Having worked with Vax-Hub over the last year, Phenotypeca is delighted to have been invited to contribute to their latest newsletter, focusing on protein production platforms for vaccine development.
Dr Chris Finnis, Phenotypeca’s founder and Research Director, was asked to introduce Phenotypeca and share insights in the article found below. The full Vax-Hub Issue 5 Newsletter is here.
How is your company contributing to vaccine technology?
Phenotypeca® was founded in late 2018, bringing together unique expertise in yeast strain development and cGMP manufacturing to develop next-generation vaccine bioprocesses. Specifically, yeast breeding and quantitative trait loci (QTL) analysis combined with proven off-patent biopharmaceutical manufacturing technology.
Yeast-derived biologics have a long, safe history of human use, with the first hepatitis B vaccine launched in 1986, followed by insulin in 1987. However, these products’ manufacturing processes are sub-optimal, and the vaccines they produce are not available to all those who need them. Phenotypeca is developing next-generation systems harnessing natural diversity for the production of recombinant proteins, initially to improve the manufacturing of HBsAg and HPV vaccines.
Most FDA-approved biologics from yeast are still made by baker’s yeast (Saccharomyces cerevisiae) despite the expression technology being patent protected for many years and not made widely available until now. Phenotypeca decreases the time for production host optimisation by using breeding, high throughput selection and critical IP from first-generation industrial systems; instead of relying solely on traditional genome engineering. Despite yields often being higher from Pichia pastoris systems, S. cerevisiae has many advantages and is much safer for large scale manufacturing, growing on simple animal-free media without the need for oxygen or a methanol-feed. Therefore, one of Phenotypeca’s main objectives is to improve product yields while retaining and enhancing the qualities already valued by manufacturers.
“Omics” studies of first-generation yeast strains making recombinant proteins showed that strain engineering can give general improvement for many recombinant protein products. However, this is often limited by more elusive bottlenecks specific to each protein (or even variants of the same protein). Therefore, off-the-shelf first-generation strains are unlikely to be optimal for all proteins. Furthermore, improving the production strain for each specific protein product or variant is laborious, costly and slow, so has only been attempted in a few cases. The Vax-Hub Feasibility Study between Phenotypeca and The Jenner Institute focuses on using rapid strain development by yeast breeding, rather than traditional genome engineering methods. While this is one example of an academic-industry collaboration facilitated by Vax-Hub, yeast breeding technology can also be applied to other proteins suited to yeast expression, which might be of interest to Vax-Hub members.
Phenotypeca typically generates around a billion genetically distinct yeast progeny for full diversity screens, through multiple breeding rounds, taking 10-14 weeks. Depending on which parent strains we chose, there can be around 100,000 SNPs (single nucleotide polymorphisms) independently segregating throughout the genome during breeding. However, experience has shown that SNPs in as few as 10-30 key loci within the genome make the most significant contributions towards any particular complex trait, such as the yield of a VLP. Therefore, screening around a billion cells (2 (to the power of 30) equals around one billion) is highly likely to give strains with improved phenotypes. Subsequent genome analysis can also reveal the causal SNPs, leading to further improvements. In almost every case tested, progeny which are better than the best parent (as well as worse than the worst parent) can be generated by breeding in this way. In contrast, relatively little genetic diversity was explored when developing our first-generation yeast strains for biologics manufacturing.
Although some improvements are expected to be specific for a particular product, some are likely to be generally useful for vaccine manufacture and can be applied to many processes. To facilitate this Phenotypeca uses industrially stable, yet exchangeable plasmids; for example, a strain improved for HPV production can quickly be tested to see if it also improves bioprocessing for another vaccine, such as polio. Initial work by Phenotypeca with Vax-Hub led to Innovate UK funding to test the feasibility of optimising strains for the production of SARS-CoV-2 antigens for bulk microbial production from S. cerevisiae.
Why is your company part of the Vax-Hub, and why do you think it is important to support collaborations between industry and academia?
Phenotypeca was born out of strong academic research combined with extensive industrial know-how. Professor Ed Louis’ yeast genomics and breeding research, first published from work at the University of Nottingham and later from the University of Leicester, has been complemented with proven non-proprietary industrial manufacturing technology, initially developed by companies such as Delta Biotechnology and Novozymes Biopharma. While this represents one example of academic technology becoming established industrial practice, it is typical of many academic innovations translated through industrial collaboration. Phenotypeca’s R&D activities are currently based in the University of Nottingham’s Synthetic Biology Research Centre, which is part of the Biodiscovery Institute. This is a vibrant research environment where multiple biotechnology start-ups benefit from close interactions with academic researchers, which for Phenotypeca has already led to fruitful collaborations in phenotypic diversity and click-chemistry. Phenotypeca also has a strong industry network, with experienced industry professionals, such as our Board Directors Patrick Florent from GSK Vaccines and CEPI, and Simon Chalk from BioPhorum; who can support academic technology commercialisation within the biopharmaceutical industry.
While Phenotypeca is a yeast biofoundry business with core expertise in yeast strain development for cGMP manufacturing, we prefer to partner with experts in different product areas, in this case, the production of VLP-based vaccines. Vax-Hub provides the perfect complement of knowledge in areas such as vaccinology, immunology, down-stream processing and LMIC (Low-to-Middle Income Country) manufacturing. During our collaborations with The Jenner Institute, Vax-Hub has provided opportunities for cooperation with various experts, increasing the likelihood of successful outcomes. For example, down-stream processing advice from UCL, useful insights on process economics from Imperial College, or factors important to manufacturing by LMICs from industry partners could all affect important strain selection decisions. The Vax-Hub Collaboration Agreement facilitates rapid knowledge exchange between its academic and industrial members, who, with shared interests and goals, stand a significantly better chance of improving vaccine manufacturing when working together.
From a personal perspective working in a biotechnology start-up company within Vax-Hub is also incredibly exciting. Since we have started exploring diverse yeast libraries for traits beneficial to recombinant protein production, we have been amazed by the diversity of phenotypes observed. It would be much harder for a relatively small company, like Phenotypeca, to follow-up on positive results like these alone, if we were not part of Vax-Hub. It also provides an excellent forum for the professional development of researchers working within Vax-Hub, whether in academia or industry.
Your company is mainly focusing on VLP vaccine development – what led the company to choose this particular research area?
Phenotypeca chose VLP vaccine development because there is a need to improve the established yeast-derived vaccine manufacturing processes, e.g. especially around cost-of-goods, sustainability and robustness; and to develop new technologies and strategies, e.g. for rapid response to emerging threats. We would also like these new technologies to be more widely available than they have been for first-generation processes, especially for LMICs.
Because S. cerevisiae is the model eukaryotic microbe, with its genome published in 1996, a wealth of academic and industrial knowledge surrounds its use as a production host, and well-established method exists for genome engineering and analysis. It is also extremely well suited to the large-scale manufacture of biologics, with a proven safety track-record and costs significantly lower than mammalian systems. It also performs the eukaryotic post-translational modifications needed for many biologics.
Yield improvement for intracellular products, such as virus-like particle (VLP) vaccines, also lends itself particularly well to our high throughput screening methods, such as fluorescence-activated cell sorting (FACS), able to sort around a billion cells in a few hours. For some VLPs, such as enveloped HBsAg VLPs, we expect this will allow strain improvement for traits such as lipid metabolism and membrane biogenesis, which are likely to be sub-optimal in first-generation processes.
We are also interested in VLPs as scaffolds for conjugation to antigens; as alternative manufacturing strategies, or in rapid response scenarios. For secreted products, Phenotypeca is optimising strains to secrete SARS-CoV-2 antigens, which could be conjugated to VLPs; and secreted therapeutic proteins such as antibody domains are also well-suited to yeast.
What is, according to you/your company, the future of vaccine technology?
There is a far greater understanding of pathogens and our immune system than there has ever been, which will boost future innovation in vaccine development. Furthermore, the recent COVID-19 pandemic has raised awareness of the societal need for improved vaccine technology and the ability of academic-industrial collaborations to deliver them. In parallel, we have seen tremendous advances in S. cerevisiae genetics and biopharmaceutical manufacturing since the first biologics processes were developed over 30-years ago, which will accelerate yeast-derived vaccine innovation.
For yeast-based manufacturing, we envisage these conditions will result in faster process development times, leading to lower-cost vaccines, more robust, simple processes, which are environmentally sustainable and practical for LMICs. It is also conceivable to manufacture VLPs in pre-validated processes for rapid conjugation to novel antigens for faster response times, e.g. during an epidemic or for seasonal vaccines.
For yeast processes there will be a continuation of best-practices, e.g. making production strains using only yeast DNA and the synthetic gene of interest, without using any antibiotic markers that might contribute to antimicrobial resistance in the environment. These will be combined with new improvements, such as genetic solutions to increase yields, allow simple feeding regimes, or to allow growth at elevated temperatures with reduced cooling water requirements.
Thus, the future of vaccine technology could not be brighter.
Dr Chris Finnis (Research Director).