Defining lncRNAs Correlated with CHO Cell Growth and IgG Productivity by RNA-Seq.

Davide Vito,Jens Christian Eriksen,Christian Skjødt,C Mark Smales,Søren K Rasmussen,Dietmar Weilguny

doi:10.1016/j.isci.2019.100785

Davide Vito, Jens Christian Eriksen + Show 4 more

Open Access

https://doi.org/10.1016/j.isci.2019.100785

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Abstract

SummaryHow the long non-coding RNA (lncRNA) genome in recombinant protein producing Chinese hamster ovary (CHO) cell lines relates to phenotype is not well described. We therefore defined the CHO cell lncRNA transcriptome from cells grown in controlled miniature bioreactors under fed-batch conditions using RNA-Seq to identify lncRNAs and how the expression of these changes throughout growth and between IgG producers. We identify lncRNAs including Adapt15, linked to ER stress, GAS5, linked to mTOR signaling/growth arrest, and PVT1, linked to Myc expression, which are differentially regulated during fed-batch culture and whose expression correlates to productivity and growth. Changes in (non)-coding RNA expression between the seed train and the equivalent day of fed-batch culture are also reported and compared with existing datasets. Collectively, we present a comprehensive lncRNA CHO cell profiling and identify targets for engineering growth and productivity characteristics of CHO cells.

Highlights

Many recombinant protein biopharmaceuticals are expressed in mammalian expression systems due to the ability of such systems to correctly fold, assemble, and undertake ‘‘human-like’’ post-translational modifications and secrete the target protein out of the cell (Walsh, 2010)
We identify long non-coding RNA (lncRNA) including Adapt15, linked to ER stress, growth-arrest-specific transcript 5 (GAS5), linked to mTOR signaling/growth arrest, and plasmacytoma variant translocation 1 (PVT1), linked to Myc expression, which are differentially regulated during fed-batch culture and whose expression correlates to productivity and growth
Following our previous landscape of lncRNA expression in Chinese hamster ovary (CHO) using microarray (Vito and Smales, 2018), we set out to provide an analysis of the lncRNA transcriptome using RNA-Seq in CHO cells producing three different model IgG1 monoclonal antibodies during fed-batch culture, defining those lncRNAs expressed in CHO cells and the flux of these during culture and between cell lines

Summary

Introduction

Many recombinant protein biopharmaceuticals are expressed in mammalian expression systems due to the ability of such systems to correctly fold, assemble, and undertake ‘‘human-like’’ post-translational modifications and secrete the target protein out of the cell (Walsh, 2010). The ambrâ cell culture system (Sartorius Stedim Biotech) has been shown to give similar cell growth and productivity data to those achieved in larger-scale stirred bioreactors, enabling more accurate predictions compared with shake flasks on the behavior of a cell line at larger scale (Alsayyari et al, 2018; Janakiraman et al, 2015; Nienow et al, 2013; Rouiller et al, 2016) This capacity to conduct small-scale experiments under controlled conditions, of a highly predictive nature at larger scale, allows the investigation of the behavior of different cell lines under alternative feeding regimes to determine how each respond. Recent reports state that the ambrâ small-scale automated and controlled bioreactor system provides an excellent scale-down model to facilitate studies on multiple cell lines under controlled industrially relevant conditions to identify robust targets linked to productivity for cell engineering and material and data for future regulatory submissions (Sandner et al, 2019)

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