Mining Data From Plasma Cell Differentiation Identified Novel Genes for Engineering of a Yeast Antibody Factory

Abstract

Saccharomyces cerevisiae is a common platform for production of therapeutic proteins, but it is not intrinsically suited for the manufacturing of antibodies. Antibodies are naturally produced by plasma cells (PCs) and studies conducted on PC differentiation provide a comprehensive blueprint for the cellular transformations needed to create an antibody factory. In this study we mined transcriptomics data from PC differentiation to improve antibody secretion by S. cerevisiae. Through data exploration, we identified several new target genes. We tested the effects of 14 genetic modifications belonging to different cellular processes on protein production. Four of the tested genes resulted in improved antibody expression. The ER stress sensor IRE1 increased the final titer by 1.8-fold and smaller effects were observed with PSA1, GOT1, and HUT1 increasing antibody titers by 1. 6-, 1. 4-, and 1.4-fold. When testing combinations of these genes, the highest increases were observed when co-expressing IRE1 with PSA1, or IRE1 with PSA1 and HUT1, resulting in 3.8-and 3.1-fold higher antibody titers. In contrast, strains expressing IRE1 alone or in combination with the other genes produced similar or lower levels of recombinantly expressed endogenous yeast acid phosphatase compared to the controls. Using a genetic UPR responsive GFP reporter construct, we show that IRE1 acts through constitutive activation of the unfolded protein response. Moreover, the positive effect of IRE1 expression was transferable to other antibody molecules. We demonstrate how data exploration from an evolutionary distant, but highly specialized cell type can pinpoint new genetic targets and provide a novel concept for rationalized cell engineering.

Production of galactosylated complex-type N-glycans in glycoengineered Saccharomyces cerevisiae

“…Thus, instead of homogeneous production of single glycoforms, the ability to produce glycan patterns comparable to current production platforms using yeast could be more advantageous. In addition to optimizing the glycosylation pattern, increasing the production levels of foreign proteins in yeast is essential in the context of therapeutic protein production, and our research group has also accomplished improvements in this area (Koskela et al 2020 ).…”

Early Emergence of Adaptive Mechanisms Sustaining Ig Production: Application to Antibody Therapy

“…Therefore, controlling ER stress could represent a complementary aspect to the monitoring one. Work mainly focused on UPR-specific genes activation has been successfully done with factors such as IRE1α ( 101 ), BiP ( 102 , 103 ) or XBP-1 ( 104 ). PDIs (protein disulfite isomerases) which are upregulated during Ig production (such as PDIA5 and PDIA6 in cluster 4; Figure 3A ) have also been shown to increase the protein secretion rate in CHO cells when overexpressed ( 105 , 106 ).…”