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Guidelines, Strategies, and Principles for the Directed Evolution of Cross-Reactive Antibodies Using Yeast Surface Display Technology

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Yeast Surface Display

Abstract

The ability of cross-reactive antibodies to bind multiple related or unrelated targets derived from different species provides not only superior therapeutic efficacy but also a better assessment of treatment toxicity, thereby facilitating the transition from preclinical models to human clinical studies. This chapter provides some guidelines for the directed evolution of cross-reactive antibodies using yeast surface display technology. Cross-reactive antibodies are initially isolated from a naïve library by combining highly avid magnetic bead separations followed by multiple cycles of flow cytometry sorting. Once initial cross-reactive clones are identified, sequential rounds of mutagenesis and two-pressure selection strategies are applied to engineer cross-reactive antibodies with improved affinity and yet retained or superior cross-reactivity.

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References

  1. Elgundi Z, Reslan M, Cruz E, Sifniotis V, Kayser V (2017) The state-of-play and future of antibody therapeutics. Adv Drug Deliv Rev 122:2–19. https://doi.org/10.1016/j.addr.2016.11.004

    Article  CAS  PubMed  Google Scholar 

  2. Bradbury ARM, Sidhu S, Dübel S, McCafferty J (2011) Beyond natural antibodies: the power of in vitro display technologies. Nat Biotechnol 29:245–254. https://doi.org/10.1038/nbt.1791

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Alfaleh MA, Alsaab HO, Mahmoud AB, Alkayyal AA, Jones ML, Mahler SM, Hashem AM (2020) Phage display derived monoclonal antibodies: from bench to bedside. Front Immunol 11:1986. https://doi.org/10.3389/fimmu.2020.01986

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Boder ET, Raeeszadeh-Sarmazdeh M, Price JV (2012) Engineering antibodies by yeast display. Arch Biochem Biophys 526:99–106. https://doi.org/10.1016/j.abb.2012.03.009

    Article  CAS  PubMed  Google Scholar 

  5. Fagète S, Ravn U, Gueneau F, Magistrelli G, Kosco-Vilbois MH, Fischer N (2009) Specificity tuning of antibody fragments to neutralize two human chemokines with a single agent. MAbs 1:288–296. https://doi.org/10.4161/mabs.1.3.8527

    Article  PubMed  PubMed Central  Google Scholar 

  6. Lee CV, Hymowitz SG, Wallweber HJ, Gordon NC, Billeci KL, Tsai SP, Compaan DM, Yin JP, Gong Q, Kelley RF, DeForge LE, Martin F, Starovasnik MA, Fuh G (2006) Synthetic anti-BR3 antibodies that mimic BAFF binding and target both human and murine B cells. Blood 108:3103–3111. https://doi.org/10.1182/blood-2006-03-011031

    Article  CAS  PubMed  Google Scholar 

  7. Liang WC, Wu X, Peale FV, Lee CV, Meng YG, Gutierrez J, Fu L, Malik AK, Gerber HP, Ferrara N, Fuh G (2006) Cross-species vascular endothelial growth factor (VEGF)-blocking antibodies completely inhibit the growth of human tumor xenografts and measure the contribution of stromal VEGF. J Biol Chem 281:951–961. https://doi.org/10.1074/jbc.M508199200

    Article  CAS  PubMed  Google Scholar 

  8. Bostrom J, Yu SF, Kan D, Appleton BA, Lee CV, Billeci K, Man W, Peale F, Ross S, Wiesmann C, Fuh G (2009) Variants of the antibody herceptin that interact with HER2 and VEGF at the antigen binding site. Science (80-) 323:1610–1614. https://doi.org/10.1126/science.1165480

    Article  CAS  Google Scholar 

  9. Angelini A, Miyabe Y, Newsted D, Kwan BH, Miyabe C, Kelly RL, Jamy MN, Luster AD, Wittrup KD (2018) Directed evolution of broadly crossreactive chemokine-blocking antibodies efficacious in arthritis. Nat Commun 9:1461. https://doi.org/10.1038/s41467-018-03687-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Garcia-Rodriguez C, Geren IN, Lou J, Conrad F, Forsyth C, Wen W, Chakraborti S, Zao H, Manzanarez G, Smith TJ, Brown J, Tepp WH, Liu N, Wijesuriya S, Tomic MT, Johnson EA, Smith LA, Marks JD (2011) Neutralizing human monoclonal antibodies binding multiple serotypes of botulinum neurotoxin. Protein Eng Des Sel 24:321–331. https://doi.org/10.1093/protein/gzq111

    Article  CAS  PubMed  Google Scholar 

  11. Garcia-Rodriguez C, Levy R, Arndt JW, Forsyth CM, Razai A, Lou J, Geren I, Stevens RC, Marks JD (2007) Molecular evolution of antibody cross-reactivity for two subtypes of type a botulinum neurotoxin. Nat Biotechnol 25:107–116. https://doi.org/10.1038/nbt1269

    Article  CAS  PubMed  Google Scholar 

  12. Hu D, Zhu Z, Li S, Deng Y, Wu Y, Zhang N, Puri V, Wang C, Zou P, Lei C, Tian X, Wang Y, Zhao Q, Li W, Prabakaran P, Feng Y, Cardosa J, Qin C, Zhou X, Dimitrov DS, Ying T (2019) A broadly neutralizing germline-like human monoclonal antibody against dengue virus envelope domain III. PLoS Pathog 15:e1007836. https://doi.org/10.1371/journal.ppat.1007836

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Lou J, Geren I, Garcia-Rodriguez C, Forsyth CM, Wen W, Knopp K, Brown J, Smith T, Smith LA, Marks JD (2010) Affinity maturation of human botulinum neurotoxin antibodies by light chain shuffling via yeast mating. Protein Eng Des Sel 23:311–319. https://doi.org/10.1093/protein/gzq001

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Mehta N, Maddineni S, Kelly RL, Lee RB, Hunter SA, Silberstein JL, Parra Sperberg RA, Miller CL, Rabe A, Labanieh L, Cochran JR (2020) An engineered antibody binds a distinct epitope and is a potent inhibitor of murine and human VISTA. Sci Rep 10:15171. https://doi.org/10.1038/s41598-020-71519-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Puri V, Streaker E, Prabakaran P, Zhu Z, Dimitrov DS (2013) Highly efficient selection of epitope specific antibody through competitive yeast display library sorting. MAbs 5:533–539. https://doi.org/10.4161/mabs.25211

    Article  PubMed  PubMed Central  Google Scholar 

  16. Rouha H, Badarau A, Visram ZC, Battles MB, Prinz B, Magyarics Z, Nagy G, Mirkina I, Stulik L, Zerbs M, Jägerhofer M, Maierhofer B, Teubenbacher A, Dolezilkova I, Gross K, Banerjee S, Zauner G, Malafa S, Zmajkovic J, Maier S, Mabry R, Krauland E, Dane Wittrup K, Gerngross TU, Nagy E (2015) Five birds, one stone: neutralization of α-hemolysin and 4 bi-component leukocidins of Staphylococcus aureus with a single human monoclonal antibody. MAbs 7:243–254. https://doi.org/10.4161/19420862.2014.985132

    Article  CAS  PubMed  Google Scholar 

  17. Orcutt KD, Wittrup KD (2010) Yeast display and selections. In: Antibody Engineering, pp 207–233. https://doi.org/10.1007/978-3-642-01144-3_15

  18. VanAntwerp JJ, Wittrup KD (2000) Fine affinity discrimination by yeast surface display and flow cytometry. Biotechnol Prog 16:31–37. https://doi.org/10.1021/bp990133s

    Article  CAS  PubMed  Google Scholar 

  19. Angelini A, Chen TF, De Picciotto S, Yang NJ, Tzeng A, Santos MS, Van Deventer JA, Traxlmayr MW, Dane Wittrup K (2015) Protein engineering and selection using yeast surface display. Methods Mol Biol 1319:3–36. https://doi.org/10.1007/978-1-4939-2748-7_1

  20. Miersch S, Sidhu SS (2012) Synthetic antibodies: concepts, potential and practical considerations. Methods 57:486–498. https://doi.org/10.1016/j.ymeth.2012.06.012

    Article  CAS  PubMed  Google Scholar 

  21. Sivasubramanian A, Estep P, Lynaugh H, Yu Y, Miles A, Eckman J, Schutz K, Piffath C, Boland N, Niles RH, Durand S, Boland T, Vásquez M, Xu Y, Abdiche Y (2017) Broad epitope coverage of a human in vitro antibody library. MAbs 9:29–42. https://doi.org/10.1080/19420862.2016.1246096

    Article  CAS  PubMed  Google Scholar 

  22. Ackerman M, Levary D, Tobon G, Hackel B, Orcutt KD, Wittrup KD (2009) Highly avid magnetic bead capture: an efficient selection method for de novo protein engineering utilizing yeast surface display. Biotechnol Prog 25:774–783. https://doi.org/10.1002/btpr.174

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Shusta EV, Holler PD, Kieke MC, Kranz DM, Wittrup KD (2000) Directed evolution of a stable scaffold for T-cell receptor engineering. Nat Biotechnol 18:754–759. https://doi.org/10.1038/77325

    Article  CAS  PubMed  Google Scholar 

  24. Traxlmayr MW, Obinger C (2012) Directed evolution of proteins for increased stability and expression using yeast display. Arch Biochem Biophys 526:174–180. https://doi.org/10.1016/j.abb.2012.04.022

    Article  CAS  PubMed  Google Scholar 

  25. Colby DW, Kellogg BA, Graff CP, Yeung YA, Swers JS, Wittrup KD (2004) Engineering antibody affinity by yeast surface display. Methods Enzymol 388:348–358. https://doi.org/10.1016/S0076-6879(04)88027-3

    Article  CAS  PubMed  Google Scholar 

  26. Swers JS, Kellogg BA, Wittrup KD (2004) Shuffled antibody libraries created by in vivo homologous recombination and yeast surface display. Nucleic Acids Res 32:e36. https://doi.org/10.1093/nar/gnh030

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Jain D, Salunke DM (2019) Antibody specificity and promiscuity. Biochem J 476:433–447. https://doi.org/10.1042/BCJ20180670

    Article  CAS  PubMed  Google Scholar 

  28. Erijman A, Aizner Y, Shifman JM (2011) Multispecific recognition: mechanism, evolution, and design. Biochemistry 50:602–611. https://doi.org/10.1021/bi101563v

    Article  CAS  PubMed  Google Scholar 

  29. Schreiber G, Keating AE (2011) Protein binding specificity versus promiscuity. Curr Opin Struct Biol 21:50–61. https://doi.org/10.1016/j.sbi.2010.10.002

    Article  CAS  PubMed  Google Scholar 

  30. Aharoni A, Gaidukov L, Khersonsky O, Gould SMQ, Roodveldt C, Tawfik DS (2005) The “evolvability” of promiscuous protein functions. Nat Genet 37:73–76. https://doi.org/10.1038/ng1482

    Article  CAS  PubMed  Google Scholar 

  31. James LC, Tawfik DS (2003) Conformational diversity and protein evolution—a 60-year-old hypothesis revisited. Trends Biochem Sci 28:361–368. https://doi.org/10.1016/S0968-0004(03)00135-X

    Article  CAS  PubMed  Google Scholar 

  32. Sethi DK, Agarwal A, Manivel V, Rao KVS, Salunke DM (2006) Differential epitope positioning within the germline antibody paratope enhances promiscuity in the primary immune response. Immunity 24:429–438. https://doi.org/10.1016/j.immuni.2006.02.010

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

We gratefully acknowledge all group members for helpful discussions and critical reading of this chapter. The financial contributions from the iCARE-2 Marie Curie fellowship cofounded by the AIRC foundation for cancer research and the European Union’s Horizon 2020 research and innovation programme to E.L.W. (grant agreement n. 800924) is gratefully acknowledged.

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Correspondence to Alessandro Angelini .

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Linciano, S. et al. (2022). Guidelines, Strategies, and Principles for the Directed Evolution of Cross-Reactive Antibodies Using Yeast Surface Display Technology. In: Traxlmayr, M.W. (eds) Yeast Surface Display. Methods in Molecular Biology, vol 2491. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2285-8_14

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  • DOI: https://doi.org/10.1007/978-1-0716-2285-8_14

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2284-1

  • Online ISBN: 978-1-0716-2285-8

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