Untargeted proteomics reveals upregulation of stress response pathways during CHO-based monoclonal antibody manufacturing process leading to disulfide bond reduction

References

• Yusufi FNK, Lakshmanan M, Ho YS, Loo BLW, Ariyaratne P, Yang Y, Ng SK, Tan TRM, Yeo HC, Lim HL, et al. Mammalian systems biotechnology reveals global cellular adaptations in a recombinant CHO cell line. Cell Syst. 2017;4(5):530–14. doi:10.1016/j.cels.2017.04.009. PMID: 28544881.
   PubMed Web of Science ®Google Scholar
• Lee H-W, Bhatia H, Park S-Y, Kamga M-H, Reimonn T, Sha S, Zhuangrong H, Galbraith S, Liu H, Yoon S. Process analytical technology and quality by design for animal cell culture. In: Lee GM, Kildegaard HF, editors. Cell culture engineering: recombinant protein production. Weinheim (Germany): Wiley-VCH Verlag GmbH & Co. KGaA; 2019. p. 365–90. doi:10.1002/9783527811410.ch15.
   Google Scholar
• Morris C, Polanco A, Yongky A, Xu J, Huang Z, Zhao J, McFarland KS, Park S-Y, Warrack B, Reily M, et al. Big data analytics identifies metabolic inhibitors and promoters for productivity improvement and optimization of monoclonal antibody (mAb) production process. Bioresour Bioprocess. 2020;7(1):1–13. doi:10.1186/s40643-020-00318-6.
   Web of Science ®Google Scholar
• Das TK, Narhi LO, Sreedhara A, Menzen T, Grapentin C, Chou DK, Antochshuk V, Filipe V. Stress factors in mAb drug substance production processes: critical assessment of impact on product quality and control strategy. J Pharm Sci. 2020;109(1):116–33. doi:10.1016/j.xphs.2019.09.023. PMID: 31593689.
   PubMed Web of Science ®Google Scholar
• Mulukutla BC, Kale J, Kalomeris T, Jacobs M, Hiller GW. Identification and control of novel growth inhibitors in fed-batch cultures of Chinese hamster ovary cells. Biotechnol Bioeng. 2017;114(8):1779–90. doi:10.1002/bit.26313. PMID: 28409820.
   PubMed Web of Science ®Google Scholar
• O’Mara B, Gao Z, Kuruganti M, Mallett R, Nayar G, Smith L, Meyer JD, Therriault J, Miller C, Cisney J, et al. Impact of depth filtration on disulfide bond reduction during downstream processing of monoclonal antibodies from CHO cell cultures. Biotechnol Bioeng. 2019;116(7):1669–83. doi:10.1002/bit.26964. PMID: 30883673.
   PubMed Web of Science ®Google Scholar
• Trexler-Schmidt M, Sargis S, Chiu J, Sze-Khoo S, Mun M, Kao Y-H, Laird MW. Identification and prevention of antibody disulfide bond reduction during cell culture manufacturing. Biotechnol Bioeng. 2010;106:452–61. doi:10.1002/bit.22699. PMID: 20178122.
   PubMed Web of Science ®Google Scholar
• Mun M, Khoo S, Do Minh A, Dvornicky J, Trexler-Schmidt M, Kao Y-H, Laird MW. Air sparging for prevention of antibody disulfide bond reduction in harvested CHO cell culture fluid. Biotechnol Bioeng. 2015;112(4):734–42. doi:10.1002/bit.25495. PMID: 25384896.
   PubMed Web of Science ®Google Scholar
• Kao Y-H, Hewitt DP, Trexler-Schmidt M, Laird MW. Mechanism of antibody reduction in cell culture production processes. Biotechnol Bioeng. 2010;107(4):622–32. doi:10.1002/bit.22848. PMID: 20589844.
   PubMed Web of Science ®Google Scholar
• Chung WK, Russell B, Yang Y, Handlogten M, Hudak S, Cao M, Wang J, Robbins D, Ahuja S, Zhu M. Effects of antibody disulfide bond reduction on purification process performance and final drug substance stability. Biotechnol Bioeng. 2017;114(6):1264–74. doi:10.1002/bit.26265. PMID: 28186329.
   PubMed Web of Science ®Google Scholar
• Du C, Huang Y, Borwankar A, Tan Z, Cura A, Yee JC, Singh N, Ludwig R, Borys M, Ghose S, et al. Using hydrogen peroxide to prevent antibody disulfide bond reduction during manufacturing process. MAbs. 2018;10(3):500–10. doi:10.1080/19420862.2018.1424609. PMID: 29336721.
   PubMed Web of Science ®Google Scholar
• Liu H, May K. Disulfide bond structures of IgG molecules: structural variations, chemical modifications and possible impacts to stability and biological function. MAbs. 2012;4(1):17–23. doi:10.4161/mabs.4.1.18347. PMID: 22327427.
   PubMed Web of Science ®Google Scholar
• Liu H, Chumsae C, Gaza-Bulseco G, Hurkmans K, Radziejewski CH. Ranking the susceptibility of disulfide bonds in human IgG1 antibodies by reduction, differential alkylation, and LC-MS analysis. Anal Chem. 2010;82(12):5219–26. doi:10.1021/ac100575n. PMID: 20491447.
   PubMed Web of Science ®Google Scholar
• Hutterer KM, Hong RW, Lull J, Zhao X, Wang T, Pei R, Le ME, Borisov O, Piper R, Liu YD, et al. Monoclonal antibody disulfide reduction during manufacturing: untangling process effects from product effects. MAbs. 2013;5(4):608–13. doi:10.4161/mabs.24725. PMID: 23751615.
   PubMed Web of Science ®Google Scholar
• Cura AJ, Xu X, Egan S, Aron K, Jenkins L, Hageman T, Huang Y, Chollangi S, Borys M, Ghose S, et al. Metabolic understanding of disulfide reduction during monoclonal antibody production. Appl Microbiol Biotechnol. 2020;104(22):9655–69. doi:10.1007/s00253-020-10916-1. PMID: 32997205.
   PubMed Web of Science ®Google Scholar
• Handlogten MW, Wang J, Ahuja S. Online control of cell culture redox potential prevents antibody interchain disulfide bond reduction. Biotechnol Bioeng. 2020;117(5):1329–36. doi:10.1002/bit.27281. PMID: 31956991.
   PubMed Web of Science ®Google Scholar
• Schneider M, Knuesting J, Birkholz O, Heinisch JJ, Scheibe R. Cytosolic GAPDH as a redox-dependent regulator of energy metabolism. BMC Plant Biol. 2018;18(1):1-14. doi:10.1186/s12870-018-1390-6. PMID: 30189844.
   PubMedGoogle Scholar
• Nakajima H, Itakura M, Kubo T, Kaneshige A, Harada N, Izawa T, Azuma Y-T, Kuwamura M, Yamaji R, Takeuchi T. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) aggregation causes mitochondrial dysfunction during oxidative stress-induced cell death. J Biol Chem. 2017;292(11):4727–42. doi:10.1074/jbc.M116.759084. PMID: 28167533.
   PubMed Web of Science ®Google Scholar
• Zhang J-Y, Zhang F, Hong C-Q, Giuliano AE, Cui X-J, Zhou G-J, Zhang G-J, Cui Y-K. Critical protein GAPDH and its regulatory mechanisms in cancer cells. Cancer Biol Med. 2015;12:10–22. doi:10.7497/j..2095-3941.2014.0019. PMID: 25859407.
   PubMed Web of Science ®Google Scholar
• Chevallier V, Andersen MR, Malphettes L. Oxidative stress‐alleviating strategies to improve recombinant protein production in CHO cells. Biotechnol Bioeng. 2020;117(4):1172–86. doi:10.1002/bit.27247. PMID: 31814104.
   PubMed Web of Science ®Google Scholar
• Senft D, Ronai ZA. UPR, autophagy, and mitochondria crosstalk underlies the ER stress response. Trends Biochem Sci. 2015;40(3):141–48. doi:10.1016/j.tibs.2015.01.002. PMID: 25656104.
   PubMed Web of Science ®Google Scholar
• Yoo DY, Bin CS, Jung HY, Kim W, Lee KY, Kim JW, Moon SM, Won MH, Choi JH, Yoon YS, et al. Protein disulfide-isomerase A3 significantly reduces ischemia-induced damage by reducing oxidative and endoplasmic reticulum stress. Neurochem Int. 2019;122:19–30. doi:10.1016/j.neuint.2018.11.002. PMID: 30399388.
   PubMed Web of Science ®Google Scholar
• Koterba KL, Borgschulte T, Laird MW. Thioredoxin 1 is responsible for antibody disulfide reduction in CHO cell culture. J Biotechnol. 2012;157(1):261–67. doi:10.1016/j.jbiotec.2011.11.009. PMID: 22138638.
   PubMed Web of Science ®Google Scholar
• Goh WWB, Wong L. Protein complex-based analysis is resistant to the obfuscating consequences of batch effects — a case study in clinical proteomics. BMC Genomics. 2017;18(2):1–15. doi:10.1186/s12864-017-3490-3. PMID: 28361693.
   PubMedGoogle Scholar
• Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P, et al. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019;47(D1):D607–D613. doi:10.1093/nar/gky1131. PMID: 30476243.
   PubMed Web of Science ®Google Scholar
• Handlogten MW, Zhu M, Ahuja S. Glutathione and thioredoxin systems contribute to recombinant monoclonal antibody interchain disulfide bond reduction during bioprocessing. Biotechnol Bioeng. 2017;114(7):1469–77. doi:10.1002/bit.26278. PMID: 28262915.
   PubMed Web of Science ®Google Scholar
• Xu N, Ma C, Ou J, Sun WW, Zhou L, Hu H, Liu XM. Comparative proteomic analysis of three Chinese hamster ovary (CHO) host cells. Biochem Eng J. 2017;124:122–29. doi:10.1016/j.bej.2017.05.007. PMID: 28736500.
   PubMed Web of Science ®Google Scholar
• Park JH, Jin JH, Lim MS, An HJ, Kim JW, Lee GM. Proteomic analysis of host cell protein dynamics in the culture supernatants of antibody-producing CHO cells. Sci Rep. 2017;7(1):44246. doi:10.1038/srep44246. PMID: 28281648.
   PubMedGoogle Scholar
• Lakshmanan M, Kok YJ, Lee AP, Kyriakopoulos S, Lim HL, Teo G, Poh SL, Tang WQ, Hong J, Tan AH, et al. Multi‐omics profiling of CHO parental hosts reveals cell line‐specific variations in bioprocessing traits. Biotechnol Bioeng. 2019;116(9):2117–29. doi:10.1002/bit.27014. PMID: 31066037.
   PubMed Web of Science ®Google Scholar
• Kantardjieff A, Jacob NM, Yee JC, Epstein E, Kok Y-J, Philp R, Betenbaugh M, Hu W-S. Transcriptome and proteome analysis of Chinese hamster ovary cells under low temperature and butyrate treatment. J Biotechnol. 2010;145(2):143–59. doi:10.1016/j.jbiotec.2009.09.008. PMID: 19770009.
   PubMed Web of Science ®Google Scholar
• Goey CH, Tsang JMH, Bell D, Kontoravdi C. Cascading effect in bioprocessing-The impact of mild hypothermia on CHO cell behavior and host cell protein composition. Biotechnol Bioeng. 2017;114(12):2771–81. doi:10.1002/bit.26437. PMID: 28843000.
   PubMed Web of Science ®Google Scholar
• Coleman O, Costello A, Henry M, Lao NT, Barron N, Clynes M, Meleady P. A proteomic profiling dataset of recombinant Chinese hamster ovary cells showing enhanced cellular growth following miR-378 depletion. Data Br. 2018;21:2679–88. doi:10.1016/j.dib.2018.11.115. PMID: 30761351.
   PubMed Web of Science ®Google Scholar
• Kallehauge TB, Li S, Pedersen LE, Ha TK, Ley D, Andersen MR, Kildegaard HF, Lee GM, Lewis NE. Ribosome profiling-guided depletion of an mRNA increases cell growth rate and protein secretion. Sci Rep. 2017;7(1):1–12. doi:10.1038/srep40388. PMID: 28091612.
   PubMedGoogle Scholar
• Kelly PS, Dorival‐García N, Paré S, Carillo S, Ta C, Alarcon Miguez A, Coleman O, Harper E, Shannon M, Henry M, et al. Improvements in single‐use bioreactor film material composition leads to robust and reliable Chinese hamster ovary cell performance. Biotechnol Prog. 2019;35(4):1–17. doi:10.1002/btpr.2824. PMID: 31017345.
   Web of Science ®Google Scholar
• Gronemeyer P, Ditz R, Strube J. DoE based integration approach of upstream and downstream processing regarding HCP and ATPE as harvest operation. Biochem Eng J. 2016;113:158–66. doi:10.1016/j.bej.2016.06.016.
   Web of Science ®Google Scholar
• Albrecht S, Kaisermayer C, Reinhart D, Ambrose M, Kunert R, Lindeberg A, Bones J. Multiple reaction monitoring targeted LC-MS analysis of potential cell death marker proteins for increased bioprocess control. Anal Bioanal Chem. 2018;410(13):3197–207. doi:10.1007/s00216-018-1029-3. PMID: 29607450.
   PubMed Web of Science ®Google Scholar
• Lakbub JC, Shipman JT, Desaire H. Recent mass spectrometry-based techniques and considerations for disulfide bond characterization in proteins. Anal Bioanal Chem. 2018;410(10):2467–84. doi:10.1007/s00216-017-0772-1. PMID: 29256076.
   PubMed Web of Science ®Google Scholar
• Hagihara Y, Saerens D. Engineering disulfide bonds within an antibody. Biochim Biophys Acta (BBA)-Proteins Proteomics. 2014;1844(11):2016–23. doi:10.1016/j.bbapap.2014.07.005. PMID: 25038323.
   PubMed Web of Science ®Google Scholar
• Xie G, Hong WX, Zhou L, Yang X, Huang H, Wu D, Huang X, Zhu W, Liu J. An investigation of methyl tert-butyl ether-induced cytotoxicity and protein profile in Chinese hamster ovary cells. Mol Med Rep. 2017;16(6):8595–604. doi:10.3892/mmr.2017.7761. PMID: 29039499.
   PubMed Web of Science ®Google Scholar
• Rapp UK, Kaufmann SHE. Glucose-regulated stress proteins and antibacterial immunity. Trends Microbiol. 2003;11(11):519–26. doi:10.1016/j.tim.2003.09.001. PMID: 14607069.
   PubMed Web of Science ®Google Scholar
• Dorner AJ, Wasley LC, Raney P, Haugejorden S, Green M, Kaufman RJ. The stress response in Chinese hamster ovary cells. Regulation of ERp72 and protein disulfide isomerase expression and secretion. J Biol Chem. 1990;265(35):22029–34. doi:10.1016/S0021-9258(18)45843-7. PMID: 2254345.
   PubMed Web of Science ®Google Scholar
• Showalter AE, Martini AC, Nierenberg D, Hosang K, Fahmi NA, Gopalan P, Khaled AS, Zhang W, Khaled AR. Investigating Chaperonin-Containing TCP-1 subunit 2 as an essential component of the chaperonin complex for tumorigenesis. Sci Rep. 2020;10(1):798. doi:10.1038/s41598-020-57602-w. PMID: 31964905.
   PubMed Web of Science ®Google Scholar
• Marzec M, Eletto D, Argon Y. GRP94: an HSP90-like protein specialized for protein folding and quality control in the endoplasmic reticulum. Biochim Biophys Acta - Mol Cell Res. 2012;1823(3):774–87. doi:10.1016/j.bbamcr.2011.10.013. PMID: 22079671.
   PubMed Web of Science ®Google Scholar
• Komatsu K, Kumon K, Arita M, Onitsuka M, Omasa T, Yohda M. Effect of the disulfide isomerase PDIa4 on the antibody production of Chinese hamster ovary cells. J Biosci Bioeng. 2020;130(6):637–43. doi:10.1016/j.jbiosc.2020.08.001. PMID: 32878739.
   PubMed Web of Science ®Google Scholar
• Meleady P, Henry M, Gammell P, Doolan P, Sinacore M, Melville M, Francullo L, Leonard M, Charlebois T, Clynes M. Proteomic profiling of CHO cells with enhanced rhBMP-2 productivity following co-expression of PACEsol. Proteomics. 2008;8(13):2611–24. doi:10.1002/pmic.200700854. PMID: 18546152.
   PubMed Web of Science ®Google Scholar
• Easton DP, Kaneko Y, Subjeck JR. The hsp110 and Grp170 stress proteins: newly recognized relatives of the Hsp70s. Cell Stress Chaperones. 2000;5(4):276–90. doi:10.1379/1466-1268(2000)005<0276:thagsp>2.0.co;2. PMID: 11048651.
   PubMed Web of Science ®Google Scholar
• Wei YYC, Naderi S, Meshram M, Budman H, Scharer JM, Ingalls BP, McConkey BJ. Proteomics analysis of Chinese hamster ovary cells undergoing apoptosis during prolonged cultivation. Cytotechnology. 2011;63(6):663–77. doi:10.1007/s10616-011-9385-2. PMID: 21853334.
   PubMed Web of Science ®Google Scholar
• Tomanek L, Podrabsky JE, Stillman JH, Tomanek L. Proteomic responses to environmentally induced oxidative stress. J Exp Biol. 2015;218(12):1867–79. doi:10.1242/jeb.116475. PMID: 26085664.
   PubMed Web of Science ®Google Scholar
• Voth W, Jakob U. Stress-activated chaperones: a first line of defense. Trends Biochem Sci. 2017;42(11):899–913. doi:10.1016/j.tibs.2017.08.006. PMID: 28893460.
   PubMed Web of Science ®Google Scholar
• Cao SS, Kaufman RJ. Endoplasmic reticulum stress and oxidative stress in cell fate decision and human disease. Antioxid Redox Signal. 2014;21(3):396–413. doi:10.1089/ars.2014.5851. PMID: 24702237.
   PubMed Web of Science ®Google Scholar
• Peksel B, Gombos I, Péter M, Veigh L, Á T, Brameshuber M, Balogh G, Schütz GJ, Horváth I, Veigh L, et al. Mild heat induces a distinct “eustress” response in Chinese Hamster Ovary cells but does not induce heat shock protein synthesis. Sci Rep. 2017;7(1):1–12. doi:10.1038/s41598-017-15821-8. PMID: 29142280.
   PubMedGoogle Scholar
• Park HG, Han SI, Oh SY, Kang HS. Cellular responses to mild heat stress. Cell Mol Life Sci. 2005;62(1):10–23. doi:10.1007/s00018-004-4208-7. PMID: 15619003.
   PubMed Web of Science ®Google Scholar
• Kang KR, Lee SY. Effect of serum and hydrogen peroxide on the Ca2+/calmodulin-dependent phosphorylation of eukaryotic elongation factor 2(eEF-2) in Chinese hamster ovary cells. Exp Mol Med. 2001;33(4):198–204. doi:10.1038/emm.2001.33. PMID: 11795480.
   PubMed Web of Science ®Google Scholar
• Kaufman RJ, Back SH, Song B, Han J, Hassler J. The unfolded protein response is required to maintain the integrity of the endoplasmic reticulum, prevent oxidative stress and preserve differentiation in β-cells. Diabetes Obes Metab. 2010;12:99–107. doi:10.1111/j.1463-1326.2010.01281.x. PMID: 21029306.
   PubMed Web of Science ®Google Scholar
• Stech M, Kubick S. Cell-free synthesis meets antibody production: a review. Antibodies. 2015;4(1):12–33. doi:10.3390/antib4010012.
   Web of Science ®Google Scholar
• Fernando MR, Nanri H, Yoshitake S, Nagata-kuno K, Minakami S. Thioredoxin regenerates proteins inactivated by oxidative stress in endothelial cells. Eur J Biochem. 1992;209(3):917–22. doi:10.1111/j.1432-1033.1992.tb17363.x. PMID: 1425698.
   PubMedGoogle Scholar
• Manteiga S, Lee K. Monoethylhexyl phthalate elicits an inflammatory response in adipocytes characterized by alterations in lipid and cytokine pathways. Environ Health Perspect. 2017;125(4):615–22. doi:10.1289/EHP464. PMID: 27384973.
   PubMed Web of Science ®Google Scholar
• Reimonn TM, Park S-Y, Agarabi CD, Brorson KA, Yoon S. Effect of amino acid supplementation on titer and glycosylation distribution in hybridoma cell cultures—Systems biology-based interpretation using genome-scale metabolic flux balance model and multivariate data analysis. Biotechnol Prog. 2016;32(5):1163–73. doi:10.1002/btpr.2335. PMID: 27452371.
   PubMed Web of Science ®Google Scholar
• Anderson MJ. A new method for non-parametric multivariate analysis of variance. Austral Ecol. 2001;26:32–46. doi:10.1111/j.1442-9993.2001.01070.pp.x.
   Web of Science ®Google Scholar
• Zar JH. Biostatistical analysis. 5th. Upper Saddle River (NJ): Prentice Hall; 2010.
   Google Scholar
• Liu Y, Li Z, Xiong H, Gao X, Wu J Understanding of internal clustering validation measures. In: Webb GI, Liu B, Zhang C, Dimitrios G, Wu X, eds. Proceedings of the 2010 IEEE 10th International Conference on Data Mining (ICDM); 2010 Dec 14-17; Sydney, Australia: IEEE Press, 2010. p. 911–16. doi: 10.1109/ICDM.2010.35.
   Google Scholar
• Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, et al. Integration of biological networks and gene expression data using cytoscape. Nat Protoc. 2007;2(10):2366–82. doi:10.1038/nprot.2007.324. PMID: 17947979.
   PubMed Web of Science ®Google Scholar