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Cell-culture optimization may see benefits from a synthetic biology-based approach that improves product titer, quality, and time.
Synthetic biology is an emerging area of interest in biologic drug development for its ability to offer new genetic solutions for use in developing targeted cell lines. The ability to develop cell lines with precisely optimized cellular machinery can pose potential advantages for upstream processing, which is largely dependent on cell culture systems.
In upstream processing, cell-culture systems still face challenges; among them is the correlation between upstream optimization and manufacturing scalability. The scalability of the cell line and process is typically addressed late in the development timeline, notes Brian Douglass, general manager, Cell Culture Media, Cytiva. While there is quite a bit of time spent on identifying the best cell line candidates, establishing clonal populations, and optimizing cell culture media as well as process parameters, all of this work is typically performed in small-scale models, but under large-scale manufacturing conditions, alternative clones and processes may emerge as better choices, he says.
A second challenge is cell culture media development and the plethora of components from which to choose. “Our understanding of interactions between the components is still a young and emerging science. Some of this aspect of process optimization is still tribal knowledge,” Douglass says.
Matthew Weinstock, chief technology officer of AbSci, a synthetic biology company that uses Escherichia coli to discover and manufacture complex therapeutic proteins, notes that the major focus of biotherapeutic manufacturing process development has been to optimize the production of full-length antibodies, which are naturally occurring proteins that native host cell machinery can express and fold without requiring sophisticated cell line engineering. However, little attention has been paid to the production of so-called next-generation therapeutics that move beyond natural antibody scaffolds. Maximizing cell-line productivity for antibody production places heavy demands on this cellular machinery, and rate-limiting steps impact titer and productivity gains, cell fitness, and other cell properties that can negatively impact cell physiology and reduce protein production.
“Over 30% of biologics in preclinical development are next-generation therapeutics, which require more sophisticated folding, disulfide bond formation, and assembly, or have other production challenges (i.e., toxicity, aggregation). These molecules routinely have titer and quality issues in standard cell-culture lines,” Weinstock states. Additionally, while there is a viable path forward for commercializing simple antibody-based drugs, current cell-culture technologies lead to long development timelines and high cost. Generally speaking, he continues, protein production bottlenecks can result from suboptimal protein stoichiometry (the ratio of heavy chain and light chain), protein folding, proteolysis, and reliance on export machinery that limit titer, quality, and productivity of cell culture strains.
Rapid results, diversity of experimental design, and robust data generation are all advantages that a synthetic biology-based approach could offer in upstream cell-culture processes, Douglass adds.
Using a synthetic biology-based approach to cell culture can potentially unlock benefits for biologic production. Synthetic biology enables systematic optimization of cell culture, Weinstock says. For instance, protein expression rates, protein folding, protein export, and metabolic engineering are aspects of protein production that can be improved beyond the native capabilities of the cell line through engineering, and doing so improves cell culture productivity. Additionally, synthetic biology enables simplification of downstream processing steps, for example, via targeted removal or reduction of host cell proteins known to create purification challenges.
The optimization of glycosylation would be a further advantage. “Uniformity of protein glycosylation is frequently a challenge in conventional cell lines, and synthetic biology will address glycan type and glycan uniformity,” Weinstock says.
The range of molecular tools at the disposal of research and process development scientists today can help facilitate a synthetic biology-based approach. For example, Douglass explains, the biopharmaceutical industry has the capability now to synthesize entire metabolic pathways and deliver it to a cell line. “Additionally, take into account the different equipment and consumable offerings that are purpose-built to drive innovation and productivity in the upstream process development space. For example, the equipment platforms from Berkeley Lights have decreased the time it takes to identify the best clones. Similarly, tailored media formulations generated in our cell-culture services have significantly improved the protein quality and titer capabilities of therapeutic manufacturers’ cell lines,” he says.
Douglass also emphasizes that the industry is at a point in time where synthetic biology-based systems in upstream cell culture are leading to new paths of biologics manufacturing. “I think biologics manufacturers understand well the variables that impact their processes and are actively working to solve them with the different tool suppliers in the life sciences industry,” he states.
Some challenges presented to biomanufacturers with a synthetic biology approach include the scalability of cell lines that have been genetically improved via this approach. Significant optimization efforts to improve cell lines identified in deep well-plate experiments may not necessarily translate to industrial fermentation scales, notes Weinstock. “It’s important to build robust cell culture scale-up and scale-down models to ensure scalability of cell-line improvements.”
Moreover, traditional research efforts to identify cell-line improvements are laborious, Weinstock stresses. Although the genetic tools (e.g., clustered regularly interspaced short palindromic repeats) to make efficient and systematic changes to cell lines have improved considerably over the past 10 years, it typically takes extensive iteration in the lab to optimize new mammalian cell lines that work generically well for protein production.
Cell culture systems can learn a great deal about strategies for cell line improvement from advances made in alternative cell lines using synthetic biology. Many biologics (including antibodies) that have historically been made in cell culture can now be made very efficiently in E. coli using advanced cell lines engineered using synthetic biology. “Earlier this year we were able to construct a high-titer cell line for the production of a COVID-19 diagnostic antibody, scale up the strain, purify material, characterize the material, generate a research cell bank, and ship to a partner in a 10-day timeframe. Using traditional cell culture techniques, that same process would have taken months,” says Weinstock, who encourages increasing adoption of synthetic biology in cell culture systems. “Synthetic biology enables exquisite control over all cellular processes that are involved in the production of proteins,” he adds.
Alison Arnold, head of Fermentation and Microbiology at Ingenza—a biotechnology company—sees the main challenge in using synthetic biology as ensuring that any cell culture processes based on this technology are compliant with appropriate regulatory guidelines. Biologics must be approved or manufactured according to good manufacturing practice (GMP) standards and fit in with regulatory guidelines. “Synthetic biology is such an exciting field, offering benefits in a huge range of areas, including cell culture for biologics. However, ensuring regulatory compliance can be a time-consuming process,” she says. “It can also be expensive to set up a synthetic biology lab and challenging to build synthetic systems quickly, if you don’t have the necessary knowhow.” Arnold says that it is necessary to have the capabilities or access to test and screen strains to take them forward to production. For these reasons, companies may be in the mindset of not wanting to change their current methodologies, despite a synthetic approach offering advantages.
Feliza Mirasol is the science editor for BioPharm International.
Vol. 34, No. 1
When referring to this article, please cite is as F. Mirasol, “Cultivating a Synthetic Biology-Based Approach to Improving Cell Culture,” BioPharm International 34 (1) 2021.