Creation of recombinant antigen-binding molecules derived from hybridomas secreting specific antibodies

Nature Protocols

Volumn 8, Issue 6, 2013, Pages 1125-1148

  Fields, Conor ^a   O'Connell, David ^a   Xiao, Sujing ^b   Lee, Gil U ^a   Billiald, Philippe ^c   Muzard, Julien ^a,d  

^a UNIVERSITY COLLEGE DUBLIN   (Ireland)

^b Genscript   (United States)

^c CNRS   (France)

^d Bioinformatique et Chimie Moléculaire   (France)

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNOGLOBULIN G ANTIBODY; MONOCLONAL ANTIBODY; RECOMBINANT ANTIBODY; SINGLE CHAIN FRAGMENT VARIABLE ANTIBODY;

ANTIBODY ENGINEERING; ARTICLE; DNA SEQUENCE; HYBRIDOMA; IMMUNOGLOBULIN HEAVY CHAIN GENE; IMMUNOGLOBULIN LIGHT CHAIN GENE; MOLECULAR CLONING; PRIORITY JOURNAL; PURIFICATION;

ANIMALS; ANTIBODIES, MONOCLONAL; CLONING, MOLECULAR; HYBRIDOMAS; IMMUNOGLOBULIN FRAGMENTS; IMMUNOGLOBULIN HEAVY CHAINS; IMMUNOGLOBULIN LIGHT CHAINS; MICE; MODELS, MOLECULAR; RECOMBINATION, GENETIC;

MURINAE; MUS;

EID: 84879371196     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2013.057     Document Type: Article

References (56)

1. Köhler, G. & Milstein, C. Continuous cultures of fused cells secreting antibody of predefned specifcity. Nature 256, 495-497 (1975).
2. Nelson, A.L. & Reichert, J.M. Development trends for therapeutic antibody fragments. Nat. Biotechnol. 27, 331-337 (2009).
3. Bird, R.E. et al. Single-chain antigen-binding proteins. Science 242, 423-426 (1988).
4. Holliger, P. & Hudson, P.J. Engineered antibody fragments and the rise of single domains. Nat. Biotechnol. 23, 1126-1136 (2005).
5. Aubrey, N. et al. Engineering of a recombinant Fab from a neutralizing IgG directed against scorpion neurotoxin AahI and functional evaluation versus other antibody fragments. Toxicon 43, 233-241 (2004).
6. Eisenhardt, S.U., Schwarz, M., Bassler, N. & Peter, K. Subtractive single-chain antibody (scFv) phage-display: tailoring phage-display for high specifcity against function-specifc conformations of cell membrane molecules. Nat. Protoc. 2, 3063-3073 (2007).
7. Chapman, A.P. PEGylated antibodies and antibody fragments for improved therapy: a review. Adv. Drug Deliv. Rev. 54, 531-545 (2002).
8. Zahid, M. et al. Design and reshaping of an scFv directed against human platelet glycoprotein VI with diagnostic potential. Anal. Biochem. 417, 274-282 (2011).
9. Dubreuil, O. et al. Fine tuning of the specifcity of an anti-progesterone antibody by frst and second sphere residue engineering. J. Biol. Chem. 280, 24880-24887 (2005).
10. Rouet, R. et al. Expression of high-affnity human antibody fragments in bacteria. Nat. Protoc. 7, 364-373 (2012).
11. Muzard, J. et al. Design and humanization of a murine scFv that blocks human platelet glycoprotein VI in vitro. FEBS J. 276, 4207-4222 (2009).
12. di Tommaso, A. et al. Diabody mixture providing full protection against experimental scorpion envenoming with crude Androctonus australis venom. J. Biol. Chem. 287, 14149-14156 (2012).
13. Kontermann, R.E. Strategies to extend plasma half-lives of recombinant antibodies. Biodrugs 23, 93-109 (2009).
14. +-channel toxins protects against experimental scorpion envenoming. Cell Mol. Life Sci. 64, 206-218 (2007).
15. Aubrey, N. et al. Design and evaluation of a diabody to improve protection against a potent scorpion neurotoxin. Cell Mol. Life Sci. 60, 617-628 (2003).
16. Nelson, A.L., Dhimolea, E. & Reichert, J.M. Development trends for human monoclonal antibody therapeutics. Nat. Rev. Drug Discov. 9, 767-774 (2010).
17. Barbas III, C.F., Burton, D.R., Scott, J.K. & Silverman, G.J. Phage Display: A laboratory Manual (Cold Spring Harbor Laboratory Press, 2004).
18. Grimm, S., Yu, F. & Nygren, P.A. Ribosome display selection of a murine IgG(1) Fab binding affbody molecule allowing species selective recovery of monoclonal antibodies. Mol. Biotechnonol. 48, 263-276 (2011).
19. Chao, G. et al. Isolating and engineering human antibodies using yeast surface display. Nat. Protoc. 1, 755-768 (2006).
20. Cotten, S.W., Zou, J., Valencia, C.A. & Liu, R. Selection of proteins with desired properties from natural proteome libraries using mRNA display. Nat. Protoc. 6, 1163-1182 (2011).
21. Mazor, Y., Blarcom, T.V., Iverson, B.L. & Georgiou, G. E-clonal antibodies: selection of full-length IgG antibodies using bacterial periplasmic display. Nat. Protoc. 3, 1766-1777 (2008).
22. Haque, A. & Tonks, K.T. The use of phage display to generate conformation-sensor recombinant antibodies. Nat. Protoc. 7, 2127-2143 (2012).
23. Lee, C.M.Y., Iorno, N., Sierro, F. & Christ, D. Selection of human antibody fragments by phage display. Nat. Protoc. 2, 3001-3008 (2007).
24. O'Connell, D., Becerril, B., Roy-Burman, A., Daws, M. & Marks, J.D. Phage versus phagemid libraries for generation of human monoclonal antibodies. J. Mol. Biol. 321, 49-56 (2002).
25. Bourbeillon, J. et al. Minimum information about a protein affnity reagent (MIAPAR). Nat. Biotechnol. 28, 650-653 (2010).
26. Borrebaeck, C.A.K. Antibody Engineering, 2nd edn. (Oxford University Press, 1994).
27. Gustafsson, C., Govindarajan, S. & Minshull, J. Codon bias and heterologous protein expression. Trends Biotechnol. 22, 346-353 (2004).
28. Sambrook, J., Fritsch, E.F. & Maniatis, T. Molecular Cloning: a Laboratory Manual 3rd edn. (eds. Sambrook, J. & Russell, D.W.) 11.98-11.133 (Cold Spring Harbor Laboratory Press, 2001).
29. Muzard, J., Loyau, S., Ajzenberg, N., Billiald, P. & Jandrot-Perrus, M. Antithrombotic recombinant antibodies. J. Soc. Biol. 200, 365-376 (2006).
30. McGregor, D.P., Molloy, P.E., Cunningham, C. & Harris, W.J. Spontaneous assembly of bivalent single chain antibody fragments in Escherichia coli. Mol. Immunol. 31, 219-226 (1994).
31. Muzard, J. Recent patent applications in antibody fragments: an academic update from the EU. Nat. Biotechnol. 29, 979 (2011).
32. Muzard, J., Fields, C., O'Mahony, J.J. & Lee, G.U. Probing the soybean Bowman Birk Inhibitor using recombinant antibody fragments. J. Agric. Food Chem. 60, 6164-6172 (2012).
33. Kortt, A.A., Dolezal, O., Power, B.E. & Hudson, P.J. Dimeric and trimeric antibodies: high avidity scFvs for cancer targeting. Biomol. Eng. 18, 95-108 (2001).
34. Muzard, J. et al. Grafting of protein L-binding activity onto recombinant antibody fragments. Anal Biochem. 388, 331-338 (2009).
35. Juste, M., Muzard, J. & Billiald, P. Cloning of the antibody κ light chain V-gene from murine hybridomas by bypassing the aberrant MOPC21-derived transcript. Anal Biochem. 349, 159-161 (2006).
36. Heo, M.A. et al. Functional expression of single-chain variable fragment antibody against c-Met in the cytoplasm of Escherichia coli. Protein Expr. Purif. 47, 203-209 (2006).
37. Tolner, B., Smith, L., Begent, R.H.J. & Chester, K.A. Production of recombinant protein in Pichia pastoris by fermentation. Nat. Protoc. 1, 1006-1021 (2006).
38. Hardiman, G. Next-generation antibody discovery platforms. Proc. Natl Acad. Sci. USA 109, 1824-1826 (2012).
39. Kabat, E.A., Wu, T.T., Perry, H., Gottesman, G. & Foeller, C. Sequences of Proteins of Immunological Interest 5th edn. US Department of Health and Human Services, Public Health Service, National Institutes of Health (NIH): NIH publication no. 91-3242 (1991).
40. Hornig, N. & Färber-Schwarz, A. Production of bispecifc antibodies: diabodies and tandem scFv. Methods Mol. Biol. 907, 713-727 (2012).
41. Ruberti, F., Cattaneo, A. & Bradbury, A. The use of the RACE method to clone hybridoma cDNA when V region primers fail. J. Immunol. Methods 173, 33-39 (1994).
42. Kaas, Q. & Lefranc, M.P. IMGT Colliers de Perles: standardized sequence-structure representations of the IgSF and MhcSF superfamily domains. Curr. Bioinformatics 2, 21-30 (2007).
43. Kaas, Q., Ehrenmanns, F. & Lefranc, M.P. IG, TR, MHC, IgSf and MhcSF: what do we learn from the IMGT Colliers de Perles? Brief. Funct. Genomic Proteomic. 6, 253-264 (2007).
44. Honegger, A. & Plückthun, A. Yet another numbering scheme for immunoglobulin variable domains: An automatic modeling and analysis tool. J. Mol. Biol. 309, 657-670 (2001).
45. Billiald, P., Motta, G. & Vaux, D.J. Production of a functional antiscorpion hemocyanin scFv in Escherichia coli. Arch. Biochem. Biophys. 317, 429-438 (1995).
46. Zhou, H., Fisher, R.J. & Papas, T.S. Optimization of primer sequences for mouse scFv repertoire display library construction. Nucleic Acids Res. 22, 888-889 (1994).
47. Ortega, C. et al. High level prokaryotic expression of anti-Müllerian inhibiting substance type II receptor diabody, a new recombinant antibody for in vivo ovarian cancer imaging. J. Immunol. Methods 387, 11-20 (2013).
48. Schaefer, J.V. & Plückthun, A. Improving expression of scFv fragments by co-expression of periplasmic chaperones. in Antibody Engineering 2nd edn. (eds. Kontermann, R. & Dübel, S.) 2, 345-361 (Springer, 2010).
49. Vincze, T., Posfai, J. & Roberts, R.J. NEBcutter: a program to cleave DNA with restriction enzymes. Nucleic Acids Res. 31, 3688-3691 (2003).
50. Ehrenmann, F., Giudicelli, V., Duroux, P. & Lefranc, M.P. IMGT/Collier de Perles: IMGT standardized representation of domains (IG, TR, and IgSF variable and constant domains, MH and MhSF groove domains). Cold Spring Harbor Protoc. 6, 726-736 (2011).
51. Martin, A.C.R. Accessing the Kabat antibody sequence database by computer PROTEINS: Structure, Function and Genetics. Proteins 25, 130-133 (1996).
52. Whitelegg, N.R.J. & Rees, A.R. WAM: an improved algorithm for modeling antibodies on the web. Protein Eng. 13, 819-824 (2000).
53. Bruccoleri, R.E. Application of systematic conformational search to protein modelling. Mol. Simul. 10, 151-174 (1993).
54. Sivasubramanian, A., Sircar, A., Chaudhury, S. & Gray, J.J. Toward highresolution homology modeling of antibody Fv regions and application to antibody-antigen docking. Proteins 74, 497-514 (2009).
55. Duhovny, D., Nussinov, R. & Wolfson, H.J. Effcient unbound docking of rigid molecules. in Proceedings of the 2nd Workshop on Algorithms in Bioinformatics (WABI), Rome, Italy; Lecture Notes in Computer Science (ed. Gusfeld et al.) 2452, 185-200 (Springer, 2002).
56. Schneidman-Duhovny, D., Inbar, Y., Nussinov, R. & Wolfson, H.J. PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Res. 33, W363-W367 (2005).