Utilizing RNA-Seq technique to improve molecular understanding of

Engineering Conferences International ECI Digital Archives Cell Culture Engineering XV Proceedings Spring 5-12-2016 Utilizing RNA-Seq technique to improve molecular understanding of Chinese Hamster ovary (CHO) cell bioprocessing Yogender Kumar Clemson University, ygowtha@clemson.edu Christpher Saski Clemson University Sarah Harcum Clemson University Follow this and additional works at: http://dc.engconfintl.org/cellculture_xv Part of the Biomedical Engineering and Bioengineering Commons Recommended Citation Yogender Kumar, Christpher Saski, and Sarah Harcum, "Utilizing RNA-Seq technique to improve molecular understanding of Chinese Hamster ovary (CHO) cell bioprocessing" in "Cell Culture Engineering XV", Robert Kiss, Genentech Sarah Harcum, Clemson University Jeff Chalmers, Ohio State University Eds, ECI Symposium Series, (2016) http://dc.engconfintl.org/cellculture_xv/171 This Abstract is brought to you for free and open access by the Proceedings at ECI Digital Archives It has been accepted for inclusion in Cell Culture Engineering XV by an authorized administrator of ECI Digital Archives For more information, please contact franco@bepress.com UTILIZING RNA-SEQ TECHNIQUE TO IMPROVE MOLECULAR UNDERSTANDING OF CHINESE HAMSTER OVARY (CHO) CELL BIOPROCESSING Yogender Kumar Gowtham, Department of Bioengineering, Clemson University ygowtha@clemson.edu Christopher A Saski, Computational Genomics Lab, Clemson University Sarah W Harcum, Department of Bioengineering, Clemson University Key Words: CHO cells, Next-generation sequencing, transcriptomics, RNA-Seq Chinese Hamster Ovary (CHO) cells are an important biopharmaceutical cell line, accounting for the production of over 70% of the approved protein therapeutics However several limitations exist with the use of CHO cell lines including low product titers Understanding of CHO cells in bioprocessing has up until now relied heavily on empirical results with a limited knowledge of the intracellular dynamics With the recent establishment of both Chinese hamster and CHO-K1 cell line genome assemblies, it is now possible to leverage the genomic resources to better understand and further improve CHO cell bioprocessing In this study, RNA-Seq, nextgeneration transcriptome sequencing, was used to characterize the gene expression profile of three different CHO cell lines under several industrially relevant conditions including low culture temperature and pH Each culture condition sample was sequenced by HiSeq 2000 and contained over 15 million short reads, which were assembled using the Chinese hamster reference genome (v1.01) Differential gene expression between conditions was statistically quantified based on generalized linear models using edgeR software for the replicate samples One of the applications of the RNA-Seq analysis method, in this study, was to observe and understand the impact of low culture temperature on CHO gene expression behavior In a CHO-K1 cell line adapted to protein-free medium, the cultures grown at 33°C had higher expression of 251 genes and lower expression of 15 genes (filter criteria were a minimum of two-fold expression change and FDR ≤ 0.05) compared to cultures grown at 37°C These genes could be utilized as potential targets for cellular and metabolic engineering to further improve CHO cell lines The current investigation presents the potential of next-generation sequencing techniques for advanced characterization of CHO cell bioprocessing  .. .UTILIZING RNA-SEQ TECHNIQUE TO IMPROVE MOLECULAR UNDERSTANDING OF CHINESE HAMSTER OVARY (CHO) CELL BIOPROCESSING Yogender Kumar Gowtham, Department of Bioengineering, Clemson... linear models using edgeR software for the replicate samples One of the applications of the RNA-Seq analysis method, in this study, was to observe and understand the impact of low culture temperature... improve CHO cell bioprocessing In this study, RNA-Seq, nextgeneration transcriptome sequencing, was used to characterize the gene expression profile of three different CHO cell lines under several