Project keywords

Cell and Tissue Engineering, Systems Biology, Systems Biotechnology, Manufacturing, Health, CHO, HEK293, MAb, Biofactory, Metabolic engineering

Project summary

Mammalian cells are important hosts for the production of a wide range of biopharmaceuticals due to their ability to produce correctly folded and glycosylated proteins. Compared to microbes and yeast, however, the productivity of mammalian cells is low because of their comparatively slow growth rate, tendency to undergo apoptosis, and low production capacities. While much effort has been invested in the engineering of mammalian cells with superior production characteristics, the success of these approaches has been limited to date. One factor responsible for this lack of success is our limited understanding of the cellular basis for high productivity, and of how discrete mechanisms within a cell contribute to the overall phenotype. Aiming to measure and characterize all cellular components at different functional levels, omics technologies have the potential to improve our understanding of mammalian cell physiology, elucidating new targets for the generation of a superior host cell line.

In the past 5 years, the release of the CHO genome and advances in omics technologies have enabled the generation of high-resolution, high-quality data, which together with advances in mammalian genome engineering tools will greatly change production of high value biopharmaceuticals. 


Song MC, Hou JJ, Nielsen LK, Gray PP (2015) Novel cell engineering of the Unfolded Protein Response to achieve efficient therapeutic protein production cell line. BMC Proceedings 9 (S9):P14. doi:10.1186/1753-6561-9-S9-P14.

Orellana CA, Marcellin E, Munro T, Gray PP, Nielsen LK (2015) Multi-omics approach for comparative studies of monoclonal antibody producing CHO cells. BMC Proceedings 9 (S9):O8. doi:10.1186/1753-6561-9-S9-O8.

Martínez VS, Buchsteiner M, Gray P, Nielsen LK, Quek LE (2015) Dynamic Metabolic Flux Analysis using B-splines to study the effects of temperature shift on CHO cell metabolism. Met Eng Comm 2: 46-57.

Orellana CA, Marcellin E, Schulz BL, Nouwens AS, Gray PP, Nielsen LK (2015) High antibody producing Chinese hamster ovary cells up-regulate intracellular protein transport and glutathione synthesis. J Proteome Res 14: 609–618. PMID: 25495469

Turner J, Quek LE, Titmarsh D, Krömer JO, Kao LP, Nielsen LK, Wolvetang E, Cooper-White J (2014) Metabolic profiling and flux analysis of MEL-2 human embryonic stem cells during exponential growth at physiological and atmospheric oxygen concentrations. PLoS ONE 9: e112757. PMID: 25412279. Online.

Fearnley LG, Davis MJ, Ragan MA, Nielsen LK (2014) Extracting Reaction Networks from Databases – Opening Pandora’s Box. Briefings in Bioinformatics 15: 973-983. PMID: 23946492. Online

Quek LE, Nielsen LK (2014) Steady-State 13C Fluxomics Using OpenFLUX. In: Krömer JO, Nielsen LK, Blank LM (eds) Metabolic Flux Analysis: Methods and Protocols. Series: Methods in Molecular Biology, vol. 1191. Chapter 13: 65-78. PMID: 25178793.

Quek LE, Nielsen LK (2014) Customization of 13C-MFA Strategy According to Cell Culture System. In: Krömer JO, Nielsen LK, Blank LM (eds) Metabolic Flux Analysis: Methods and Protocols. Series: Methods in Molecular Biology, vol. 1191. Chapter 5: 81-90. PMID: 25178785.

Martinez VS, Nielsen LK (2014) NExT: Integration of Thermodynamic Constraints and Metabolomics Data into a Metabolic Network. In: Krömer JO, Nielsen LK, Blank LM (eds) Metabolic Flux Analysis: Methods and Protocols. Series: Methods in Molecular Biology, vol. 1191. Chapter 4: 209-224. PMID: 25178784.

Quek LE, Nielsen LK (2014) A depth-first search algorithm to compute elementary flux modes by linear programming. BMC Systems Biology 8:94. PMID: 25074068. Online.

Martínez VS, Quek LE, Nielsen LK ( 2014) Network thermodynamic curation of human and yeast genome-scale metabolic models. Biophys J 107:493-503. PMID: 25028891.

Quek LE, Dietmair S, Hanscho M, Martinez VS, Borth N, Nielsen LK (2014) Reducing Recon 2 for steady-state flux analysis of HEK cell culture. J Biotech 184: 172-178. PMID: 24907410.

Mercer TR, Clark MB, Crawford J, Brunck ME, Gerhardt D, Taft R, Nielsen LK, Dinger M, Mattick JS (2014) Targeted sequencing for gene discovery and quantification using RNA CaptureSeq. Nat Protoc 9: 989-1009. PMID: 24705597

Fearnley LG, Ragan MA, Nielsen LK (2014) Towards a Large Integrated Model of Signal Transduction and Gene Regulation Events in Mammalian Cells. In: Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, pg 117-122.

Mercer TR, Edwards SL, Clark MB, Neph SJ, Wang H, Stergachis AB, John S, Sandstrom R, Li G, Sandhu KS, Ruan Y, Nielsen LK, Mattick JS, Stamatoyannopoulos JA (2013) DNase I-hypersensitive exons co-localize with promoters and distal regulatory elements. Nature Genetics 45:852-9. PMID: 23793028

Dietmair S, Hodson MP, Quek L-E, Timmins NE, Gray P, Nielsen LK (2012) A multi-omics analysis of recombinant protein production in Hek293 cells. PLoS ONE 7(8):e43394. PMID: 22937046. PMC3427347

Fearnley LG, Nielsen LK (2012) PATHLOGIC-S: A scalable Boolean framework for modelling cellular signalling. PLoS ONE 7(8): e41977. PMID: 22879903. PMC3413702

Martinez VS, Dietmair S, Quek L-E, Hodson MP, Gray P, Nielsen LK (2012) Flux balance analysis of CHO cells before and after a metabolic switch from lactate production to consumption. Biotechnol. Bioeng. 110: 660-666. PMID: 22991240

Dietmair S, Hodson MP, Quek LE, Timmins NE, Chrysanthopoulos P, Jacob SS, Gray P, Nielsen LK (2012)Metabolite profiling of CHO cells with different growth characteristics. Biotechnol. Bioeng. 109: 1404-1414. PMID: 22407794

Dietmair S, Timmins NE, Chrysanthopoulos P, Gray PP, Kr?mer JO, Nielsen LK (2012) Metabolomic analysis of CHO cultures with different growth characteristics - Development of a metabolite extraction protocol for suspension adapted mammalian cells In N. Jenkins, N Barron, PM Alves (Ed.) Proceedings of the 21st Annual Meeting of the European Society for Animal Cell Technology (ESACT), Dublin, Ireland, June 7-10, 2009 (pp. 37-41) Dordrecht, Netherlands: Springer.

Li J, Wijffels G, Yu Y, Nielsen LK, Niemeyer DO, Fisher AD, Ferguson DM, Schirra HJ (2011) Altered Fatty Acid Metabolism in Long Duration Road Transport: An NMR-based Metabonomics Study in Sheep. J Proteome Res. 10: 1073-87. PMID: 21142080.

Krömer JO, Dietmair S, Jacob SS, Nielsen LK (2011) Quantification of L-alanyl-L-glutamine in mammalian cell culture broth - evaluation of different detectors. Analytical Biochemistry 416:129-31. PMID: 21651886.

Dietmair S, Nielsen LK, Timmins NE (2010) Engineering a mammalian super producer. Journal of Chemical Technology & Biotechnology 86: 905–914.

Dietmair S, Timmins NE, Gray PP, Nielsen LK, Krömer JO (2010) Toward quantitative metabolomics of mammalian cells: Development of a metabolite extraction protocol. Analytical Biochemistry 404:155-164. PMID: 20435011.

Quek L-E, Dietmair S; Krömer JO, Nielsen LK (2010) Metabolic flux analysis in mammalian cell culture. Metabolic Engineering 12: 161-171. PMID: 19833223.

Quek L-E, Nielsen LK (2009) Metabolic engineering of mammalian cells. In: The Metabolic Pathway Engineering Handbook, ed. CD Smolke. CRC Press. Chapter 26. ISBN 978-1-4398-0296-0.  Publication Date: 28/07/2009.

Quek L-E, Wittmann C, Nielsen LK, Krömer JO (2009) OpenFLUX: Efficient Modelling Software for 13C-Based Metabolic Flux Analysis. Microbial Cell Factories 8:25. PMID: 19409084.

Quek L-E, Nielsen LK (2008) On the reconstruction of the Mus musculus genome-scale metabolic network model. Genome Informatics 21:89-100.

Dinnis DM, Stansfield SH, Schlatter S, Smales CM, Alete D, Birch JR, Racher AJ, Marshall CT, Nielsen LK, James DC (2006) Functional proteomic analysis of GS-NS0 murine myeloma cell lines with varying recombinant monoclonal antibody production rate. Biotechnology and Bioengineering 94: 830-841. DOI 10.1002/bit. 20899

Sheikh K, Förster J, Nielsen LK (2005) Modeling Hybridoma Cell Metabolism Using a Generic Genome-Scale Metabolic Model of Mus musculus. Biotechnology Progress 21:112-121. DOI: 10.1021/bp0498138

Project contacts

Lead investigator Professor Lars Nielsen
Research group AIBN Systems & Synthetic Biology
Contact email


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