Chemometric identification of canonical metabolites linking critical process parameters to monoclonal antibody production during bioprocess development

doi:10.1016/j.cjche.2018.10.009

Chinese Journal of Chemical Engineering ›› 2019, Vol. 27 ›› Issue (5): 1171-1176.DOI: 10.1016/j.cjche.2018.10.009

• Biotechnology and Bioengineering • Previous Articles Next Articles

Chemometric identification of canonical metabolites linking critical process parameters to monoclonal antibody production during bioprocess development

Lijuan Shen¹, Xu Yan¹, Lei Nie^1,2, Wenyan Xu², Shiwei Miao², Haibin Wang², H. Fai Poon², Haibin Qu¹

1 Pharmaceutical Informatics Institute, College of Pharmaceutical Science, Zhejiang University, Hangzhou 310058, China;
2 Zhejiang Hisun Pharmaceutical Co., Ltd., Fuyang, Hangzhou 311404, China

Received:2018-08-09 Revised:2018-09-26 Online:2019-06-27 Published:2019-05-28
Contact: Haibin Qu
Supported by:
Supported by the Science and Technology Development Program of Zhejiang Province (2017C03003).

Chemometric identification of canonical metabolites linking critical process parameters to monoclonal antibody production during bioprocess development

Lijuan Shen¹, Xu Yan¹, Lei Nie^1,2, Wenyan Xu², Shiwei Miao², Haibin Wang², H. Fai Poon², Haibin Qu¹

1 Pharmaceutical Informatics Institute, College of Pharmaceutical Science, Zhejiang University, Hangzhou 310058, China;
2 Zhejiang Hisun Pharmaceutical Co., Ltd., Fuyang, Hangzhou 311404, China

通讯作者: Haibin Qu
基金资助:
Supported by the Science and Technology Development Program of Zhejiang Province (2017C03003).

Abstract

Abstract: A deeper understanding of the biological events occurring when bioprocess parameters changed will be of great value in improving the monoclonal antibodies (mAbs) production. Design of experiment (DoE) was applied to investigate the effect of process parameters (pH, temperature shift and dissolve oxygen (DO)) on protein titer. The key metabolites connecting the critical process parameters (CPPs) with monoclonal antibody production were identified by different chemometrics tools. Finally, the biological events of marker metabolites relating with titer improvement were concluded. pH and temperature shift were identified as CPPs that affect the target protein titer. A series of metabolites influenced by the altered CPPs and correlated with protein titer were screened by principal component analysis (PCA) and Pearson' correlation test. The marker metabolites and their pathways linking CPPs to target protein titer in different culture phases were summarized. Metabolomics and chemometrics are promising data-driven tools to shine light into the biological black box between the bioprocess parameters and process performance.

Key words: Canonical metabolites, Chemometrics, Critical process parameters, Metabolomics, Protein titer

摘要： A deeper understanding of the biological events occurring when bioprocess parameters changed will be of great value in improving the monoclonal antibodies (mAbs) production. Design of experiment (DoE) was applied to investigate the effect of process parameters (pH, temperature shift and dissolve oxygen (DO)) on protein titer. The key metabolites connecting the critical process parameters (CPPs) with monoclonal antibody production were identified by different chemometrics tools. Finally, the biological events of marker metabolites relating with titer improvement were concluded. pH and temperature shift were identified as CPPs that affect the target protein titer. A series of metabolites influenced by the altered CPPs and correlated with protein titer were screened by principal component analysis (PCA) and Pearson' correlation test. The marker metabolites and their pathways linking CPPs to target protein titer in different culture phases were summarized. Metabolomics and chemometrics are promising data-driven tools to shine light into the biological black box between the bioprocess parameters and process performance.

关键词: Canonical metabolites, Chemometrics, Critical process parameters, Metabolomics, Protein titer

Lijuan Shen, Xu Yan, Lei Nie, Wenyan Xu, Shiwei Miao, Haibin Wang, H. Fai Poon, Haibin Qu. Chemometric identification of canonical metabolites linking critical process parameters to monoclonal antibody production during bioprocess development[J]. Chinese Journal of Chemical Engineering, 2019, 27(5): 1171-1176.

References

[1] F.M. Wurm, Production of recombinant protein therapeutics in cultivated mammalian cells, Nat. Biotechnol. 22(2004) 1393-1398.
[2] T.R. Davis, T.J. Wickham, K.A. Mckenna, R.R. Granados, M.L. Shuler, H.A. Wood, Comparative recombinant protein production of eight insect cell lines, In Vitro Cell. Dev. Biol. Anim. 29a (1993) 388-390.
[3] S. Oguchi, H. Saito, M. Tsukahara, H. Tsumura, pH condition in temperature shift cultivation enhances cell longevity and specific hMab productivity in CHO culture, Cytotechnology 52(2006) 199-207.
[4] P. Gammell, N. Barron, N. Kumar, M. Clynes, Initial identification of low temperature and culture stage induction of miRNA expression in suspension CHO-K1 cells, J. Biotechnol. 130(2007) 213-218.
[5] F. Zhang, M.A. Saarinen, L.J. Itle, S.C. Lang, D.W. Murhammer, R.J. Linhardt, The effect of dissolved oxygen (DO) concentration on the glycosylation of recombinant protein produced by the insect cell-baculovirus expression system, Biotechnol. Bioeng. 77(2002) 219-224.
[6] L. Maranga, A. Cunha, J. Clemente, C.P. Mjt, Scale-up of virus-like particles production:Effects of sparging, agitation and bioreactor scale on cell growth, infection kinetics and productivity, J. Biotechnol. 107(2004) 55-64.
[7] Z. Ying, J.V. Cuenca, W. Zhou, V. Amit, NS0 cell damage by high gas velocity sparging in protein-free and cholesterol-free cultures, Biotechnol. Bioeng. 101(2008) 751-760.
[8] S. Dietmair, M.P. Hodson, L.E. Quek, N.E. Timmins, P. Chrysanthopoulos, S.S. Jacob, P. Gray, L.K. Nielsen, Metabolite profiling of CHO cells with different growth characteristics, Biotechnol. Bioeng. 109(2012) 1404-1414.
[9] N. Carinhas, T.M. Duarte, L.C. Barreiro, M.J.T. Carrondo, P.M. Alves, A.P. Teixeira, Metabolic signatures of GS-CHO cell clones associated with butyrate treatment and culture phase transition, Biotechnol. Bioeng. 110(2013) 3244-3257.
[10] H. Zhang, H. Wang, M. Liu, T. Zhang, J. Zhang, X. Wang, W. Xiang, Rational development of a serum-free medium and fed-batch process for a GS-CHO cell line expressing recombinant antibody, Cytotechnology 65(2013) 363-378.
[11] A.S. Rathore, QbD/PAT for bioprocessing:moving from theory to implementation, Curr. Opin. Chem. Eng. 6(2014) 1-8.
[12] W.S. Ahn, J.J. Jeon, Y.R. Jeong, S.J. Lee, S.K. Yoon, Effect of culture temperature on erythropoietin production and glycosylation in a perfusion culture of recombinant CHO cells, Biotechnol. Bioeng. 101(2008) 1234-1244.
[13] M.A. Hanson, X. Ge, Y. Kostov, K.A. Brorson, A.R. Moreira, G. Rao, Comparisons of optical pH and dissolved oxygen sensors with traditional electrochemical probes during mammalian cell culture, Biotechnol. Bioeng. 97(2007) 833-841.
[14] V. Restelli, M.D. Wang, N. Huzel, M. Ethier, H. Perreault, M. Butler, The effect of dissolved oxygen on the production and the glycosylation profile of recombinant human erythropoietin produced from CHO cells, Biotechnol. Bioeng. 94(2006) 481-494.
[15] J. Dean, P. Reddy, Metabolic analysis of antibody producing CHO cells in fed-batch production, Biotechnol. Bioeng. 110(2013) 1735-1747.
[16] D.M. Wuest, S.W. Harcum, K.H. Lee, Genomics in mammalian cell culture bioprocessing, Biotechnol. Adv. 30(2011) 629-638.
[17] A. Bedoyalópez, K. Estrada, A. Sanchezflores, O.T. Ramírez, C. Altamirano, L. Segovia, J. Mirandaríos, M.A. Trujilloroldán, N.A. Valdezcruz, Effect of temperature downshift on the transcriptomic responses of Chinese hamster ovary cells using recombinant human tissue plasminogen activator production culture, PLoS One 11(2016), e0151529..
[18] Y. Gao, S. Ray, S. Dai, A.R. Ivanov, N.R. Abu Absi, A.M. Lewis, Z. Huang, Z. Xing, M.C. Borys, Z.J. Li, Combined metabolomics and proteomics reveals hypoxia as a cause of lower productivity on scale-up to a 5000-liter CHO bioprocess, Biotechnol. J. (2016) 1190-1200.
[19] F. Poon, V.S. Mathura, Introduction to proteomics, Bioinformatics:A Concept-based Introduction 2009, pp. 107-113.
[20] P.K. Chrysanthopoulos, C.T. Goudar, M.I. Klapa, Metabolomics for high-resolution monitoring of the cellular physiological state in cell culture engineering, Metab. Eng 12(2010) 212-222.
[21] S. Kang, Z. Zhang, J. Richardson, B. Shah, S. Gupta, C.J. Huang, J. Qiu, N. Le, H. Lin, P.V. Bondarenko, Metabolic markers associated with high mannose glycan levels of therapeutic recombinant monoclonal antibodies, J. Biotechnol. 203(2015) 22-31.
[22] N. Sengupta, S.T. Rose, J.A. Morgan, Metabolic flux analysis of CHO cell metabolism in the late non-growth phase, Biotechnol. Bioeng. 108(2011) 82-92.
[23] S.K. Yoon, S.L. Choi, J.Y. Song, G.M. Lee, Effect of culture pH on erythropoietin production by Chinese hamster ovary cells grown in suspension at 32.5 and 37.0℃, Biotechnol. Bioeng. 89(2005) 345-356.
[24] M. Bollati Fogolín, G. Forno, M. Nimtz, H.S. Conradt, M. Etcheverrigaray, R. Kratje, Temperature reduction in cultures of hGM-CSF-expressing CHO cells:Effect on productivity and product quality, Biotechnol. Prog. 21(2005) 17-21.
[25] K. Furukawa, K. Ohsuye, Effect of culture temperature on a recombinant CHO cell line producing a C-terminal α-amidating enzyme, Cytotechnology 26(1998) 153-164.
[26] F. Chen, L. Fan, J. Wang, Y. Zhou, Z. Ye, L. Zhao, W. Tan, Insight into the roles of hypoxanthine and thydimine on cultivating antibody-producing CHO cells:Cell growth, antibody production and long-term stability, Appl. Microbiol. Biotechnol. 93(2012) 169-178.
[27] T. Kou, L. Fan, Y. Zhou, Z. Ye, L. Zhao, W. Tan, Increasing the productivity of TNFR-Fc in GS-CHO cells at reduced culture temperatures, Biotechnol. Bioprocess Eng. 16(2011) 136-143.
[28] J. Richardson, B. Shah, P.V. Bondarenko, P. Bhebe, Z. Zhang, M. Nicklaus, M.C. Kombe, Metabolomics analysis of soy hydrolysates for the identification of productivity markers of mammalian cells for manufacturing therapeutic proteins, Biotechnol. Prog. 31(2015) 522-531.
[29] J.I. Sagara, K. Miura, S. Bannai, Cystine uptake and glutathione level in fetal brain cells in primary culture and in suspension, J. Neurochem. 61(1993) 1667-1671.
[30] R.A. Tobey, K.D. Ley, Regulation of initiation of DNA synthesis in Chinese hamster cells. I. Production of stable, reversible G1-arrested populations in suspension culture, J. Cell Biol. 46(1970) 151-157.
[31] J.K. Hong, S.M. Cho, S.K. Yoon, Substitution of glutamine by glutamate enhances production and galactosylation of recombinant IgG in Chinese hamster ovary cells, Appl. Microbiol. Biotechnol. 88(2010) 869-876.
[32] W.P. Chong, S.G. Reddy, F.N. Yusufi, D. Lee, N.S. Wong, C.K. Heng, M.G. Yap, Y.S. Ho, Metabolomics-driven approach for the improvement of Chinese hamster ovary cell growth:overexpression of malate dehydrogenase Ⅱ, J. Biotechnol. 147(2010) 116-121.
[33] M. Zhou, Y. Crawford, D. Ng, J. Tung, A.F. Pynn, A. Meier, I.H. Yuk, N. Vijayasankaran, K. Leach, J. Joly, Decreasing lactate level and increasing antibody production in Chinese Hamster Ovary cells (CHO) by reducing the expression of lactate dehydrogenase and pyruvate dehydrogenase kinases, J. Biotechnol. 153(2011) 27-34.

Chemometric identification of canonical metabolites linking critical process parameters to monoclonal antibody production during bioprocess development

Chemometric identification of canonical metabolites linking critical process parameters to monoclonal antibody production during bioprocess development

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 2

Recommended Articles

Metrics

Comments

[1]	Tao Sun, Shubin Li, Guangsheng Pei, Lei Chen, Weiwen Zhang. Towards understanding the mechanism of n-hexane tolerance in Synechocystis sp. PCC 6803 [J]. Chinese Journal of Chemical Engineering, 2023, 59(7): 128-134.
[2]	Xingchu Gong, Junlin Guo, Jingjing Pan, Zhenfeng Wu. The development of Fructus corni quality standard considering the effects of processing [J]. Chinese Journal of Chemical Engineering, 2021, 29(1): 77-84.