Advertisement

Selection and Characterization of Anti-idiotypic Shark Antibody Domains

  • Doreen Könning
  • Stefan Zielonka
  • Anna Kaempffe
  • Sebastian Jäger
  • Harald Kolmar
  • Christian SchröterEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2070)

Abstract

The antibody repertoire of cartilaginous fish comprises an additional heavy-chain-only antibody isotype that is referred to as IgNAR (immunoglobulin novel antigen receptor). Its antigen-binding site consists of one single domain (vNAR) that is reportedly able to engage a respective antigen with affinities similar to those achieved by conventional antibodies. While vNAR domains offer a reduced size, which is often favorable for applications in a therapeutic as well as a biotechnological setup, they also exhibit a high physicochemical stability. Together with their ability to target difficult-to-address antigens such as virus particles or toxins, these shark-derived antibody domains seem to be predestined as tools for biotechnological and diagnostic applications. In the following chapter, we will describe the isolation of anti-idiotypic vNAR domains targeting monoclonal antibody paratopes from semi-synthetic, yeast-displayed libraries. Anti-idiotypic vNAR variants could be employed for the characterization of antibody-based therapeutics (such as antibody-drug conjugates) or as positive controls in immunogenicity assays. Peculiarly, when using semi-synthetic vNAR libraries, we found that it is not necessary to deplete the libraries using unrelated antibody targets, which enables a fast and facile screening procedure that exclusively delivers anti-idiotypic binders.

Key words

Shark IgNAR vNAR Yeast surface display Antibody engineering Protein engineering Anti-idiotypic Anti-ID Single-domain antibody 

References

  1. 1.
    Hammerschlag N (2006) Osmoregulation in elasmobranchs: a review for fish biologists, behaviourists and ecologists. Mar Behav Physiol 39:209–228CrossRefGoogle Scholar
  2. 2.
    Greenberg AS, Avila D, Hughes M et al (1995) A new antigen receptor gene family that undergoes rearrangement and extensive somatic diversification in sharks. Nature 374:168–173CrossRefGoogle Scholar
  3. 3.
    Zielonka S, Empting M, Grzeschik J et al (2015) Structural insights and biomedical potential of IgNAR scaffolds from sharks. MAbs 7:15–25CrossRefGoogle Scholar
  4. 4.
    Kovaleva M, Ferguson L, Steven J et al (2014) Shark variable new antigen receptor biologics—a novel technology platform for therapeutic drug development. Expert Opin Biol Ther 14:1527–1539CrossRefGoogle Scholar
  5. 5.
    Stanfield RL, Dooley H, Verdino P et al (2007) Maturation of Shark Single-domain (IgNAR) antibodies: evidence for induced-fit binding. J Mol Biol 367:358–372CrossRefGoogle Scholar
  6. 6.
    Dooley H, Flajnik MF (2006) Antibody repertoire development in cartilaginous fish. Dev Comp Immunol 30:43–56CrossRefGoogle Scholar
  7. 7.
    Stanfield RL, Dooley H, Flajnik MF et al (2004) Crystal structure of a shark single-domain antibody V region in complex with lysozyme. Science 305:1770–1773CrossRefGoogle Scholar
  8. 8.
    Goodchild SA, Dooley H, Schoepp RJ et al (2011) Isolation and characterisation of Ebolavirus-specific recombinant antibody fragments from murine and shark immune libraries. Mol Immunol 48:2027–2037CrossRefGoogle Scholar
  9. 9.
    Walsh R, Nuttall S, Revill P et al (2011) Targeting the hepatitis B virus precore antigen with a novel IgNAR single variable domain intrabody. Virology 411:132–141CrossRefGoogle Scholar
  10. 10.
    Liu JL, Anderson GP, Delehanty JB et al (2007) Selection of cholera toxin specific IgNAR single-domain antibodies from a naïve shark library. Mol Immunol 44:1775–1783CrossRefGoogle Scholar
  11. 11.
    Liu JL, Anderson GP, Goldman ER (2007) Isolation of anti-toxin single domain antibodies from a semi-synthetic spiny dogfish shark display library. BMC Biotechnol 7:78CrossRefGoogle Scholar
  12. 12.
    Ubah OC, Steven J, Kovaleva M et al (2017) Novel, Anti-hTNF-α variable new antigen receptor formats with enhanced neutralizing potency and multifunctionality, generated for therapeutic development. Front Immunol 8:1780CrossRefGoogle Scholar
  13. 13.
    Kovaleva M, Johnson K, Steven J et al (2017) Therapeutic potential of shark Anti-ICOSL VNAR domains is exemplified in a murine model of autoimmune non-infectious uveitis. Front Immunol 8:1121CrossRefGoogle Scholar
  14. 14.
    Zielonka S, Weber N, Becker S et al (2014) Shark attack: high affinity binding proteins derived from shark vNAR domains by stepwise in vitro affinity maturation. J Biotechnol 191:236–245CrossRefGoogle Scholar
  15. 15.
    Zielonka S, Empting M, Könning D et al (2015) The shark strikes twice: hypervariable loop 2 of shark IgNAR antibody variable domains and its potential to function as an autonomous paratope. Mar Biotechnol (NY) 17:386–392CrossRefGoogle Scholar
  16. 16.
    Camacho-Villegas T, Mata-González M, García-Ubbelohd W et al (2018) Intraocular penetration of a vNAR: in vivo and in vitro VEGF165 neutralization. Mar Drugs 16:113CrossRefGoogle Scholar
  17. 17.
    Könning D, Zielonka S, Sellmann C et al (2016) Isolation of a pH-sensitive IgNAR variable domain from a yeast-displayed, histidine-doped master library. Mar Biotechnol (NY) 18:161–167CrossRefGoogle Scholar
  18. 18.
    Könning D, Hinz SC, Grzeschik J et al (2018) Construction of histidine-enriched shark IgNAR variable domain antibody libraries for the isolation of pH-sensitive vNAR fragments. In: Hust M, Lin T (eds) Phage display. methods in molecular biology. Humana Press, New York, NY, pp 109–127Google Scholar
  19. 19.
    Matz H, Dooley H (2019) Shark IgNAR-derived binding domains as potential diagnostic and therapeutic agents. Dev Comp Immunol 90:100–107CrossRefGoogle Scholar
  20. 20.
    Könning D, Rhiel L, Empting M et al (2017) Semi-synthetic vNAR libraries screened against therapeutic antibodies primarily deliver anti-idiotypic binders. Sci Rep 7:1–13CrossRefGoogle Scholar
  21. 21.
    Simmons DP, Streltsov VA, Dolezal O et al (2008) Shark IgNAR antibody mimotopes target a murine immunoglobulin through extended CDR3 loop structures. Proteins 71:119–130CrossRefGoogle Scholar
  22. 22.
    Tornetta M, Fisher D, O’Neil K et al (2007) Isolation of human anti-idiotypic antibodies by phage display for clinical immune response assays. J Immunol Methods 328:34–44CrossRefGoogle Scholar
  23. 23.
    Godar M, Morello V, Sadi A et al (2016) Dual anti-idiotypic purification of a novel, native-format biparatopic anti-MET antibody with improved in vitro and in vivo efficacy. Sci Rep 6:31621CrossRefGoogle Scholar
  24. 24.
    Ladjemi MZ (2012) Anti-idiotypic antibodies as cancer vaccines: achievements and future improvements. Front Oncol 2:158CrossRefGoogle Scholar
  25. 25.
    Alvarez-Rueda N, Ladjemi MZ, Béhar G et al (2009) A llama single domain anti-idiotypic antibody mimicking HER2 as a vaccine: Immunogenicity and efficacy. Vaccine 27:4826–4833CrossRefGoogle Scholar
  26. 26.
    Sanches J de S, de Aguiar RB, Parise CB et al (2016) Anti-bevacizumab idiotype antibody vaccination is effective in inducing vascular endothelial growth factor-binding response, impairing tumor outgrowth. Cancer Sci 107:551–555CrossRefGoogle Scholar
  27. 27.
    Hartmann C, Müller N, Blaukat A et al (2010) Peptide mimotopes recognized by antibodies cetuximab and matuzumab induce a functionally equivalent anti-EGFR immune response. Oncogene 29:4517–4527CrossRefGoogle Scholar
  28. 28.
    Grzeschik J, Könning D, Hinz SC et al (2018) Generation of semi-synthetic shark ignar single-domain antibody libraries. In: Hust H, Lin T (eds) Phage display. Methods in molecular biology. Humana Press, New York, NY, pp 147–167CrossRefGoogle Scholar
  29. 29.
    Dickgiesser S, Rasche N, Nasu D et al (2015) Self-assembled hybrid aptamer-Fc conjugates for targeted delivery: a modular chemoenzymatic approach. ACS Chem Biol 10:2158–2165CrossRefGoogle Scholar
  30. 30.
    Van Deventer JA, Wittrup KD (2014) Yeast surface display for antibody isolation: library construction, library screening, and affinity maturation. In: Ossipow V, Fischer N (eds) Monoclonal antibodies. Methods in molecular biology (methods and protocols). Springer, Totowa, NJ, pp 151–181CrossRefGoogle Scholar
  31. 31.
    Chao G, Lau WL, Hackel BJ et al (2006) Isolating and engineering human antibodies using yeast surface display. Nat Protoc 1:755–768CrossRefGoogle Scholar
  32. 32.
    Gera N, Hussain M, Rao BM (2013) Protein selection using yeast surface display. Methods 60:15–26CrossRefGoogle Scholar
  33. 33.
    Pettersen EF, Goddard TD, Huang CC et al (2004) UCSF Chimera—a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612CrossRefGoogle Scholar
  34. 34.
    Könning D, Kolmar H (2018) Beyond antibody engineering: directed evolution of alternative binding scaffolds and enzymes using yeast surface display. Microb Cell Factories 17:32CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • Doreen Könning
    • 1
  • Stefan Zielonka
    • 2
  • Anna Kaempffe
    • 1
    • 3
  • Sebastian Jäger
    • 1
    • 3
  • Harald Kolmar
    • 3
  • Christian Schröter
    • 1
    Email author
  1. 1.Antibody-Drug Conjugates and Targeted NBE TherapeuticsMerck KGaADarmstadtGermany
  2. 2.Protein Engineering and Antibody Technologies (PEAT)Merck KGaADarmstadtGermany
  3. 3.Institute for Organic Chemistry and BiochemistryTechnische Universität DarmstadtDarmstadtGermany

Personalised recommendations