(466e) Epigenomic Analysis on Chinese Hamster Ovary (CHO) Cells for Enhanced Production Cell Line Stability

For a biomanufacturing of protein therapeutics, the producing CHO cell line must have high expression level of the product gene. This is mostly achieved through a gene amplification process that increases the copy number of transgene in the genome. The increased mRNA expression of the transgene leads to high protein production, but often results in unstable cell lines that lose the productivity over long-term culture. Many have pursued the construction of robust production cell lines in which the transgene is integrated in a single, active and stable site in the genome. Ideally, such integration sites are rationally selected. The stability of the expression of transgene is affected by the structural integrity and vulnerability of the locus of integration as well as many factors affecting gene expression, among them epigenetic regulation. We surveyed the epigenetic landscape in multiple CHO cell lines to better understand the relationship between epigenetic status and cell line stability.

Chromatin accessibility is a strong indicator of regulatory activity in the genome. Local chromatin can become exposed by RNA polymerase occupancy at promoters and transcription factor occupancy at enhancers. To assess chromatin accessibility we employed Assay for Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) that uses a hyperactive Tn5 transposase to insert sequencing adapters preferentially into open chromatin. We found that the presence of ATAC-seq peaks near transcription start sites correlated with gene expression data. We also identified clusters of open chromatin peaks with very high ATAC-seq signal, commonly known as super-enhancers. These features are thought to mediate high transcription of cell-type specific genes. We hypothesize that integrating transgenes into loci with high ATAC-seq signal will confer increased expression stability due to reduced likelihood of epigenetic silencing.

This study provides a global view of transcriptional regulatory signatures and their potential for mediating strong transgene expression. Epigenomic analysis can benefit cell line development processes by identifying loci that maintain transgene stability without compromising transcriptional activity.