Evaluating Metabolite Profiles of Protein Hydrolysates for Cell Culture Media Applications

Abstract

Cell culture media development is an ongoing endeavour across biopharmaceutical and cultivated meat industries, often accounting for the majority of production costs. To relieve these costs, protein hydrolysates may be used as a cost-effective additive that provides a variety of beneficial nutrients to cell culture media. However, relatively unknown compositions and potential batch-to-batch variability add levels of uncertainty to the overall reproducibility of cell cultures when hydrolysates are introduced. To address this, this work performs a comprehensive analysis of hydrolysate products — encompassing four of the five non-animal derived sources and a variety of yeast products available through Kerry Group — to determine their composition via metabolomics and their impact on cell cultures. Nuclear magnetic resonance (NMR) metabolomics was able to establish a baseline composition of small metabolites within hydrolysates, identifying significant differences between hydrolysate products. On the other hand, batch-to-batch variance was identified as relatively low, where select metabolites account for the majority of the variability within any given product. These trends were also observed in targeted mass spectrometry (MS) metabolomic data, which compared 21 metabolites consistent to both methods. These comparisons further showcased the benefits of MS sensitivity, with greater consistency in identifying metabolites and overall lower coefficients of variance, highlighting the benefits of using multiple methods for characterization. To evaluate the product differences and low batch variance observed using metabolomics, hydrolysate effects were analysed in mixture design-of-experiments and within various culture media. In general, plant hydrolysates observed positive effects on cell growth when in combination, where cotton and wheat together or Hy-Yest™ 466 alone were the highest performing hydrolysates overall. While the hydrolysates fully replaced serum in classical media, which was otherwise unable to support cell growth, they inhibited overall growth when used in undisclosed commercial media, indicating an excess of nutrients and underscoring the importance of known media compositions. Furthermore, despite low metabolomic variance, significant differences in cell density were observed when comparing cell cultures with different yeast hydrolysate batches. This work serves as a basis for hydrolysate characterization, aiming to address perceived challenges in hydrolysate use to support further development in cost-effective cell culture media.