Between Dec 19, 2024 and Jan 2, 2025, datasets can be submitted to DRUM but will not be processed until after the break. Staff will not be available to answer email during this period, and will not be able to provide DOIs until after Jan 2. If you are in need of a DOI during this period, consider Dryad or OpenICPSR. Submission responses to the UDC may also be delayed during this time.
 

High-throughput transcriptomic analysis of resource-poor mammalian cell lines for recombinant protein production

Loading...
Thumbnail Image

Persistent link to this item

Statistics
View Statistics

Journal Title

Journal ISSN

Volume Title

Title

High-throughput transcriptomic analysis of resource-poor mammalian cell lines for recombinant protein production

Published Date

2013-10

Publisher

Type

Thesis or Dissertation

Abstract

Over the past 30 years, mammalian cell culture has enabled the production of recombinant protein therapeutics for treatment of a broad range of debilitating or life-threatening diseases. Continual improvements in cell and process engineering have facilitated the attainment of once unheard-of product titers, and improvements in molecular analysis techniques and process analytic technologies have been employed with great success for cell culture process characterization. High-throughput transcriptomic analysis tools such as microarrays and next-generation RNA sequencing (RNA-seq) provide access to gene expression information by simultaneously measuring the expression levels of tens of thousands of genes. However, until recently such tools have not been used to their full advantage in mammalian cell culture processes due to limitations in available reference sequences for the industrially important Chinese hamster ovary (CHO) and baby hamster kidney (BHK) cell lines. We employed high-throughput RNA sequencing in several CHO cell lines to identify and interrogate a class of small non-coding RNAs called microRNAs (miRNAs), which mediate post-transcriptional repression of protein-coding genes. We annotated and analyzed the expression and genomic conservation of several hundred of these small RNAs. We also employed RNA sequencing to build a comprehensive reference transcriptome for a recombinant protein-producing BHK cell lines. We utilized the BHK reference sequence to enable analysis of gene expression levels in the BHK cell line and two Syrian hamster tissues. We designed an expression microarray from the BHK sequence and utilized it to analyze the transcriptome profiles of BHK cells at several time points in perfusion culture at manufacturing scale. Implementation of several functional analysis tools revealed a consistent time-dependent change in the transcriptome profile that involved down-regulation of extracellular matrix components and changes to calcium signaling genes. The transcriptomic reference sequences we developed in this research and the detailed studies they have enabled will enhance our ability to understand and further optimize cell culture processes.

Description

University of Minnesota Ph.D. dissertation. October 2013. Major: Chemical Engineering. Advisor: Wei-Shou Hu. 1 computer file (PDF); ix, 149 pages, appendices A-B.

Related to

Replaces

License

Collections

Series/Report Number

Funding information

Isbn identifier

Doi identifier

Previously Published Citation

Other identifiers

Suggested citation

Johnson, Kathryn Christine. (2013). High-throughput transcriptomic analysis of resource-poor mammalian cell lines for recombinant protein production. Retrieved from the University Digital Conservancy, https://hdl.handle.net/11299/161008.

Content distributed via the University Digital Conservancy may be subject to additional license and use restrictions applied by the depositor. By using these files, users agree to the Terms of Use. Materials in the UDC may contain content that is disturbing and/or harmful. For more information, please see our statement on harmful content in digital repositories.