QTL technology combines Phenotypeca’s proprietary breeding method with genomic based screening to optimise strains for a given protein and the requirements of its market.
The technology targets specific variations of critical locations in the genome – otherwise known as quantitative trait loci (QTL) – that functionally drive key aspects of protein manufacture. These variations are like letters in an alphabet which QTL technology can uniquely identify to exploit the full power of biology, delivering an optimal protein and manufacturing method.
The optimised strain is protected by Phenotypeca’s patent estate. This covers the breeding process as well as the specific quantitative trait loci. No one else can use patented quantitative trait loci to develop rival products.
Phenotypeca has access to strains of baker’s yeast (Saccharomyces cerevisiae) which evolved in Japanese sake and European wine processes. Others were found in diverse geographical locations such as West Africa. Guided by proprietary genomic knowledge and the needs of each project, we draw on this diverse library to select appropriate parent strains for initial breeding.
Genomic optimisation screening
Initial breeding results in billions of different progeny strains that are screened using specially tailored assays to identify the best performers. QTL analysis on the best performers informs which parent strains are selected for the next round of breeding.
The optimisation process of breeding, screening and QTL analysis is then continuously iterated. Billions more progeny are generated in each round to keep improving performance. The process concludes when the project’s objectives have been satisfied, and/or when progeny strain performance hits a plateau, indicating that the ceiling of biological capability has been reached.
Why we use Saccharomyces cerevisiae
Until recently, old patents kept S. cerevisiae off-limits for certain aspects of recombinant protein manufacture. Therefore, the industry turned to alternatives such as Chinese hamster ovary cells and Pichia pastoris, which have significant limitations for multi-parameter optimisation.
The patents that restricted S. cerevisiae innovation have now expired. This puts Phenotypeca in a strategic position to leverage its proprietary knowledge based on decades of functional genomic research using S. cerevisiae, opening up the entire genome for optimisation.
The fast breeding cycle of S. cerevisiae and the billions more progeny it produces compared to mammalian cells, make exploration and optimisation pragmatically feasible. The greater dexterity of S. cerevisiae also brings critical advantages to protein folding and upstream adjustments, enabling optimisation to reduce downstream processing steps.
QTL technology is currently focused on S. cerevisiae, but the patents also cover variants in other eukaryote cells.
Strain characteristics optimised
QTL technology can optimise a range of strain characteristics to provide numerous recombinant protein manufacturing advantages, including:
- High protein titre
- Reduced downstream processing
- Protease reduction
- Mitochondrial fitness
- Reduced cell lysis
- Crabtree effect control
- High genetic stability for continuous manufacturing
What other methods lack
Conventional methods such as rational strain engineering and mutagenesis are not equipped to compete with QTL technology when multi-parameter optimisation is required to create a premium recombinant protein manufacturing process tailored for its market. In these circumstances, the chances of delivering an optimum process using the rival methods are statistically remote and often financially unviable at the scale required. They use only a small part of a single genome, and the number of strains available for screening is orders of magnitude less. They also frequently generate sick strains due to adverse side effects, making them unreliable and ill-suited for commercially scalable manufacture.