Systems biology analysis of CHO cell clonal variation

In this study, we employed recent cell line development tools, including Beacon, CRISPR, and recombinase-mediated cassette exchange, for site-specific transgene insertion with the goal of decreasing clonal variability. By adopting a systems biology perspective, incorporating proteomics and transcriptomics, we examined sixteen CHO cell lines and found considerable clonal variation, which hinders the analysis of transgene expression, particularly that of Factor IX. The integration of proteomic and transcriptomic analyses, coupled with bootstrapping and Data Integration Analysis for Biomarker Discovery Using Latent components (DIABLO) modelling, has revealed potential signatures of clonal variation. These insights contribute to our understanding of the complex causes of clonal variation. They also highlight the metabolic shifts that CHO cells undergo during development, which may inform strategies for future CHO cell line development. This study advances our understanding of the persistent clonal variation in CHO cells when creating transgene-expressing cell lines.