The Epigenetics (Histone PTMs) of Therapeutic Protein Production in CHO Cells

Chinese hamster ovary (CHO) cells are an important host cell system for the manufacturing of biopharmaceuticals. Epigenetics have been shown to have an important role in controlling gene expression in CHO cells, and thus affect the rate of protein production. It is hoped that by understanding the role of epigenetics in CHO cells improvements can be made in the production of biopharmaceuticals. In this work we have studied how histone PTMs differ between cell lines and throughout culture. These changes have then been correlated with growth rate, cell size and specific productivity.
Mass spectrometry (MS) has been used as an unbiased quantitative technique to study how histone PTMs differ between four cell lines and throughout cell culture. The data generated in this study is the first global analysis of histone PTMs in CHO cells to date. The relative abundances of histone PTM were compared across different CHO-S and CHO-K1 cell lines with different productivities. Similar patterns of histone PTMs were observed. The most abundant modifications identified included H3K9me3, H4K20me2 and H3K27me1. Furthermore the results show no significant differences between different clones within a lineage, but the abundance of H3K23ac differed between lineages.
In addition, the relative abundances of histone PTM for the different cell lines were compared throughout batch culture. Over 20 proteoforms were identified having different abundances at different stages of culture. The most prominent change was on H4K20 where methylation was progressive. The majority of the modifications that changed were associated with quiescence such as H3K9me3K14ac and H3K27me3 which increased through culture. Given that changes occurred through culture these were then correlated with the cellular phenotypes of growth rate, cell size and specific productivity. H3K27me3 and acetylation of H4 which correlated with growth rate were identified as possible engineering targets.
Finally alterations to the epigenetic profile of CHO cells were made by small molecule inhibitors targeting methyltransferases and Histone deacetylases with the aim of improving specific productivity and growth rates of CHO cells. The results showed that addition of the small molecules inhibitors affected the growth rate through altering the epigenetic profile but in an unpredictable manner as multiple modification need to be altered to successfully alter the phenotype.