Dynamic mRNA and miRNA profiling of CHO-K1 suspension cell cultures

Authors

  • Dr. Juan A. Hernández Bort,

    Corresponding author
    1. Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Austria
    • Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Muthgasse 18, 1190 Vienna, Austria
    Search for more papers by this author
    • *

      These authors contributed equally to this study and share first authorship.

  • Matthias Hackl,

    Corresponding author
    1. Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Austria
    • Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Muthgasse 18, 1190 Vienna, Austria
    Search for more papers by this author
    • *

      These authors contributed equally to this study and share first authorship.

  • Helga Höflmayer,

    1. Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Austria
    Search for more papers by this author
  • Vaibhav Jadhav,

    1. Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Austria
    Search for more papers by this author
  • Eva Harreither,

    1. Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Austria
    Search for more papers by this author
  • Niraj Kumar,

    1. Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Austria
    Search for more papers by this author
  • Wolfgang Ernst,

    1. Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Austria
    2. ACIB GmbH, Austrian Centre of Industrial Biotechnology, Graz, Austria
    Search for more papers by this author
  • Johannes Grillari,

    1. Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Austria
    Search for more papers by this author
  • Nicole Borth

    1. Department of Biotechnology, University of Natural Resources and Applied Life Sciences, Vienna, Austria
    2. ACIB GmbH, Austrian Centre of Industrial Biotechnology, Graz, Austria
    Search for more papers by this author

Abstract

In spite of the importance of Chinese hamster ovary (CHO) cells for recombinant protein production, very little is known about the molecular and gene regulatory mechanisms that control cellular phenotypes such as enhanced growth under serum-free conditions or high productivity. Most microarray analyses to this purpose are performed with samples taken during the exponential growth phase. However, the cellular transcriptome is dynamic, changing in response to external and internal stimuli and thus reflecting the current functional capacity of cells as well as their ability to adapt to a changing environment. Therefore, during batch or fed-batch cultivations it can be expected that the transcription pattern of genes will change and that such changes may give indications on the cellular state in terms of viability, growth, and productivity. In the current study we monitored the change in expression patterns of mRNAs and microRNAs (miRNA) during lag, exponential, and stationary phases in CHO-K1 suspension cell cultures. In total, over 1400 mRNAs and more than 100 miRNAs were differentially regulated (p<0.05) relative to the batch culture at the starting point. Functional clustering revealed groups of genes with similar expression patterns, which were subjected to functional pathway analysis. In addition, as miRNAs generally act as negative post-transcriptional regulators of mRNAs, we looked for changes in their expression that were inverse to those of their predicted target mRNAs.

Ancillary