Skip to main content

The Use of Somatic Hypermutation for the Affinity Maturation of Therapeutic Antibodies

  • Protocol
  • First Online:
Book cover Antibody Engineering

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1827))

Abstract

The engineering of antibodies and antibody fragments for affinity maturation, stability, and other biophysical characteristics is a common aspect of therapeutic development. Maturation of antibodies in B cells during the adaptive immune response is the result of a process called somatic hypermutation (SHM), in which the activation-induced cytidine deaminase (AID) acts to introduce mutations into immunoglobulin (Ig) genes. Iterative selection and clonal expansion of B cells containing affinity-enhancing mutations drive an increase in the overall affinity of antibodies. Here we describe the use of SHM coupled with mammalian cell surface display for the maturation of antibodies in vitro and the complementarity of these methods with the mining of immune lineages using next-generation sequencing (NGS).

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

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 279.99
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

Institutional subscriptions

References

  1. Ecker DM, Jones SD, Levine HL (2015) The therapeutic monoclonal antibody market. MAbs 7(1):9–14. https://doi.org/10.4161/19420862.2015.989042

    Article  PubMed  CAS  Google Scholar 

  2. Weiner LM, Surana R, Wang SZ (2010) Monoclonal antibodies: versatile platforms for cancer immunotherapy. Nat Rev Immunol 10(5):317–327. https://doi.org/10.1038/nri2744

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  3. Spiess C, Zhai Q, Carter PJ (2015) Alternative molecular formats and therapeutic applications for bispecific antibodies. Mol Immunol 67(2 Pt A):95–106. https://doi.org/10.1016/j.molimm.2015.01.003

    Article  PubMed  CAS  Google Scholar 

  4. Julian MC, Li L, Garde S, Wilen R, Tessier PM (2017) Efficient affinity maturation of antibody variable domains requires co-selection of compensatory mutations to maintain thermodynamic stability. Sci Rep 7:45259. https://doi.org/10.1038/srep45259

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  5. Tas JM, Mesin L, Pasqual G, Targ S, Jacobsen JT, Mano YM, Chen CS, Weill JC, Reynaud CA, Browne EP, Meyer-Hermann M, Victora GD (2016) Visualizing antibody affinity maturation in germinal centers. Science 351(6277):1048–1054. https://doi.org/10.1126/science.aad3439

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  6. Queen C, Schneider WP, Selick HE, Payne PW, Landolfi NF, Duncan JF, Avdalovic NM, Levitt M, Junghans RP, Waldmann TA (1989) A humanized antibody that binds to the interleukin-2 receptor. Proc Natl Acad Sci U S A 86(24):10029–10033. https://doi.org/10.1073/pnas.86.24.10029

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  7. Kettleborough CA, Saldanha J, Heath VJ, Morrison CJ, Bendig MM (1991) Humanization of a mouse monoclonal-antibody by Cdr-grafting - the importance of framework residues on loop conformation. Protein Eng 4(7):773–783. https://doi.org/10.1093/protein/4.7.773

    Article  PubMed  CAS  Google Scholar 

  8. Wu HR, Nie Y, Huse WD, Watkins JD (1999) Humanization of a murine monoclonal antibody by simultaneous optimisation of framework and CDR residues. J Mol Biol 294(1):151–162. https://doi.org/10.1006/jmbi.1999.3141

    Article  PubMed  CAS  Google Scholar 

  9. Boder ET, Midelfort KS, Wittrup KD (2000) Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity. Proc Natl Acad Sci U S A 97(20):10701–10705. https://doi.org/10.1073/pnas.170297297

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  10. Bowers PM, Neben TY, Tomlinson GL, Dalton JL, Altobell L, Zhang X, Macomber JL, Wu BF, Toobian RM, McConnell AD, Verdino P, Chau B, Horlick RA, King DJ (2013) Humanization of antibodies using heavy chain complementarity-determining region 3 grafting coupled with in vitro somatic hypermutation. J Biol Chem 288(11):7688–7696. https://doi.org/10.1074/jbc.M112.445502

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  11. Bowers PM, Horlick RA, Neben TY, Toobian RM, Tomlinson GL, Dalton JL, Jones HA, Chen A, Altobell L, Zhang X, Macomber JL, Krapf IP, Wu BF, McConnell A, Chau B, Holland T, Berkebile AD, Neben SS, Boyle WJ, King DJ (2011) Coupling mammalian cell surface display with somatic hypermutation for the discovery and maturation of human antibodies. Proc Natl Acad Sci U S A 108(51):20455–20460. https://doi.org/10.1073/pnas.1114010108

    Article  PubMed  PubMed Central  Google Scholar 

  12. Bowers PM, Horlick RA, Kehry MR, Neben TY, Tomlinson GL, Altobell L, Zhang X, Macomber JL, Krapf IP, Wu BF, McConnell AD, Chau B, Berkebile AD, Hare E, Verdino P, King DJ (2014) Mammalian cell display for the discovery and optimization of antibody therapeutics. Methods 65(1):44–56. https://doi.org/10.1016/j.ymeth.2013.06.010

    Article  PubMed  CAS  Google Scholar 

  13. Cumbers SJ, Williams GT, Davies SL, Grenfell RL, Takeda S, Batista FD, Sale JE, Neuberger MS (2002) Generation and iterative affinity maturation of antibodies in vitro using hypermutating B-cell lines. Nat Biotechnol 20(11):1129–1134. https://doi.org/10.1038/nbt752

    Article  PubMed  CAS  Google Scholar 

  14. Petersen-Mahrt SK, Harris RS, Neuberger MS (2002) AID mutates E-coli suggesting a DNA deamination mechanism for antibody diversification. Nature 418(6893):99–103. https://doi.org/10.1038/nature00862

    Article  PubMed  CAS  Google Scholar 

  15. Peled JU, Kuang FL, Iglesias-Ussel MD, Roa S, Kalis SL, Goodman ME, Scharff MD (2008) The biochemistry of somatic hypermutation. Annu Rev Immunol 26:481–511. https://doi.org/10.1146/annurev.immunol.26.021607.090236

    Article  PubMed  CAS  Google Scholar 

  16. Mazor Y, Van Blarcom T, Mabry R, Iverson BL, Georgiou G (2007) Isolation of engineered, full-length antibodies from libraries expressed in Escherichia coli. Nat Biotechnol 25(5):563–565. https://doi.org/10.1038/nbt1296

    Article  PubMed  CAS  Google Scholar 

  17. Feldhaus MJ, Siegel RW, Opresko LK, Coleman JR, Feldhaus JMW, Yeung YA, Cochran JR, Heinzelman P, Colby D, Swers J, Graff C, Wiley HS, Wittrup KD (2003) Flow-cytometric isolation of human antibodies from a nonimmune Saccharomyces cerevisiae surface display library. Nat Biotechnol 21(2):163–170. https://doi.org/10.1038/nbt785

    Article  PubMed  CAS  Google Scholar 

  18. Bowers PM, Verdino P, Wang ZY, Correia JD, Chhoa M, Macondray G, Do M, Neben TY, Horlick RA, Stanfield RL, Wilson IA, King DJ (2014) Nucleotide insertions and deletions complement point mutations to massively expand the diversity created by somatic hypermutation of antibodies. J Biol Chem 289(48):33557–33567. https://doi.org/10.1074/jbc.M114.607176

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  19. Damjanovich S, Tron L, Szollosi J, Zidovetzki R, Vaz WLC, Regateiro F, Arndtjovin DJ, Jovin TM (1983) Distribution and mobility of murine histocompatibility H-2kk antigen in the cytoplasmic membrane. Proc Natl Acad Sci Biol 80(19):5985–5989. https://doi.org/10.1073/pnas.80.19.5985

    Article  CAS  Google Scholar 

  20. Park SR (2012) Activation-induced cytidine deaminase in B cell immunity and cancers. Immune Netw 12(6):230–239. https://doi.org/10.4110/in.2012.12.6.230

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  21. van den Beucken T, Pieters H, Steukers M, van der Vaart M, Ladner RC, Hoogenboom HR, Hufton SE (2003) Affinity maturation of fab antibody fragments by fluorescent-activated cell sorting of yeast-displayed libraries. FEBS Lett 546(2–3):288–294

    Article  CAS  PubMed  Google Scholar 

  22. Hu D, Hu S, Wan W, Xu M, Du R, Zhao W, Gao X, Liu J, Liu H, Hong J (2015) Effective optimization of antibody affinity by phage display integrated with high-throughput DNA synthesis and sequencing technologies. PLoS One 10(6):e0129125. https://doi.org/10.1371/journal.pone.0129125

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  23. Hotzel I, Theil FP, Bernstein LJ, Prabhu S, Deng R, Quintana L, Lutman J, Sibia R, Chan P, Bumbaca D, Fielder P, Carter PJ, Kelley RF (2012) A strategy for risk mitigation of antibodies with fast clearance. MAbs 4(6):753–760. https://doi.org/10.4161/mabs.22189

    Article  PubMed  PubMed Central  Google Scholar 

  24. Dudgeon K, Rouet R, Kokmeijer I, Schofield P, Stolp J, Langley D, Stock D, Christ D (2012) General strategy for the generation of human antibody variable domains with increased aggregation resistance. Proc Natl Acad Sci U S A 109(27):10879–10884. https://doi.org/10.1073/pnas.1202866109

    Article  PubMed  PubMed Central  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Peter M. Bowers .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Bowers, P.M., Boyle, W.J., Damoiseaux, R. (2018). The Use of Somatic Hypermutation for the Affinity Maturation of Therapeutic Antibodies. In: Nevoltris, D., Chames, P. (eds) Antibody Engineering. Methods in Molecular Biology, vol 1827. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8648-4_24

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-8648-4_24

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8647-7

  • Online ISBN: 978-1-4939-8648-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics