Investigation of Trancriptome and methylome changes in Chinese Hamster Ovary cells after single cell cloning

Chinese hamster ovary (CHO) cells are the most extensively used mammalian production system for biologics intended for use in humans. A critical step in the establishment of production cell lines is single cell cloning, with the objective of achieving high productivity and product quality. Despite general use, knowledge of the effects of this process is limited. Importantly, single cell cloned cells display a wide array of observed phenotypes, which so far was attributed to the instability and variability of the CHO genome. In this study we present evidence that the reason for the generation of subclones with diverse phenotypes are changes in DNA methylation patterns and transcriptomes that occur during the subcloning process. These results indicate that epigenetic regulation is a hidden player in cell line development with an important role in the establishment of high performing clones with improved characteristics for bioprocessing.