Tracing production instability in a clonally derived CHO cell line using single‐cell transcriptomics

• Published in: Biotechnology and bioengineering Vol. 118; no. 5; pp. 2016 - 2030
• Main Authors: Tzani, Ioanna, Herrmann, Nicholas, Carillo, Sara, Spargo, Cathy A., Hagan, Ryan, Barron, Niall, Bones, Jonathan, Shannon Dillmore, W., Clarke, Colin
• Format: Journal Article
• Language: English
• Published: United States Wiley Subscription Services, Inc 01.05.2021
• Subjects: Animals; Antibodies, Monoclonal - analysis; Antibodies, Monoclonal - genetics; Antibodies, Monoclonal - metabolism; Apoptosis; Biotechnology; Cell lines; Chains; Chinese hamster ovary; CHO Cells; Cricetinae; Cricetulus; Gene expression; Gene Expression Profiling - methods; Gene silencing; heterogeneity; High-Throughput Nucleotide Sequencing; Monoclonal antibodies; next‐generation sequencing; Oxidative stress; Reduction; Single-Cell Analysis - methods; single‐cell RNA‐seq; Transcriptome - genetics; transcriptomics; Transgenes; Transgenes - genetics; transcriptomics; single-cell RNA-seq; Chinese hamster ovary; next-generation sequencing; heterogeneity
• ISSN: 0006-3592; 1097-0290
• DOI: 10.1002/bit.27715

A variety of mechanisms including transcriptional silencing, gene copy loss, and increased susceptibility to cellular stress have been associated with a sudden or gradual loss of monoclonal antibody (mAb) production in Chinese hamster ovary (CHO) cell lines. In this study, we utilized single‐cell RNA‐seq (scRNA‐seq) to study a clonally derived CHO cell line that underwent production instability leading to a dramatic reduction of the levels of mAb produced. From the scRNA‐seq data, we identified subclusters associated with variations in the mAb transgenes and observed that heavy chain gene expression was significantly lower than that of the light chain across the population. Using trajectory inference, the evolution of the cell line was reconstructed and was found to correlate with a reduction in heavy and light chain gene expression. Genes encoding for proteins involved in the response to oxidative stress and apoptosis were found to increase in expression as cells progressed along the trajectory. Future studies of CHO cell lines using this technology have the potential to dramatically enhance our understanding of the characteristics underpinning efficient manufacturing performance as well as product quality. Tzani and co‐workers report the use of single cell transcriptomics to capture > 3,800 gene expression profiles from a clonally derived monoclonal antibody producing CHO cell line that had undergone production instability. Analysis of the resulting data enabled the study of transgene and host cell gene expression patterns at unprecedented resolution. The authors were also able to trace the evolution of the cell line, capturing the divergence of the population over its lifetime in culture.