Skip to main content
SpringerLink
Log in
Book cover

Genotype Phenotype Coupling pp 191–209Cite as

Selection and Characterization of Anti-idiotypic Shark Antibody Domains

  • Protocol
  • First Online:

Part of the book series: Methods in Molecular Biology ((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.

This is a preview of subscription content, log in via an institution.

Protocol
USD   49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

References

  1. Hammerschlag N (2006) Osmoregulation in elasmobranchs: a review for fish biologists, behaviourists and ecologists. Mar Behav Physiol 39:209–228

    Article  CAS  Google Scholar 

  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 374:168–173

    Article  CAS  Google Scholar 

  3. Zielonka S, Empting M, Grzeschik J et al (2015) Structural insights and biomedical potential of IgNAR scaffolds from sharks. MAbs 7:15–25

    Article  CAS  Google Scholar 

  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 14:1527–1539

    Article  CAS  Google Scholar 

  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 367:358–372

    Article  CAS  Google Scholar 

  6. Dooley H, Flajnik MF (2006) Antibody repertoire development in cartilaginous fish. Dev Comp Immunol 30:43–56

    Article  CAS  Google Scholar 

  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 305:1770–1773

    Article  CAS  Google Scholar 

  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 48:2027–2037

    Article  CAS  Google Scholar 

  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 411:132–141

    Article  CAS  Google Scholar 

  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 44:1775–1783

    Article  CAS  Google Scholar 

  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 7:78

    Article  Google Scholar 

  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 8:1780

    Article  Google Scholar 

  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 8:1121

    Article  Google Scholar 

  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 191:236–245

    Article  CAS  Google Scholar 

  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) 17:386–392

    Article  CAS  Google Scholar 

  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 16:113

    Article  Google Scholar 

  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) 18:161–167

    Article  Google Scholar 

  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 109–127

    Google Scholar 

  19. Matz H, Dooley H (2019) Shark IgNAR-derived binding domains as potential diagnostic and therapeutic agents. Dev Comp Immunol 90:100–107

    Article  CAS  Google Scholar 

  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 7:1–13

    Article  Google Scholar 

  21. Simmons DP, Streltsov VA, Dolezal O et al (2008) Shark IgNAR antibody mimotopes target a murine immunoglobulin through extended CDR3 loop structures. Proteins 71:119–130

    Article  CAS  Google Scholar 

  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 328:34–44

    Article  CAS  Google Scholar 

  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 6:31621

    Article  CAS  Google Scholar 

  24. Ladjemi MZ (2012) Anti-idiotypic antibodies as cancer vaccines: achievements and future improvements. Front Oncol 2:158

    Article  Google Scholar 

  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 27:4826–4833

    Article  CAS  Google Scholar 

  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 107:551–555

    Article  Google Scholar 

  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 29:4517–4527

    Article  CAS  Google Scholar 

  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 147–167

    Chapter  Google Scholar 

  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 10:2158–2165

    Article  CAS  Google Scholar 

  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 151–181

    Chapter  Google Scholar 

  31. Chao G, Lau WL, Hackel BJ et al (2006) Isolating and engineering human antibodies using yeast surface display. Nat Protoc 1:755–768

    Article  CAS  Google Scholar 

  32. Gera N, Hussain M, Rao BM (2013) Protein selection using yeast surface display. Methods 60:15–26

    Article  CAS  Google Scholar 

  33. Pettersen EF, Goddard TD, Huang CC et al (2004) UCSF Chimera—a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612

    Article  CAS  Google Scholar 

  34. Könning D, Kolmar H (2018) Beyond antibody engineering: directed evolution of alternative binding scaffolds and enzymes using yeast surface display. Microb Cell Factories 17:32

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Antibody-Drug Conjugates and Targeted NBE Therapeutics, Merck KGaA, Darmstadt, Germany

    Doreen Könning, Anna Kaempffe, Sebastian Jäger & Christian Schröter

  2. Protein Engineering and Antibody Technologies (PEAT), Merck KGaA, Darmstadt, Germany

    Stefan Zielonka

  3. Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany

    Anna Kaempffe, Sebastian Jäger & Harald Kolmar

Authors
  1. Doreen Könning
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Stefan Zielonka
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Anna Kaempffe
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Sebastian Jäger
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Harald Kolmar
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Christian Schröter
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Christian Schröter .

Editor information

Editors and Affiliations

  1. Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany

    Stefan Zielonka

  2. Protein Engineering and Antibody Technologies, Merck KGaA, Darmstadt, Germany

    Simon Krah

Rights and permissions

Reprints and permissions

Copyright information

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

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Könning, D., Zielonka, S., Kaempffe, A., Jäger, S., Kolmar, H., Schröter, C. (2020). Selection and Characterization of Anti-idiotypic Shark Antibody Domains. In: Zielonka, S., Krah, S. (eds) Genotype Phenotype Coupling. Methods in Molecular Biology, vol 2070. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9853-1_11

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-9853-1_11

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-4939-9852-4

  • Online ISBN: 978-1-4939-9853-1

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation