Molecular Profiling for Improved Biologics Production in Pichia Pastoris

The GlycoFi Pichia pastoris platform is an important component of Merck's biologics production strategy, and it features engineered yeast strains capable of expressing functional and non-immunogenic human proteins. This is made possible by the elimination of several endogenous glycosylation enzymes and the incorporation of mammalian enzymes instead. A major goal for this platform is to further maximize the viability of the resulting strains during high cell density fermentations such that additional productivity gains can be realized. Furthermore, significant savings in time and resources could be achieved if the currently required strain selection process to identify the most robust strains was simplified.

To address this challenge, molecular profiling tools have recently been applied to better understand recombinant biologics production in Pichia pastoris. Such work has focused in part upon developing a predictive gene expression signature for cell death that can also inform and suggest strain and bioprocess engineering strategies for increasing cell robustness and biologics production. First, a gene expression signature was developed to predict Pichia pastoris cell robustness at a larger scale from smaller scale fermentations. Next, this signature was biologically annotated in order to develop hypotheses for strain and process improvements. This process of assigning biological meaning to a myriad of observed changes and to recommend specific actions for production improvement is an ongoing challenge in applying molecular profiling to bioprocess improvement. Leveraging both an internal bioinformatics database and the external Saccharomyces Genome Database, signature genes were identified as homologous to Saccharomyces cerevisiae genes implicated in a variety of biological processes. Specific recommendations for genetic interventions as well as bioprocess changes were prioritized and delivered based upon the corresponding yeast literature.

These and future molecular profiling studies will continue to deliver critical knowledge and suggestions for improved and lower cost Pichia pastoris biologics production at Merck.