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Open Access Highly Accessed Research article

Integrated miRNA, mRNA and protein expression analysis reveals the role of post-transcriptional regulation in controlling CHO cell growth rate

Colin Clarke1*, Michael Henry1, Padraig Doolan1, Shane Kelly1, Sinead Aherne12, Noelia Sanchez1, Paul Kelly1, Paula Kinsella1, Laura Breen1, Stephen F Madden12, Lin Zhang3, Mark Leonard3, Martin Clynes1, Paula Meleady1* and Niall Barron1*

Author affiliations

1 National Institute for Cellular Biotechnology, Dublin City University, Dublin 9, Ireland

2 Molecular Therapeutics for Cancer Ireland, Dublin City University, Dublin 9, Ireland

3 Bioprocess R&D, Pfizer Inc., Andover, Massachusetts, USA

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Citation and License

BMC Genomics 2012, 13:656  doi:10.1186/1471-2164-13-656

Published: 21 November 2012

Abstract

Background

To study the role of microRNA (miRNA) in the regulation of Chinese hamster ovary (CHO) cell growth, qPCR, microarray and quantitative LC-MS/MS analysis were utilised for simultaneous expression profiling of miRNA, mRNA and protein. The sample set under investigation consisted of clones with variable cellular growth rates derived from the same population. In addition to providing a systems level perspective on cell growth, the integration of multiple profiling datasets can facilitate the identification of non-seed miRNA targets, complement computational prediction tools and reduce false positive and false negative rates.

Results

51 miRNAs were associated with increased growth rate (35 miRNAs upregulated and 16 miRNAs downregulated). Gene ontology (GO) analysis of genes (n=432) and proteins (n=285) found to be differentially expressed (DE) identified biological processes driving proliferation including mRNA processing and translation. To investigate the influence of miRNA on these processes we combined the proteomic and transcriptomic data into two groups. The first set contained candidates where evidence of translational repression was observed (n=158). The second group was a mixture of proteins and mRNAs where evidence of translational repression was less clear (n=515). The TargetScan algorithm was utilised to predict potential targets within these two groups for anti-correlated DE miRNAs.

Conclusions

The evidence presented in this study indicates that biological processes such as mRNA processing and protein synthesis are correlated with growth rate in CHO cells. Through the integration of expression data from multiple levels of the biological system a number of proteins central to these processes including several hnRNPs and components of the ribosome were found to be post-transcriptionally regulated. We utilised the expression data in conjunction with in-silico tools to identify potential miRNA-mediated regulation of mRNA/proteins involved in CHO cell growth rate. These data have allowed us to prioritise candidates for cell engineering and/or biomarkers relevant to industrial cell culture. We also expect the knowledge gained from this study to be applicable to other fields investigating the role of miRNAs in mammalian cell growth.

Keywords:
Chinese hamster ovary; CHO cells; Growth rate; MicroRNA; mRNA; Microarray; Proteomics