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

Lise Marie Grav, Daria Sergeeva, Jae Seong Lee, Igor Marín de Mas, Nathan E. Lewis, Mikael Rørdam Andersen, Lars Keld Nielsen, Gyun Min Lee, Helene Faustrup Kildegaard*

*Corresponding author for this work

Research output: Contribution to journalJournal articleResearchpeer-review


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.
Original languageEnglish
JournalA C S Synthetic Biology
Issue number9
Pages (from-to)2148-2159
Publication statusPublished - 2018


  • Clonal variation
  • CRISPR/Cas9
  • Mammalian cells
  • Recombinase-mediated cassette exchange
  • Targeted integration
  • Transcriptome


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