Predicting cell-specific productivity from CHO gene expression.
Improving the rate of recombinant protein production in Chinese hamster ovary (CHO) cells is an important consideration in controlling the cost of biopharmaceuticals. We present the first predictive model of productivity in CHO bioprocess culture based on gene expression profiles. The dataset used to construct the model consisted of transcriptomic data from 70 stationary phase, temperature-shifted CHO production cell line samples, for which the cell-specific productivity had been determined. These samples were utilised to investigate gene expression over a range of high to low monoclonal antibody and fc-fusion-producing CHO cell lines. We utilised a supervised regression algorithm, partial least squares (PLS) incorporating jackknife gene selection, to produce a model of cell-specific productivity (Qp) capable of predicting Qp to within 4.44 pg/cell/day root mean squared error in cross model validation (RMSE(CMV)). The final model, consisting of 287 genes, was capable of accurately predicting Qp in a further panel of 10 additional samples which were incorporated as an independent validation. Several of the genes constituting the model are linked with biological processes relevant to protein metabolism.
National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland. colin.clarke@dcu.ie
Colin
C
Clarke
Padraig
P
Doolan
Niall
N
Barron
Paula
P
Meleady
Finbarr
F
O'Sullivan
Patrick
P
Gammell
Mark
M
Melville
Mark
M
Leonard
Martin
M
Clynes
D000465:Algorithms; D000818:Animals; D016466:CHO Cells; D002460:Cell Line; D002851:Chromatography, High Pressure Liquid; D019295:Computational Biology / Q000379:methods; D006224:Cricetinae; D003412:Cricetulus; D015870:Gene Expression; D020869:Gene Expression Profiling; D016018:Least-Squares Analysis; D020411:Oligonucleotide Array Sequence Analysis; D010641:Phenotype; D013696:Temperature