Harnessing secretory pathway differences between HEK293 and CHO to rescue production of difficult to express proteins

• Published in: Metabolic engineering Vol. 72; pp. 171 - 187
• Main Authors: Malm, Magdalena, Kuo, Chih-Chung, Barzadd, Mona Moradi, Mebrahtu, Aman, Wistbacka, Num, Razavi, Ronia, Volk, Anna-Luisa, Lundqvist, Magnus, Kotol, David, Tegel, Hanna, Hober, Sophia, Edfors, Fredrik, Gräslund, Torbjörn, Chotteau, Veronique, Field, Ray, Varley, Paul G., Roth, Robert G., Lewis, Nathan E., Hatton, Diane, Rockberg, Johan
• Format: Journal Article
• Language: English
• Published: Belgium Elsevier Inc 01.07.2022
• Subjects: Bioproduction; CHO; Differential gene expression analysis; HEK293; Protein secretion; Secretory pathway; Transcriptomics; HEK293; Protein secretion; Transcriptomics; Differential gene expression analysis; CHO; Bioproduction; Secretory pathway
• ISSN: 1096-7176; 1096-7184; 1096-7184
• DOI: 10.1016/j.ymben.2022.03.009

Biologics represent the fastest growing group of therapeutics, but many advanced recombinant protein moieties remain difficult to produce. Here, we identify metabolic engineering targets limiting expression of recombinant human proteins through a systems biology analysis of the transcriptomes of CHO and HEK293 during recombinant expression. In an expression comparison of 24 difficult to express proteins, one third of the challenging human proteins displayed improved secretion upon host cell swapping from CHO to HEK293. Guided by a comprehensive transcriptomics comparison between cell lines, especially highlighting differences in secretory pathway utilization, a co-expression screening of 21 secretory pathway components validated ATF4, SRP9, JUN, PDIA3 and HSPA8 as productivity boosters in CHO. Moreover, more heavily glycosylated products benefitted more from the elevated activities of the N- and O-glycosyltransferases found in HEK293. Collectively, our results demonstrate the utilization of HEK293 for expression rescue of human proteins and suggest a methodology for identification of secretory pathway components for metabolic engineering of HEK293 and CHO. •We report a first cross-species systems analysis of two of the most common mammalian cell factories, CHO and HEK293.•Comprehensive transcriptomic and productivity data set with 5 host cell lines and 24 human difficult to express proteins.•HEK293 can rescue the expression of several human proteins that are difficult to express in CHO.•Metabolic engineering of key secretory pathway bottleneck genes boosted bioproduction up to three-fold in CHO.•More heavily glycosylated proteins benefit from increased glycosyltransferase expression found in HEK293.