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Genetic analysis of heterogeneous sub-clones in recombinant Chinese hamster ovary cells

  • Genomics, transcriptomics, proteomics
  • Published:
Applied Microbiology and Biotechnology Aims and scope Submit manuscript

Abstract

Chinese hamster ovary (CHO) cells have been widely used for production of recombinant proteins and therapeutic antibodies. However, owing to the instability and heterogeneity of CHO cells, the development of stable and high-expression recombinant CHO cell lines is often time-consuming. To investigate the mechanisms associated with heterogeneity in protein productivity, we performed transcriptome analysis on the subclones derived from a stable parental CHO clone. Two high-expression subclones and one low-expression subclone were selected based on their similar genomic background and subjected to RNA-seq analysis. Over 100 differentially expressed genes were identified between the subclones with high and low productivity. The molecular functions of the differentially expressed genes were enriched for translational elongation, sterol biosynthetic process, and regulation of secretion. In addition, analyses of the two subclones with high protein expression levels identified over 300 differentially expressed genes involved in DNA metabolic processes, cellular macromolecule catabolic processes, cell cycle, protein catabolic processes, and RNA processing and transcription. A subset of the differentially expressed genes was overexpressed in CHO cells to identify their effects on protein production. Together, these results indicate that transcriptome variation can cause significant inter-cellular heterogeneity in CHO cells and a better understanding of the molecular mechanism underlying heterogeneity might help to improve the production of recombinant proteins by CHO cells.

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Acknowledgements

This study was supported by grants from National Natural Science Foundation of China (31270987, 31470896, 81402399), National Basic Research Program of China (973 Program) 2015CB553706 and Suzhou Applicational Basic Project, China (SYG201509). We would like to thank Editage [www.editage.cn] for the English language editing.

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Authors and Affiliations

  1. School of Life Sciences and Technology, Tongji University, Shanghai, China

    Kaiming Chen, Dong Li, Hongwen Li, Bing Li, Jie Li, Lei Huang, Renhao Li, Xiaoqing Xu, Lingxiao Jiang, Cizhong Jiang, Hua Gu & Jianmin Fang

  2. Shanghai Tongji Hospital, Tongji University, Shanghai, China

    Jianmin Fang

  3. Tongji University Suzhou Institute, Suzhou, Jiangsu, China

    Jianmin Fang

  4. Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China

    Jianmin Fang

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  1. Kaiming Chen
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  2. Dong Li
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Correspondence to Jianmin Fang.

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Chen, K., Li, D., Li, H. et al. Genetic analysis of heterogeneous sub-clones in recombinant Chinese hamster ovary cells. Appl Microbiol Biotechnol 101, 5785–5797 (2017). https://doi.org/10.1007/s00253-017-8331-4

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