New insights into genetic instability of an industrial CHO cell line by orthogonal omics

Abstract Cell line instability can pose a challenge from both regulatory and business needs perspectives. The regulatory guidelines of International Conference on Harmonization require manufacturers to evaluate the cell substrate with respect to the consistent production of the intended product and perform tests of stability during cell cultivation. In an effort to develop strategies for stabilizing cell lines, we applied RNA-seq-based transcriptomics and NMR and LCMS-based metabolomics to analyze an industrial monoclonal antibody-producing Chinese hamster ovary (CHO) cell line that was genetically unstable. The cells adapted well to environmental and nutritional changes during passaging and maintained robust cell growth, however, the omics data demonstrated that lysosome pathway, redox balancing, and lipid peroxidation and beta-oxidation were enhanced in aged cells. The genes involved in lysosome pathway activation up-regulated cellular recycling and scavenging activities, and reactive oxidative species production. While the genes associated with DNA damage were up-regulated and cell cycle was correspondingly inhibited, surprisingly those related to DNA repair machinery were down-regulated over time. This previously unrecognized disconnect between DNA damage recognition and the needed DNA repair highlights potential directions to stabilize cell lines by formulating inoculum media with increased antioxidant capacity or by maintaining a robust DNA repair system in CHO cells. Both directions require further study.