are largely known, their combinatorial effects are far less understood. Experiments varying one component at a time cannot identify combinatorial effects, and analysis of the large number of experiments required to decipher such effects is challenging. Machine learning algorithms can help in the analysis of such datasets to identify multi-component interactions. Zinc toxicity in vitro is known to change depending on amino acid concentration in the extracellular medium. Multiple amino acids are known to be involved in this protection. Thirty-two amino acid compositions were formulated to evaluate their effect on the growth of CHO cells under high zinc conditions. A sequential machine learning analysis methodology was used, which led to the identification of a set of amino acids (threonine, proline, glutamate, aspartate, asparagine, and tryptophan) contributing to protection from zinc. Our results suggest that a decrease in availability of these set of amino acids due to consumption may affect cell growth in media formulated with high zinc concentrations, and in contrast, normal levels of these amino acids are associated with better tolerance to high zinc concentration. Our sequential analysis method may be similarly employed for high throughput medium design and optimization experiments to identify interactions among a large number of cell culture medium components.

Sodium acetate increases the productivity of HEK293 cells expressing the ECD-Her1 protein in batch cultures: experimental results and metabolic flux analysis

Human Embryonic Kidney cells (HEK293) are a popular host for recombinant protein expression and production in the biotechnological industry. This has driven within both, the scientific and the engineering communities, the search for strategies to increase their protein productivity. The present work is inserted into this search exploring the impact of adding sodium acetate (NaAc) into a batch culture of HEK293 cells. We monitored, as a function of time, the cell density, many external metabolites, and the supernatant concentration of the heterologous extra-cellular domain ECD-Her1 protein, a protein used to produce a candidate prostate cancer vaccine. We observed that by adding different concentrations of NaAc (0, 4, 6 and 8 mM), the production of ECD-Her1 protein increases consistently with increasing concentration, whereas the carrying capacity of the medium decreases. To understand these results we exploited a combination of experimental and computational techniques. Metabolic Flux Analysis (MFA) was used to infer intracellular metabolic fluxes from the concentration of external metabolites. Moreover, we measured independently the extracellular acidification rate and oxygen consumption rate of the cells. Both approaches support the idea that the addition of NaAc to the culture has a significant impact on the metabolism of the HEK293 cells and that, if properly tuned, enhances the productivity of the heterologous ECD-Her1 protein.

In vitro modelling of bacterial pneumonia: a comparative analysis of widely applied complex cell culture models

Bacterial pneumonia greatly contributes to the disease burden and mortality of lower respiratory tract infections among all age groups and risk profiles. Therefore, laboratory modelling of bacterial pneumonia remains important for elucidating the complex host-pathogen interactions and to determine drug efficacy and toxicity. In vitro cell culture enables for the creation of high-throughput, specific disease models in a tightly controlled environment. Advanced human cell culture models specifically, can bridge the research gap between the classical two-dimensional cell models and animal models. This review provides an overview of the current status of the development of complex cellular in vitro models to study bacterial pneumonia infections, with a focus on air-liquid interface models, spheroid, organoid, and lung-on-a-chip models. For the wide scale, comparative literature search, we selected six clinically highly relevant bacteria (Pseudomonas aeruginosa, Mycoplasma pneumoniae, Haemophilus influenzae, Mycobacterium tuberculosis, Streptococcus pneumoniae, and Staphylococcus aureus). We reviewed the cell lines that are commonly used, as well as trends and discrepancies in the methodology, ranging from cell infection parameters to assay read-outs. We also highlighted the importance of model validation and data transparency in guiding the research field towards more complex infection models.

Debottlenecking and reformulating feed media for improved CHO cell growth and titer by data-driven and model-guided analyses

Designing and selecting cell culture media along with their feeding are a key strategy to maximize culture performance in biopharmaceutical processes. However, the sensitivity of mammalian cells to their culture environment necessitates specific nutritional requirements for their growth and the production of high-quality proteins such as antibodies, depending on the cell lines and operational conditions employed. In this regard, previously we developed a data-driven and in-silico model-guided systematic framework to investigate the effect of growth media on Chinese hamster ovary (CHO) cell culture performance, allowing us to design and reformulate basal media. To expand our exploration for media development research, we evaluated two chemically defined feed media, A and B, using a monoclonal antibody-producing CHO-K1 cell line in ambr15 bioreactor runs. We observed a significant impact of the feed media on various aspects of cell culture, including growth, longevity, viability, productivity, and the production of toxic metabolites. Specifically, the concentrated feed A was inadequate in sustaining prolonged cell culture and achieving high titers when compared to feed B. Within our framework, we systematically investigated the major metabolic bottlenecks in the tricarboxylic acid cycle and relevant amino acid transferase reactions. This analysis identified target components that play a crucial role in alleviating bottlenecks and designing highly productive cell cultures, specifically the addition of glutamate to feed A and asparagine to feed B. Based on our findings, we reformulated the feeds by adjusting the amounts of the targeted amino acids and successfully validated the effectiveness of the strategy in promoting cell growth, life span, and/or titer.

Application of Formulation Principles to Stability Issues Encountered During Processing, Manufacturing, and Storage of Drug Substance and Drug Product Protein Therapeutics

The field of formulation and stabilization of protein therapeutics has become rather extensive. However, most of the focus has been on stabilization of the final drug product. Yet, proteins experience stress and degradation through the manufacturing process, starting with fermentaition. This review describes how formulation principles can be applied to stabilize biopharmaceutical proteins during bioprocessing and manufacturing, considering each unit operation involved in prepration of the drug substance. In addition, the impact of the container on stabilty is discussed as well.

A review of algorithmic approaches for cell culture media optimization

Cell culture media composition and culture conditions play a crucial role in product yield, quality and cost of production. Culture media optimization is the technique of improving media composition and culture conditions to achieve desired product outcomes. To achieve this, there have been many algorithmic methods proposed and used for culture media optimization in the literature. To help readers evaluate and decide on a method that best suits their specific application, we carried out a systematic review of the different methods from an algorithmic perspective that classifies, explains and compares the available methods. We also examine the trends and new developments in the area. This review provides recommendations to researchers regarding the suitable media optimization algorithm for their applications and we hope to also promote the development of new cell culture media optimization methods that are better suited to existing and upcoming challenges in this biotechnology field, which will be essential for more efficient production of various cell culture products.

His-tagged lactate oxidase production for industrial applications using fed-batch fermentation

L-lactate oxidase (LOX) is a biotechnologically important enzyme used in biosensors and colorimetric kits to detect lactate, a key biomarker in clinical diagnostics, sports medicine and the food industry. In this work, we produced a recombinant His-tagged Aerococcus viridans LOX (rLOX) in Escherichia coli and carried out its functional characterization for industrial applications. Our rLOX was evaluated in a colorimetric kit for human diagnostics and in an amperometric biosensor to measure the lactic acid in food products. The rLOX was fully functional for both applications, with a performance comparable to commercial untagged LOXs. As the industrial use of LOX enzyme requires a large-scale production, we scaled up the rLOX production in a fed-batch bioreactor culture and obtained a yield approximately ten times higher than that of the Erlenmeyer scale. The His-tag allowed an easy and highly efficient purification process, and a high-purity rLOX was recovered after this one-step affinity purification. In this study, we described a simple, rapid and cost-competitive approach for the production of a recombinant His-tagged LOX enzyme suitable for industrial use.

Machine learning and hypothesis driven optimization of bull semen cryopreservation media

Cryopreservation provides a critical tool for dairy herd genetics management. Due to widely varying inter- and within-bull post thaw fertility, recent research on cryoprotectant extender medium has not dramatically improved suboptimal post-thaw recovery in industry. This progress is stymied by the interactions between samples and the many components of extender media and is often compounded by industry irrelevant sample sizes. To address these challenges, here we demonstrate blank-slate optimization of bull sperm cryopreservation media by supervised machine learning. We considered two supervised learning models: artificial neural networks and Gaussian process regression (GPR). Eleven media components and initial concentrations were identified from publications in bull semen cryopreservation, and an initial 200 extender-post-thaw motility pairs were used to train and 32 extender-post-thaw motility pairs to test the machine learning algorithms. The median post-thaw motility after coupling differential evolution with GPR the increased from 52.6 ± 6.9% to 68.3 ± 6.0% at generations 7 and 17 respectively, with several media performing dramatically better than control media counterparts. This is the first study in which machine learning was used to determine the best combination of constituents to optimize bull sperm cryopreservation media, and provides a template for optimization in other cell types.

Se(XY) matters: the importance of incorporating sex in microphysiological models

The development of microphysiological models is currently at the forefront of preclinical research. Although these 3D tissue models are being developed to mimic physiological organ function and diseases, which are often sexually dimorphic, sex is usually neglected as a biological variable. For decades, national research agencies have required government-funded clinical trials to include both male and female participants as a means of eliminating male bias. However, this is not the case in preclinical trials, which have been shown to favor male rodents in animal studies and male cell types in in vitro studies. In this Opinion, we highlight the importance of considering sex as a biological variable and outline five approaches for incorporating sex-specific features into current microphysiological models.

Bioprocess development as a sustainable platform for eco-friendly alkaline phosphatase production: an approach towards crab shells waste management

Background

There are substantial environmental and health risks associated with the seafood industry's waste of crab shells. In light of these facts, shellfish waste management is critical for environmental protection against hazardous waste produced from the processing industries. Undoubtedly, improved green production strategies, which are based on the notion of "Green Chemistry," are receiving a lot of attention. Therefore, this investigation shed light on green remediation of the potential hazardous crab shell waste for eco-friendly production of bacterial alkaline phosphatase (ALP) through bioprocessing development strategies.

Results

It was discovered that by utilizing sequential statistical experimental designs, commencing with Plackett–Burman design and ending with spherical central composite design, and then followed by pH-uncontrolled cultivation conditions in a 7 L bench-top bioreactor, an innovative medium formulation could be developed that boosted ALP production from Bacillus licheniformis strain ALP3 to 212 U L⁻¹. The highest yield of ALP was obtained after 22 h of incubation time with yield coefficient Y_p/s of 795 U g⁻¹, which was 4.35-fold higher than those obtained in the shake-flask system. ALP activity has a substantial impact on the volatilization of crab shell particles, as shown by the results of several analytical techniques such as atomic absorption spectrometry, TGA, DSC, EDS, FTIR, and XRD.

Conclusions

We highlighted in the current study that the biovalorization of crab shell waste and the production of cost-effective ALP were being combined and that this was accomplished via the use of a new and innovative medium formulation design for seafood waste management as well as scaling up production of ALP on the bench-top scale.

Antibody charge variant modulation by in vitro enzymatic treatment in different CHO cell cultures

Charge variants represent a critical quality attribute that must be controlled during the development and manufacturing of monoclonal antibodies (mAb). Previously, we reported the development of a cost-effective enzymatic treatment capable of removing the C-terminal lysine from a mAb produced by a Chinese hamster ovary (CHO) GS cell line. This treatment resulted in a significant decrease in basic charge variants and a corresponding improvement in the main peak, enabling a longer cell culture production duration for titer improvement. Here, we describe this enzymatic treatment protocol in detail and demonstrate its applicability to two additional mAbs produced by distinct industrial cell lines. The simple addition of carboxypeptidase B (CpB) at a ratio of 1:10,000 (w/w) to whole cell cultures significantly improved the main peaks for both mAbs without affecting other critical quality attributes, including size exclusion chromatography impurities and N-glycans. Our results demonstrate that this in vitro CpB treatment protocol can be used as a platform strategy to improve main peak for mAbs that exhibit high levels of basic variants attributable to C-terminal lysines. An in vitro enzymatic treatment in general may be another good addition to existing in vivo CHO cell culture strategies for titer improvement and control of critical quality attributes. This article is protected by copyright. All rights reserved.

Improved Titer in Late-Stage Mammalian Cell Culture Manufacturing by Re-Cloning

Improving productivity to reduce the cost of biologics manufacturing and ensure that therapeutics can reach more patients remains a major challenge faced by the biopharmaceutical industry. Chinese hamster ovary (CHO) cell lines are commonly prepared for biomanufacturing by single cell cloning post-transfection and recovery, followed by lead clone screening, generation of a research cell bank (RCB), cell culture process development, and manufacturing of a master cell bank (MCB) to be used in early phase clinical manufacturing. In this study, it was found that an additional round of cloning and clone selection from an established monoclonal RCB or MCB (i.e., re-cloning) significantly improved titer for multiple late phase monoclonal antibody upstream processes. Quality attributes remained comparable between the processes using the parental clones and the re-clones. For two CHO cells expressing different antibodies, the re-clone performance was successfully scaled up at 500-L or at 2000-L bioreactor scales, demonstrating for the first time that the re-clone is suitable for late phase and commercial manufacturing processes for improvement of titer while maintaining comparable product quality to the early phase process.

Incorporating Transcriptomic-Metabolomic analysis reveal the effect of ultrasound on ethanol production in Saccharomyces Cerevisiae

This study reports an enhancement of ethanol yield in Saccharomyces cerevisiae with low-intensity ultrasonic irradiation using fixed mode frequency generated by a self-developed six-frequencies (20, 23, 25, 28, 33, 40 kHz) ultrasonic device in our group. After sonication treatment, the ethanol production potential was determined. Under the optimal conditions of ultrasonic treatment (ultrasonic frequency 28 kHz, power density 180 W/L, and treatment time 24 h), the maximum ethanol yield increased by 34.87% compared to the control. Transcriptome sequencing showed that the ultrasonic treatment had expressional regulations on genes involved in pyruvate metabolism, glycolysis, pentose phosphate pathway, glucose transport, and reducing power production. The quantitative real-time polymerase chain reaction (qRT-PCR) further confirmed the changes in gene expression (up- or down-regulation). Metabolomics revealed that ultrasonic treatments increased intracellular glucose and nicotinamide adenine dinucleotide (NADH) contents, which are key metabolites for ethanol synthesis. Besides, ultrasonic treatments decreased the acetate and its derivatives resulting in lowered reverse consumption of pyruvate and thus promoted ethanol synthesis. These changes in gene expression and metabolites content might be the main reason why the ethanol yield in Saccharomyces cerevisiae increased after ultrasonic irradiation.

Modular development enables rapid design of media for alternative hosts

Developing media to sustain cell growth and production is an essential and ongoing activity in bioprocess development. Modifications to media can often address host or product‐specific challenges, such as low productivity or poor product quality. For other applications, systematic design of new media can facilitate the adoption of new industrially relevant alternative hosts. Despite manifold existing methods, common approaches for optimization often remain time and labor‐intensive. We present here a novel approach to conventional media blending that leverages stable, simple, concentrated stock solutions to enable rapid improvement of measurable phenotypes of interest. We applied this modular methodology to generate high‐performing media for two phenotypes of interest: biomass accumulation and heterologous protein production, using high‐throughput, milliliter‐scale batch fermentations of Pichia pastoris as a model system. In addition to these examples, we also created a flexible open‐source package for modular blending automation on a low‐cost liquid handling system to facilitate wide use of this method. Our modular blending method enables rapid, flexible media development, requiring minimal labor investment and prior knowledge of the host organism, and should enable developing improved media for other hosts and phenotypes of interest.

Systematically gap-filling the genome-scale metabolic model of CHO cells

OBJECTIVE

Chinese hamster ovary (CHO) cells are the leading cell factories for producing recombinant proteins in the biopharmaceutical industry. In this regard, constraint-based metabolic models are useful platforms to perform computational analysis of cell metabolism. These models need to be regularly updated in order to include the latest biochemical data of the cells, and to increase their predictive power. Here, we provide an update to iCHO1766, the metabolic model of CHO cells.

RESULTS

We expanded the existing model of Chinese hamster metabolism with the help of four gap-filling approaches, leading to the addition of 773 new reactions and 335 new genes. We incorporated these into an updated genome-scale metabolic network model of CHO cells, named iCHO2101. In this updated model, the number of reactions and pathways capable of carrying flux is substantially increased.

CONCLUSIONS

The present CHO model is an important step towards more complete metabolic models of CHO cells.

Development of an intensified fed-batch production platform with doubled titers using N-1 perfusion seed for cell culture manufacturing

The goal of cell culture process intensification is to increase volumetric productivity, generally by increasing viable cell density (VCD), cell specific productivity or production bioreactor utilization in manufacturing. In our previous study, process intensification in fed-batch production with higher titer or shorter duration was demonstrated by increasing the inoculation seeding density (SD) from ~ 0.6 (Process A) to 3–6 × 106 cells/mL (Process B) in combination with media enrichment. In this study, we further increased SD to 10–20 × 106 cells/mL (Process C) using perfusion N-1 seed cultures, which increased titers already at industrially relevant levels by 100% in 10–14 day bioreactor durations for four different mAb-expressing CHO cell lines. Redesigned basal and feed media were critical for maintaining higher VCD and cell specific productivity during the entire production duration, while medium enrichment, feeding strategies and temperature shift optimization to accommodate high VCDs were also important. The intensified Process C was successfully scaled up in 500-L bioreactors for 3 of the 4 mAbs, and quality attributes were similar to the corresponding Process A or Process B at 1000-L scale. The fed-batch process intensification strategies developed in this study could be applied for manufacturing of other mAbs using CHO and other host cells.

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.

Systems biology approach in the formulation of chemically defined media for recombinant protein overproduction

The cell culture medium is an intricate mixture of components which has a tremendous effect on cell growth and recombinant protein production. Regular cell culture medium includes various components, and the decision about which component should be included in the formulation and its optimum amount is an underlying issue in biotechnology industries. Applying conventional techniques to design an optimal medium for the production of a recombinant protein requires meticulous and immense research. Moreover, since the medium formulation for the production of one protein could not be the best choice for another protein, hence, the most suitable media should be determined for each recombinant cell line. Accordingly, medium formulation becomes a laborious, time-consuming, and costly process in biomanufacturing of recombinant protein, and finding alternative strategies for medium development seems to be crucial. In silico modeling is an attractive concept to be adapted for medium formulation due to its high potential to supersede laboratory examinations. By emerging the high-throughput datasets, scientists can disclose the knowledge about the effect of medium components on cell growth and metabolism, and via applying this information through systems biology approach, medium formulation optimization could be accomplished in silico with no need of significant amount of experimentation. This review demonstrates some of the applications of systems biology as a powerful tool for medium development and illustrates the effect of medium optimization with system-level analysis on the production of recombinant proteins in different host cells.