Minimizing Clonal Variation during Mammalian Cell Line Engineering for Improved Systems Biology Data Generation

Mammalian cells are widely used to
express genes for basic biology studies and biopharmaceuticals. Current
methods for generation of engineered cell lines introduce high genomic
and phenotypic diversity, which hamper studies of gene functions and
discovery of novel cellular mechanisms. Here, we minimized clonal
variation by integrating a landing pad for recombinase-mediated cassette
exchange site-specifically into the genome of CHO cells using CRISPR
and generated subclones expressing four different recombinant proteins.
The subclones showed low clonal variation with high consistency in
growth, transgene transcript levels and global transcriptional response
to recombinant protein expression, enabling improved studies of the
impact of transgenes on the host transcriptome. Little variation over
time in subclone phenotypes and transcriptomes was observed when controlling
environmental culture conditions. The platform enables robust comparative
studies of genome engineered CHO cell lines and can be applied to
other mammalian cells for diverse biological, biomedical
and biotechnological applications.