Elimination of the Warburg effect in Chinese hamster ovary (CHO) cells improves cell phenotype as a protein production platform

Lactate is a common metabolite and is central to many important processes. One of its more prominent roles is in the Warburg effect, in which cancer cells exhibit high rates of glycolytic flux followed by secretion of lactate, even in the presence of oxygen. This fermentation of pyruvate to lactate via lactate dehydrogenase (Ldh) accompanies increased proliferation of cancer cells and several other types of rapidly proliferating cell types in immune cell activation and embryonic development. Aerobic glycolysis is also prominent in biotherapeutic protein production, where mammalian production cells often secrete high levels of lactate. The accumulation of lactate is deleterious for cell growth, viability, product formation, and quality, both directly via acidification of the media and indirectly through base addition to control culture pH. Despite a clear genetic target, efforts to eliminate lactate secretion via knockout of Ldh(s) in mammalian cells have been unsuccessful, pointing to the essentiality of Ldh mediated NAD regeneration. A wide variety of approaches have been utilized to limit lactate accumulation in culture, including knockdown or inhibition of Ldh, replacement of glucose with alternate sugars, controlled feeding strategies, and many others, however none have proven successful in eliminating the Warburg effect. We report the elimination of the Warburg effect in a CHO cell line by using CRISPR/Cas9-based engineering to simultaneously knockout enzymes responsible for lactate production and ancillary regulators. The resulting cell lines remain proliferative while consuming significantly less glucose and can be used to generate protein producing lines using standard industrial processes. In a pH-controlled fedbatch process, the Warburg null cells require minimal base addition to maintain a stable pH, allowing an extended growth phase. The knockout strategy was also successfully applied to a CHO cell line producing Rituximab, again resulting in a prolonged growth phase. Additionally, protein production was maintained, while product quality was improved with increased glycan galactosylation. Thus, CHO cells without the capacity of Warburg metabolism may be useful for engineering production cell lines with enhanced bioproduction traits

Elimination of the “Essential” Warburg effect in CHO cells through a multiplex genome engineering strategy

The Warburg effect has posed a constant challenge in mammalian bioprocessing since the field began. Indeed, the predisposition of mammalian cells to secrete large quantities of lactic acid through the Warburg effect leads to premature cell death, reduced product yields, and often lower quality products. Thus, over the past decades, numerous innovations in the mammalian cell culture field have focused on mitigating lactate secretion, including through media optimization, feeding control, chemical inhibition, etc. Despite extensive efforts from many researchers, complete elimination of lactic acid production has not yet been obtained. Specifically, several independent efforts to knock out lactate dehydrogenase (the enzyme responsible for producing lactic acid from pyruvate) have been unsuccessful, as it has seemed essential for immortalized cell growth. Here I present our work in which we discovered a panel of genes involved in a genetic feedback circuit that controls lactic acid secretion in mammalian cells. Knocking out individual genes in serial was unsuccessful since LdhA and other targets are essential for CHO cell growth. However, we knocked out these genes simultaneously and overcame the “essentiality” of these genes, leading to the successful elimination of lactic acid secretion in Chinese hamster ovary cells. Since many hypotheses have been proposed regarding the essentiality of lactic acid secretion for rapid cell proliferation in cancer, immune cell activation, and embryonic development, we were interested to study how the complete elimination of the Warburg effect impacts CHO cells. Surprisingly, the cells show improved metabolic and growth phenotypes, despite the elimination of this fundamental metabolic activity. To understand how immortalized mammalian cells can cope without this seemingly essential metabolic process, we conducted a comprehensive analysis of these cell lines using time-course RNA-Seq, metabolomics, and analysis with a genome-scale metabolic network model developed for Chinese hamster ovary cells1. We further characterized its impact on recombinant drug production yields and quality. Thus, through a multiplex metabolic engineering effort and comprehensive systems biology analysis, we have been able to engineer out a leading challenge in protein biotherapeutic development and begin to understand now a cell can survive without a seemingly essential process. 1. Hefzi, H. et al. A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. Cell Syst. 3, 434–443.e8 (2016)