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Beyond natural antibodies: the power of in vitro display technologies

Abstract

In vitro display technologies, best exemplified by phage and yeast display, were first described for the selection of antibodies some 20 years ago. Since then, many antibodies have been selected and improved upon using these methods. Although it is not widely recognized, many of the antibodies derived using in vitro display methods have properties that would be extremely difficult, if not impossible, to obtain by immunizing animals. The first antibodies derived using in vitro display methods are now in the clinic, with many more waiting in the wings. Unlike immunization, in vitro display permits the use of defined selection conditions and provides immediate availability of the sequence encoding the antibody. The amenability of in vitro display to high-throughput applications broadens the prospects for their wider use in basic and applied research.

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Figure 1: The unique capabilities of in vitro selection offer advantages over the immunization of animals for antibody generation.
Figure 2: In vitro selected antibodies can recognize minute differences in small molecules.
Figure 3: Mechanisms for blocking or activating receptor signaling using antibodies.
Figure 4: An engineered dual specificity synthetic Fab.

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  1. Love, J.C., Ronan, J.L., Grotenbreg, G.M., van der Veen, A.G. & Ploegh, H.L. A microengraving method for rapid selection of single cells producing antigen-specific antibodies. Nat. Biotechnol. 24, 703–707 (2006).

    CAS  PubMed  Google Scholar 

  2. Jin, A. et al. A rapid and efficient single-cell manipulation method for screening antigen-specific antibody-secreting cells from human peripheral blood. Nat. Med. 15, 1088–1092 (2009).

    CAS  PubMed  Google Scholar 

  3. Reddy, S.T. et al. Monoclonal antibodies isolated without screening by analyzing the variable-gene repertoire of plasma cells. Nat. Biotechnol. 28, 965–969 (2010).

    CAS  PubMed  Google Scholar 

  4. Smith, G.P. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228, 1315–1317 (1985).

    CAS  PubMed  Google Scholar 

  5. Scott, J.K. & Smith, G.P. Searching for peptide ligands with an epitope library. Science 249, 386–390 (1990).

    CAS  PubMed  Google Scholar 

  6. Skerra, A. & Pluckthun, A. Assembly of a functional immunoglobulin Fv fragment in Escherichia coli. Science 240, 1038–1041 (1988).

    CAS  PubMed  Google Scholar 

  7. Larrick, J.W. et al. Rapid cloning of rearranged immunoglobulin genes from human hybridoma cells using mixed primers and the polymerase chain reaction. Biochem. Biophys. Res. Commun. 160, 1250–1256 (1989).

    CAS  PubMed  Google Scholar 

  8. Marks, J.D. et al. By-passing immunization. Human antibodies from V-gene libraries displayed on phage. J. Mol. Biol. 222, 581–597 (1991).

    CAS  PubMed  Google Scholar 

  9. Orlandi, R., Gussow, D.H., Jones, P.T. & Winter, G. Cloning immunoglobulin variable domains for expression by the polymerase chain reaction. Proc. Natl. Acad. Sci. USA 86, 3833–3837 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Huse, W.D. et al. Generation of a large combinatorial library of the immunoglobulin repertoire in phage lambda. Science 246, 1275–1281 (1989).

    CAS  PubMed  Google Scholar 

  11. Sastry, L. et al. Cloning of the immunological repertoire in Escherichia coli for generation of monoclonal catalytic antibodies: construction of a heavy chain variable region-specific cDNA library. Proc. Natl. Acad. Sci. USA 86, 5728–5732 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. McCafferty, J., Griffiths, A.D., Winter, G. & Chiswell, D.J. Phage antibodies: filamentous phage displaying antibody variable domains. Nature 348, 552–554 (1990).

    CAS  PubMed  Google Scholar 

  13. Breitling, F., Dübel, S., Seehaus, T., Klewinghaus, I. & Little, M. A surface expression vector for antibody screening. Gene 104, 147–153 (1991).

    CAS  PubMed  Google Scholar 

  14. Boder, E.T. & Wittrup, K.D. Yeast surface display for screening combinatorial polypeptide libraries. Nat. Biotechnol. 15, 553–557 (1997).

    CAS  PubMed  Google Scholar 

  15. Feldhaus, M.J. et al. Flow-cytometric isolation of human antibodies from a nonimmune Saccharomyces cerevisiae surface display library. Nat. Biotechnol. 21, 163–170 (2003).

    CAS  PubMed  Google Scholar 

  16. Bordeaux, J. et al. Antibody validation. Biotechniques 48, 197–209 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Jositsch, G. et al. Suitability of muscarinic acetylcholine receptor antibodies for immunohistochemistry evaluated on tissue sections of receptor gene-deficient mice. Naunyn Schmiedebergs Arch. Pharmacol. 379, 389–395 (2009).

    CAS  PubMed  Google Scholar 

  18. Jensen, B.C., Swigart, P.M. & Simpson, P.C. Ten commercial antibodies for alpha-1-adrenergic receptor subtypes are nonspecific. Naunyn Schmiedebergs Arch. Pharmacol. 379, 409–412 (2009).

    CAS  PubMed  Google Scholar 

  19. Spicer, S.S., Spivey, M.A., Ito, M. & Schulte, B.A. Some ascites monoclonal antibody preparations contain contaminants that bind to selected Golgi zones or mast cells. J. Histochem. Cytochem. 42, 213–221 (1994).

    CAS  PubMed  Google Scholar 

  20. Pozner-Moulis, S., Cregger, M., Camp, R.L. & Rimm, D.L. Antibody validation by quantitative analysis of protein expression using expression of Met in breast cancer as a model. Lab. Invest. 87, 251–260 (2007).

    CAS  PubMed  Google Scholar 

  21. Grimsey, N.L. et al. Specific detection of CB1 receptors; cannabinoid CB1 receptor antibodies are not all created equal! J. Neurosci. Methods 171, 78–86 (2008).

    CAS  PubMed  Google Scholar 

  22. Saper, C.B. An open letter to our readers on the use of antibodies. J. Comp. Neurol. 493, 477–478 (2005).

    PubMed  Google Scholar 

  23. Paschke, M. Phage display systems and their applications. Appl. Microbiol. Biotechnol. 70, 2–11 (2006).

    CAS  PubMed  Google Scholar 

  24. Zahnd, C., Amstutz, P. & Pluckthun, A. Ribosome display: selecting and evolving proteins in vitro that specifically bind to a target. Nat. Methods 4, 269–279 (2007).

    CAS  PubMed  Google Scholar 

  25. Chao, G. et al. Isolating and engineering human antibodies using yeast surface display. Nat. Protoc. 1, 755–768 (2006).

    CAS  PubMed  Google Scholar 

  26. Binz, H.K., Amstutz, P. & Pluckthun, A. Engineering novel binding proteins from nonimmunoglobulin domains. Nat. Biotechnol. 23, 1257–1268 (2005).

    CAS  PubMed  Google Scholar 

  27. Binz, H.K. & Pluckthun, A. Engineered proteins as specific binding reagents. Curr. Opin. Biotechnol. 16, 459–469 (2005).

    CAS  PubMed  Google Scholar 

  28. Skerra, A. Alternative non-antibody scaffolds for molecular recognition. Curr. Opin. Biotechnol. 18, 295–304 (2007).

    CAS  PubMed  Google Scholar 

  29. Bradbury, A.R. & Marks, J.D. Antibodies from phage antibody libraries. J. Immunol. Methods 290, 29–49 (2004).

    CAS  PubMed  Google Scholar 

  30. Throsby, M. et al. Heterosubtypic neutralizing monoclonal antibodies cross-protective against H5N1 and H1N1 recovered from human IgM+ memory B cells. PLoS ONE 3, e3942 (2008).

    PubMed  PubMed Central  Google Scholar 

  31. Razai, A. et al. Molecular evolution of antibody affinity for sensitive detection of botulinum neurotoxin type A. J. Mol. Biol. 351, 158–169 (2005).

    CAS  PubMed  Google Scholar 

  32. Lee, C.V. et al. High-affinity human antibodies from phage-displayed synthetic Fab libraries with a single framework scaffold. J. Mol. Biol. 340, 1073–1093 (2004).

    CAS  PubMed  Google Scholar 

  33. Hanes, J., Schaffitzel, C., Knappik, A. & Pluckthun, A. Picomolar affinity antibodies from a fully synthetic naive library selected and evolved by ribosome display. Nat. Biotechnol. 18, 1287–1292 (2000).

    CAS  PubMed  Google Scholar 

  34. Schier, R. et al. Isolation of picomolar affinity anti-c-erbB-2 single-chain Fv by molecular evolution of the complementarity determining regions in the center of the antibody binding site. J. Mol. Biol. 263, 551–567 (1996).

    CAS  PubMed  Google Scholar 

  35. Yang, W.P. et al. CDR walking mutagenesis for the affinity maturation of a potent human anti-HIV-1 antibody into the picomolar range. J. Mol. Biol. 254, 392–403 (1995).

    CAS  PubMed  Google Scholar 

  36. Boder, E.T., Midelfort, K.S. & Wittrup, K.D. Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity. Proc. Natl. Acad. Sci. USA 97, 10701–10705 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Foote, J. & Eisen, H.N. Breaking the affinity ceiling for antibodies and T cell receptors. Proc. Natl. Acad. Sci. USA 97, 10679–10681 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Batista, F.D. & Neuberger, M.S. Affinity dependence of the B cell response to antigen: a threshold, a ceiling, and the importance of off-rate. Immunity 8, 751–759 (1998).

    CAS  PubMed  Google Scholar 

  39. Schofield, D.J. et al. Application of phage display to high throughput antibody generation and characterization. Genome Biol. 8, R254 (2007).

    PubMed  PubMed Central  Google Scholar 

  40. Dübel, S., Stoevesandt, O., Taussig, M.J. & Hust, M. Generating recombinant antibodies to the complete human proteome. Trends Biotechnol. 28, 333–339 (2010).

    PubMed  Google Scholar 

  41. Koide, A., Bailey, C.W., Huang, X. & Koide, S. The fibronectin type III domain as a scaffold for novel binding proteins. J. Mol. Biol. 284, 1141–1151 (1998).

    CAS  PubMed  Google Scholar 

  42. Philibert, P. et al. A focused antibody library for selecting scFvs expressed at high levels in the cytoplasm. BMC Biotechnol. 7, 81 (2007).

    PubMed  PubMed Central  Google Scholar 

  43. Parsons, H.L. et al. Directing phage selections towards specific epitopes. Protein Eng. 9, 1043–1049 (1996).

    CAS  PubMed  Google Scholar 

  44. Lassen, K.S., Bradbury, A.R., Rehfeld, J.F. & Heegaard, N.H. Microscale characterization of the binding specificity and affinity of a monoclonal antisulfotyrosyl IgG antibody. Electrophoresis 29, 2557–2564 (2008).

    CAS  PubMed  Google Scholar 

  45. Kehoe, J.W. et al. Using phage display to select antibodies recognizing post-translational modifications independently of sequence context. Mol. Cell. Proteomics 5, 2350–2363 (2006).

    CAS  PubMed  Google Scholar 

  46. Hoffhines, A.J., Damoc, E., Bridges, K.G., Leary, J.A. & Moore, K.L. Detection and purification of tyrosine-sulfated proteins using a novel anti-sulfotyrosine monoclonal antibody. J. Biol. Chem. 281, 37877–37887 (2006).

    CAS  PubMed  Google Scholar 

  47. Grunewald, J. et al. Mechanistic studies of the immunochemical termination of self-tolerance with unnatural amino acids. Proc. Natl. Acad. Sci. USA 106, 4337–4342 (2009).

    PubMed  PubMed Central  Google Scholar 

  48. Dalum, I. et al. Therapeutic antibodies elicited by immunization against TNF-alpha. Nat. Biotechnol. 17, 666–669 (1999).

    CAS  PubMed  Google Scholar 

  49. Hust, M. et al. A human scFv antibody generation pipeline for proteome research. J. Biotechnol. published online, doi:10.1016/j.jbiotec.2010.09.945 (29 September 2010).

  50. Lloyd, C. et al. Modelling the human immune response: performance of a 1011 human antibody repertoire against a broad panel of therapeutically relevant antigens. Protein Eng. Des. Sel. 22, 159–168 (2009).

    CAS  PubMed  Google Scholar 

  51. Wright, K., Collins, D.C. & Preedy, J.R. Comparative specificity of antisera raised against estrone, estradiol-17 and estriol using 6–0-carboxy-methyloxime bovine serum albumin derivatives. Steroids 21, 755–769 (1973).

    CAS  PubMed  Google Scholar 

  52. Haning, R. et al. The evolution of titer and specificity of aldosterone binding antibodies in hyperimmunized sheep. Steroids 20, 73–88 (1972).

    CAS  PubMed  Google Scholar 

  53. Exley, D., Johnson, M.W. & Dean, P.D. Antisera highly specific for 17-oestradiol. Steroids 18, 605–620 (1971).

    CAS  PubMed  Google Scholar 

  54. Tateishi, K., Hamaoka, T., Takatsu, K. & Hayashi, C. A novel immunization procedure for production of anti-testosterone and anti-5 alpha-dihydrotestosterone antisera of low cross-reactivity. J. Steroid Biochem. 13, 951–959 (1980).

    CAS  PubMed  Google Scholar 

  55. Smith, T.W. & Skubitz, K.M. Kinetics in interactions between antibodies and haptens. Biochemistry 14, 1496–1502 (1975).

    CAS  PubMed  Google Scholar 

  56. Monigatti, F., Gasteiger, E., Bairoch, A. & Jung, E. The Sulfinator: predicting tyrosine sulfation sites in protein sequences. Bioinformatics 18, 769–770 (2002).

    CAS  PubMed  Google Scholar 

  57. Sako, D. et al. A sulfated peptide segment at the amino terminus of PSGL-1 is critical for P-selectin binding. Cell 83, 323–331 (1995).

    CAS  PubMed  Google Scholar 

  58. Rigby, P.W., Gething, M.J. & Hartley, B.S. Construction of intergeneric hybrids using bacteriophage P1CM: transfer of the Klebsiella aerogenes ribitol dehydrogenase gene to Escherichia coli. J. Bacteriol. 125, 728–738 (1976).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Ayriss, J., Woods, T., Bradbury, A. & Pavlik, P. High-throughput screening of single-chain antibodies using multiplexed flow cytometry. J. Proteome Res. 6, 1072–1082 (2007).

    CAS  PubMed  Google Scholar 

  60. Pershad, K. et al. Generating a panel of highly specific antibodies to 20 human SH2 domains by phage display. Protein Eng. Des. Sel. 23, 279–288 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Mersmann, M. et al. Towards proteome scale antibody selections using phage display. New Biotechnol. 27, 118–128 (2009).

    Google Scholar 

  62. Velappan, N. et al. Selection and characterization of scFv antibodies against the Sin Nombre hantavirus nucleocapsid protein. J. Immunol. Methods 321, 60–69 (2007).

    CAS  PubMed  Google Scholar 

  63. Cabezas, S. et al. Phage-displayed antibody fragments recognizing dengue 3 and dengue 4 viruses as tools for viral serotyping in sera from infected individuals. Arch. Virol. 154, 1035–1045 (2009).

    CAS  PubMed  Google Scholar 

  64. Lim, A.P. et al. Neutralizing human monoclonal antibody against H5N1 influenza HA selected from a Fab-phage display library. Virol. J. 5, 130 (2008).

    PubMed  PubMed Central  Google Scholar 

  65. Okada, J. et al. Monoclonal antibodies in man that neutralized H3N2 influenza viruses were classified into three groups with distinct strain specificity: 1968–1973, 1977–1993 and 1997–2003. Virology 397, 322–330 (2010).

    CAS  PubMed  Google Scholar 

  66. Meissner, F. et al. Detection of antibodies against the four subtypes of Ebola virus in sera from any species using a novel antibody-phage indicator assay. Virology 300, 236–243 (2002).

    CAS  PubMed  Google Scholar 

  67. Kirsch, M.I. et al. Development of human antibody fragments using antibody phage display for the detection and diagnosis of Venezuelan equine encephalitis virus (VEEV). BMC Biotechnol. 8, 66 (2008).

    PubMed  PubMed Central  Google Scholar 

  68. Maynard, J.A. et al. Protection against anthrax toxin by recombinant antibody fragments correlates with antigen affinity. Nat. Biotechnol. 20, 597–601 (2002).

    CAS  PubMed  Google Scholar 

  69. Mabry, R. et al. Passive protection against anthrax by using a high-affinity antitoxin antibody fragment lacking an Fc region. Infect. Immun. 73, 8362–8368 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Wild, M.A. et al. Human antibodies from immunized donors are protective against anthrax toxin in vivo. Nat. Biotechnol. 21, 1305–1306 (2003).

    CAS  PubMed  Google Scholar 

  71. Hayhurst, A. et al. Isolation and expression of recombinant antibody fragments to the biological warfare pathogen Brucella melitensis. J. Immunol. Methods 276, 185–196 (2003).

    CAS  PubMed  Google Scholar 

  72. Zou, N., Newsome, T., Li, B., Tsai, S. & Lo, S.C. Human single-chain Fv antibodies against Burkholderia mallei and Burkholderia pseudomallei. Exp. Biol. Med. 232, 550–556 (2007).

    CAS  Google Scholar 

  73. Steiniger, S.C., Altobell, L.J. III, Zhou, B. & Janda, K.D. Selection of human antibodies against cell surface-associated oligomeric anthrax protective antigen. Mol. Immunol. 44, 2749–2755 (2007).

    CAS  PubMed  Google Scholar 

  74. Cirino, N.M. et al. Disruption of anthrax toxin binding with the use of human antibodies and competitive inhibitors. Infect. Immun. 67, 2957–2963 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Zhou, B., Wirsching, P. & Janda, K.D. Human antibodies against spores of the genus Bacillus: a model study for detection of and protection against anthrax and the bioterrorist threat. Proc. Natl. Acad. Sci. USA 99, 5241–5246 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  76. Garcia-Rodriguez, C. et al. Molecular evolution of antibody cross-reactivity for two subtypes of type A botulinum neurotoxin. Nat. Biotechnol. 25, 107–116 (2007).

    CAS  PubMed  Google Scholar 

  77. Huie, M.A. et al. Antibodies to human fetal erythroid cells from a nonimmune phage antibody library. Proc. Natl. Acad. Sci. USA 98, 2682–2687 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  78. Nizak, C. et al. Recombinant antibodies to the small GTPase Rab6 as conformation sensors. Science 300, 984–987 (2003).

    CAS  PubMed  Google Scholar 

  79. Gao, J., Sidhu, S.S. & Wells, J.A. Two-state selection of conformation-specific antibodies. Proc. Natl. Acad. Sci. USA 106, 3071–3076 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  80. Eisenhardt, S.U., Schwarz, M., Bassler, N. & Peter, K. Subtractive single-chain antibody (scFv) phage-display: tailoring phage-display for high specificity against function-specific conformations of cell membrane molecules. Nat. Protoc. 2, 3063–3073 (2007).

    CAS  PubMed  Google Scholar 

  81. Ye, J.D. et al. Synthetic antibodies for specific recognition and crystallization of structured RNA. Proc. Natl. Acad. Sci. USA 105, 82–87 (2008).

    CAS  PubMed  Google Scholar 

  82. Edwards, B.M. et al. The remarkable flexibility of the human antibody repertoire; isolation of over one thousand different antibodies to a single protein, BLyS. J. Mol. Biol. 334, 103–118 (2003).

    CAS  PubMed  Google Scholar 

  83. Baker, K.P. et al. Generation and characterization of LymphoStat-B, a human monoclonal antibody that antagonizes the bioactivities of B lymphocyte stimulator. Arthritis Rheum. 48, 3253–3265 (2003).

    CAS  PubMed  Google Scholar 

  84. Runnels, H.A. et al. Human monoclonal antibodies to the insulin-like growth factor 1 receptor inhibit receptor activation and tumor growth in preclinical studies. Adv. Ther. 27, 458–475 (2010).

    CAS  PubMed  Google Scholar 

  85. Peipp, M., Dechant, M. & Valerius, T. Effector mechanisms of therapeutic antibodies against ErbB receptors. Curr. Opin. Immunol. 20, 436–443 (2008).

    CAS  PubMed  Google Scholar 

  86. Li, K. et al. Modulation of Notch signaling by antibodies specific for the extracellular negative regulatory region of NOTCH3. J. Biol. Chem. 283, 8046–8054 (2008).

    CAS  PubMed  Google Scholar 

  87. Wu, Y. et al. Therapeutic antibody targeting of individual Notch receptors. Nature 464, 1052–1057 (2010).

    CAS  PubMed  Google Scholar 

  88. Martens, T. et al. A novel one-armed anti-c-Met antibody inhibits glioblastoma growth in vivo. Clin. Cancer Res. 12, 6144–6152 (2006).

    CAS  PubMed  Google Scholar 

  89. Dobson, C.L. et al. Human monomeric antibody fragments to TRAIL-R1 and TRAIL-R2 that display potent in vitro agonism. MAbs 1, 552–562 (2009).

    PubMed  PubMed Central  Google Scholar 

  90. Sui, J. et al. Structural and functional bases for broad-spectrum neutralization of avian and human influenza A viruses. Nat. Struct. Mol. Biol. 16, 265–273 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  91. Sun, L. et al. Generation, characterization and epitope mapping of two neutralizing and protective human recombinant antibodies against influenza A H5N1 viruses. PLoS ONE 4, e5476 (2009).

    PubMed  PubMed Central  Google Scholar 

  92. Poul, M.A., Becerril, B., Nielsen, U.B., Morisson, P. & Marks, J.D. Selection of tumor-specific internalizing human antibodies from phage libraries. J. Mol. Biol. 301, 1149–1161 (2000).

    CAS  PubMed  Google Scholar 

  93. Heitner, T. et al. Selection of cell binding and internalizing epidermal growth factor receptor antibodies from a phage display library. J. Immunol. Methods 248, 17–30 (2001).

    CAS  PubMed  Google Scholar 

  94. Zhou, Y., Zou, H., Zhang, S. & Marks, J.D. Internalizing cancer antibodies from phage libraries selected on tumor cells and yeast-displayed tumor antigens. J. Mol. Biol. 404, 88–99 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  95. Park, J.W. et al. Tumor targeting using anti-her2 immunoliposomes. J. Control. Release 74, 95–113 (2001).

    CAS  PubMed  Google Scholar 

  96. Nielsen, U.B. et al. Therapeutic efficacy of anti-ErbB2 immunoliposomes targeted by a phage antibody selected for cellular endocytosis. Biochim. Biophys. Acta 1591, 109–118 (2002).

    CAS  PubMed  Google Scholar 

  97. Wu, H. et al. Stepwise in vitro affinity maturation of Vitaxin, an alphav beta3-specific humanized mAb. Proc. Natl. Acad. Sci. USA 95, 6037–6042 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  98. Lippow, S.M., Wittrup, K.D. & Tidor, B. Computational design of antibody-affinity improvement beyond in vivo maturation. Nat. Biotechnol. 25, 1171–1176 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  99. Fellouse, F.A., Wiesmann, C. & Sidhu, S.S. Synthetic antibodies from a four-amino-acid code: a dominant role for tyrosine in antigen recognition. Proc. Natl. Acad. Sci. USA 101, 12467–12472 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  100. Liang, W.C. et al. 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 (2006).

    CAS  PubMed  Google Scholar 

  101. Lee, C.V. et al. Synthetic anti-BR3 antibodies that mimic BAFF binding and target both human and murine B cells. Blood 108, 3103–3111 (2006).

    CAS  PubMed  Google Scholar 

  102. Fagete, S. et al. Specificity tuning of antibody fragments to neutralize two human chemokines with a single agent. MAbs 1, 288–296 (2009).

    PubMed  PubMed Central  Google Scholar 

  103. Bostrom, J. et al. Variants of the antibody Herceptin that interact with HER2 and VEGF at the antigen binding site. Science 323, 1610–1614 (2009).

    CAS  PubMed  Google Scholar 

  104. Volk, W.A., Bizzini, B., Snyder, R.M., Bernhard, E. & Wagner, R.R. Neutralization of tetanus toxin by distinct monoclonal antibodies binding to multiple epitopes on the toxin molecule. Infect. Immun. 45, 604–609 (1984).

    CAS  PubMed  PubMed Central  Google Scholar 

  105. Marks, J.D. Deciphering antibody properties that lead to potent botulinum neurotoxin neutralization. Mov. Disord. 19 Suppl 8, S101–S108 (2004).

    PubMed  Google Scholar 

  106. Nowakowski, A. et al. Potent neutralization of botulinum neurotoxin by recombinant oligoclonal antibody. Proc. Natl. Acad. Sci. USA 99, 11346–11350 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  107. Kalb, S.R. et al. Extraction of BoNT/A, /B, /E, and /F with a single, high affinity monoclonal antibody for detection of botulinum neurotoxin by Endopep-MS. PLoS ONE 5, e12237 (2010).

    PubMed  PubMed Central  Google Scholar 

  108. Garcia-Rodriguez, C. et al. Neutralizing human monoclonal antibodies binding multiple serotypes of botulinum neurotoxin. Protein Eng. Des. Sel. published online, doi:10.1093/protein/gzq111 (12 December 2010).

  109. de Kruif, J. & Logtenberg, T. Leucine zipper dimerized bivalent and bispecific scFv antibodies from a semi-synthetic antibody phage display library. J. Biol. Chem. 271, 7630–7634 (1996).

    CAS  PubMed  Google Scholar 

  110. Hudson, P.J. & Kortt, A.A. High avidity scFv multimers; diabodies and triabodies. J. Immunol. Methods 231, 177–189 (1999).

    CAS  PubMed  Google Scholar 

  111. Dübel, S. et al. Bifunctional and multimeric complexes of streptavidin fused to single chain antibodies (scFv). J. Immunol. Methods 178, 201–209 (1995).

    PubMed  Google Scholar 

  112. Griep, R.A. et al. pSKAP/S: An expression vector for the production of single-chain Fv alkaline phosphatase fusion proteins. Protein Expr. Purif. 16, 63–69 (1999).

    CAS  PubMed  Google Scholar 

  113. Cloutier, S.M. et al. Streptabody, a high avidity molecule made by tetramerization of in vivo biotinylated, phage display-selected scFv fragments on streptavidin. Mol. Immunol. 37, 1067–1077 (2000).

    CAS  PubMed  Google Scholar 

  114. Casey, J.L., Coley, A.M., Tilley, L.M. & Foley, M. Green fluorescent antibodies: novel in vitro tools. Protein Eng. 13, 445–452 (2000).

    CAS  PubMed  Google Scholar 

  115. Thie, H., Binius, S., Schirrmann, T., Hust, M. & Dübel, S. Multimerization domains for antibody phage display and antibody production. New Biotechnol. 26, 314–321 (2009).

    CAS  Google Scholar 

  116. Persic, L. et al. An integrated vector system for the eukaryotic expression of antibodies or their fragments after selection from phage display libraries. Gene 187, 9–18 (1997).

    CAS  PubMed  Google Scholar 

  117. Hu, S. et al. Minibody: A novel engineered anti-carcinoembryonic antigen antibody fragment (single-chain Fv-CH3) which exhibits rapid, high-level targeting of xenografts. Cancer Res. 56, 3055–3061 (1996).

    CAS  PubMed  Google Scholar 

  118. Beck, A. et al. Trends in glycosylation, glycoanalysis and glycoengineering of therapeutic antibodies and Fc-fusion proteins. Curr. Pharm. Biotechnol. 9, 482–501 (2008).

    CAS  PubMed  Google Scholar 

  119. Presta, L.G. Molecular engineering and design of therapeutic antibodies. Curr. Opin. Immunol. 20, 460–470 (2008).

    CAS  PubMed  Google Scholar 

  120. Merchant, A.M. et al. An efficient route to human bispecific IgG. Nat. Biotechnol. 16, 677–681 (1998).

    CAS  PubMed  Google Scholar 

  121. Ridgway, J.B., Presta, L.G. & Carter, P. 'Knobs-into-holes' engineering of antibody CH3 domains for heavy chain heterodimerization. Protein Eng. 9, 617–621 (1996).

    CAS  PubMed  Google Scholar 

  122. Perisic, O., Webb, P.A., Holliger, P., Winter, G. & Williams, R.L. Crystal structure of a diabody, a bivalent antibody fragment. Structure 2, 1217–1226 (1994).

    CAS  PubMed  Google Scholar 

  123. Atwell, J.L. et al. scFv multimers of the anti-neuraminidase antibody NC10: length of the linker between VH and VL domains dictates precisely the transition between diabodies and triabodies. Protein Eng. 12, 597–604 (1999).

    CAS  PubMed  Google Scholar 

  124. Pei, X.Y., Holliger, P., Murzin, A.G. & Williams, R.L. The 2.0-A resolution crystal structure of a trimeric antibody fragment with noncognate VH-VL domain pairs shows a rearrangement of VH CDR3. Proc. Natl. Acad. Sci. USA 94, 9637–9642 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  125. Le Gall, F., Kipriyanov, S.M., Moldenhauer, G. & Little, M. Di-, tri- and tetrameric single chain Fv antibody fragments against human CD19: effect of valency on cell binding. FEBS Lett. 453, 164–168 (1999).

    CAS  PubMed  Google Scholar 

  126. Muller, D. & Kontermann, R.E. Bispecific antibodies for cancer immunotherapy: Current perspectives. BioDrugs 24, 89–98 (2010).

    PubMed  Google Scholar 

  127. Xiang, J. Targeting cytokines to tumors to induce active antitumor immune responses by recombinant fusion proteins. Hum. Antibodies 9, 23–36 (1999).

    CAS  PubMed  Google Scholar 

  128. Schliemann, C. & Neri, D. Antibody-based targeting of the tumor vasculature. Biochim. Biophys. Acta 1776, 175–192 (2007).

    CAS  PubMed  Google Scholar 

  129. Deckert, P.M. Current constructs and targets in clinical development for antibody-based cancer therapy. Curr. Drug Targets 10, 158–175 (2009).

    CAS  PubMed  Google Scholar 

  130. Fuchs, H. & Bachran, C. Targeted tumor therapies at a glance. Curr. Drug Targets 10, 89–93 (2009).

    CAS  PubMed  Google Scholar 

  131. Gawlitta, W., Osborn, M. & Weber, K. Coiling of intermediate filaments induced by microinjection of a vimentin-specific antibody does not interfere with locomotion and mitosis. Eur. J. Cell Biol. 26, 83–90 (1981).

    CAS  PubMed  Google Scholar 

  132. Kontermann, R.E. Intrabodies as therapeutic agents. Methods 34, 163–170 (2004).

    CAS  PubMed  Google Scholar 

  133. Beerli, R.R., Wels, W. & Hynes, N.E. Intracellular expression of single chain antibodies reverts ErbB-2 transformation. J. Biol. Chem. 269, 23931–23936 (1994).

    CAS  PubMed  Google Scholar 

  134. Richardson, J.H., Sodroski, J.G., Waldmann, T.A. & Marasco, W.A. Phenotypic knockout of the high-affinity human interleukin 2 receptor by intracellular single-chain antibodies against the alpha subunit of the receptor. Proc. Natl. Acad. Sci. USA 92, 3137–3141 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  135. Paganetti, P., Calanca, V., Galli, C., Stefani, M. & Molinari, M. beta-site specific intrabodies to decrease and prevent generation of Alzheimer's Abeta peptide. J. Cell Biol. 168, 863–868 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  136. Strebe, N. et al. Functional knockdown of VCAM-1 at the posttranslational level with ER retained antibodies. J. Immunol. Methods 341, 30–40 (2009).

    CAS  PubMed  Google Scholar 

  137. Biocca, S. & Cattaneo, A. Intracellular immunization: antibody targeting to subcellular compartments. Trends Cell Biol. 5, 248–252 (1995).

    CAS  PubMed  Google Scholar 

  138. Biocca, S., Pierandrei-Amaldi, P., Campioni, N. & Cattaneo, A. Intracellular immunization with cytosolic recombinant antibodies. Nat. Biotechnol. 12, 396–399 (1994).

    CAS  Google Scholar 

  139. Desiderio, A. et al. A semi-synthetic repertoire of intrinsically stable antibody fragments derived from a single-framework scaffold. J. Mol. Biol. 310, 603–615 (2001).

    CAS  PubMed  Google Scholar 

  140. der Maur, A.A. et al. Direct in vivo screening of intrabody libraries constructed on a highly stable single-chain framework. J. Biol. Chem. 277, 45075–45085 (2002).

    PubMed  Google Scholar 

  141. Tanaka, T., Chung, G.T., Forster, A., Lobato, M.N. & Rabbitts, T.H. De novo production of diverse intracellular antibody libraries. Nucleic Acids Res. 31, e23 (2003).

    PubMed  PubMed Central  Google Scholar 

  142. Auf der Maur, A., Escher, D. & Barberis, A. Antigen-independent selection of stable intracellular single-chain antibodies. FEBS Lett. 508, 407–412 (2001).

    CAS  PubMed  Google Scholar 

  143. Visintin, M., Tse, E., Axelson, H., Rabbitts, T.H. & Cattaneo, A. Selection of antibodies for intracellular function using a two-hybrid in vivo system. Proc. Natl. Acad. Sci. USA 96, 11723–11728 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  144. Amstutz, P. et al. Intracellular kinase inhibitors selected from combinatorial libraries of designed ankyrin repeat proteins. J. Biol. Chem. 280, 24715–24722 (2005).

    CAS  PubMed  Google Scholar 

  145. Kohl, A. et al. Allosteric inhibition of aminoglycoside phosphotransferase by a designed ankyrin repeat protein. Structure 13, 1131–1141 (2005).

    CAS  PubMed  Google Scholar 

  146. Rizk, S.S. et al. An engineered substance P variant for receptor-mediated delivery of synthetic antibodies into tumor cells. Proc. Natl. Acad. Sci. USA 106, 11011–11015 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  147. Hallborn, J. & Carlsson, R. Automated screening procedure for high-throughput generation of antibody fragments. Biotechniques Suppl, 30–37 (2002).

  148. Turunen, L., Takkinen, K., Soderlund, H. & Pulli, T. Automated panning and screening procedure on microplates for antibody generation from phage display libraries. J. Biomol. Screen. 14, 282–293 (2009).

    CAS  PubMed  Google Scholar 

  149. Lou, J. et al. Antibodies in haystacks: how selection strategy influences the outcome of selection from molecular diversity libraries. J. Immunol. Methods 253, 233–242 (2001).

    CAS  PubMed  Google Scholar 

  150. Storz, U. IP issues in the therapeutic antibody industry. in Antibody Engineering (eds. Kontermann, R. & Dübel, S.) 517–581 (Springer, 2010).

  151. Kreitman, R.J. et al. Phase I trial of recombinant immunotoxin anti-Tac(Fv)-PE38 (LMB-2) in patients with hematologic malignancies. J. Clin. Oncol. 18, 1622–1636 (2000).

    CAS  PubMed  Google Scholar 

  152. Fellouse, F.A. et al. High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries. J. Mol. Biol. 373, 924–940 (2007).

    CAS  PubMed  Google Scholar 

  153. Hamilton, S.R. & Gerngross, T.U. Glycosylation engineering in yeast: the advent of fully humanized yeast. Curr. Opin. Biotechnol. 18, 387–392 (2007).

    CAS  PubMed  Google Scholar 

  154. Moghaddam, A. et al. Identification of scFv antibody fragments that specifically recognise the heroin metabolite 6-monoacetylmorphine but not morphine. J. Immunol. Methods 280, 139–155 (2003).

    CAS  PubMed  Google Scholar 

  155. Dorsam, H. et al. Antibodies to steroids from a small human naive IgM library. FEBS Lett. 414, 7–13 (1997).

    CAS  PubMed  Google Scholar 

  156. Pope, A. et al. In vitro selection of a high affinity antibody to oestradiol using a phage display human antibody library. Immunotechnology 2, 209–217 (1996).

    CAS  PubMed  Google Scholar 

  157. Hemminki, A., Niemi, S., Hautoniemi, L., Soderlund, H. & Takkinen, K. Fine tuning of an anti-testosterone antibody binding site by stepwise optimisation of the CDRs. Immunotechnology 4, 59–69 (1998).

    CAS  PubMed  Google Scholar 

  158. Saviranta, P. et al. Engineering the steroid-specificity of an anti-17beta-estradiol Fab by random mutagenesis and competitive phage panning. Protein Eng. 11, 143–152 (1998).

    CAS  PubMed  Google Scholar 

  159. Chames, P., Coulon, S. & Baty, D. Improving the affinity and the fine specificity of an anti-cortisol antibody by parsimonious mutagenesis and phage display. J. Immunol. 161, 5421–5429 (1998).

    CAS  PubMed  Google Scholar 

  160. Bikker, F.J., Mars-Groenendijk, R.H., Noort, D., Fidder, A. & van der Schans, G.P. Detection of sulfur mustard adducts in human callus by phage antibodies. Chem. Biol. Drug Des. 69, 314–320 (2007).

    CAS  PubMed  Google Scholar 

  161. Szent-Gyorgyi, C. et al. Fluorogen-activating single-chain antibodies for imaging cell surface proteins. Nat. Biotechnol. 26, 235–240 (2008).

    CAS  PubMed  Google Scholar 

  162. Watanabe, H., Nakanishi, T., Umetsu, M. & Kumagai, I. Human anti-gold antibodies: biofunctionalization of gold nanoparticles and surfaces with anti-gold antibodies. J. Biol. Chem. 283, 36031–36038 (2008).

    CAS  PubMed  Google Scholar 

  163. Dadaglio, G., Nelson, C.A., Deck, M.B., Petzold, S.J. & Unanue, E.R. Characterization and quantitation of peptide-MHC complexes produced from hen egg lysozyme using a monoclonal antibody. Immunity 6, 727–738 (1997).

    CAS  PubMed  Google Scholar 

  164. Krogsgaard, M. et al. Visualization of myelin basic protein (MBP) T cell epitopes in multiple sclerosis lesions using a monoclonal antibody specific for the human histocompatibility leukocyte antigen (HLA)-DR2-MBP 85–99 complex. J. Exp. Med. 191, 1395–1412 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  165. Mutuberria, R. et al. Isolation of human antibodies to tumor-associated endothelial cell markers by in vitro human endothelial cell selection with phage display libraries. J. Immunol. Methods 287, 31–47 (2004).

    CAS  PubMed  Google Scholar 

  166. Cohen, C.J., Denkberg, G., Lev, A., Epel, M. & Reiter, Y. Recombinant antibodies with MHC-restricted, peptide-specific, T-cell receptor-like specificity: new tools to study antigen presentation and TCR-peptide-MHC interactions. J. Mol. Recognit. 16, 324–332 (2003).

    CAS  PubMed  Google Scholar 

  167. Engberg, J., Krogsgaard, M. & Fugger, L. Recombinant antibodies with the antigen-specific, MHC restricted specificity of T cells: novel reagents for basic and clinical investigations and immunotherapy. Immunotechnology 4, 273–278 (1999).

    CAS  PubMed  Google Scholar 

  168. Stryhn, A. et al. Shared fine specificity between T-cell receptors and an antibody recognizing a peptide/major histocompatibility class I complex. Proc. Natl. Acad. Sci. USA 93, 10338–10342 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  169. Villa, A. et al. A high-affinity human monoclonal antibody specific to the alternatively spliced EDA domain of fibronectin efficiently targets tumor neo-vasculature in vivo. Int. J. Cancer 122, 2405–2413 (2008).

    CAS  PubMed  Google Scholar 

  170. Pini, A. et al. Design and use of a phage display library. Human antibodies with subnanomolar affinity against a marker of angiogenesis eluted from a two-dimensional gel. J. Biol. Chem. 273, 21769–21776 (1998).

    CAS  PubMed  Google Scholar 

  171. Schliemann, C. & Neri, D. Antibody-based vascular tumor targeting. Recent Results Cancer Res. 180, 201–216 (2010).

    CAS  PubMed  Google Scholar 

  172. Rothlisberger, D., Pos, K.M. & Pluckthun, A. An antibody library for stabilizing and crystallizing membrane proteins–selecting binders to the citrate carrier CitS. FEBS Lett. 564, 340–348 (2004).

    CAS  PubMed  Google Scholar 

  173. Uysal, S. et al. Crystal structure of full-length KcsA in its closed conformation. Proc. Natl. Acad. Sci. USA 106, 6644–6649 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  174. Osbourn, J., Groves, M. & Vaughan, T. From rodent reagents to human therapeutics using antibody guided selection. Methods 36, 61–68 (2005).

    CAS  PubMed  Google Scholar 

  175. Jespers, L.S., Roberts, A., Mahler, S.M., Winter, G. & Hoogenboom, H.R. Guiding the selection of human antibodies from phage display repertoires to a single epitope of an antigen. Bio/Technology 12, 899–903 (1994).

    CAS  Google Scholar 

  176. Xie, M.H., Yuan, J., Adams, C. & Gurney, A. Direct demonstration of MuSK involvement in acetylcholine receptor clustering through identification of agonist ScFv. Nat. Biotechnol. 15, 768–771 (1997).

    CAS  PubMed  Google Scholar 

  177. Ellmark, P., Andersson, H., Abayneh, S., Fenyo, E.M. & Borrebaeck, C.A. Identification of a strongly activating human anti-CD40 antibody that suppresses HIV type 1 infection. AIDS Res. Hum. Retroviruses 24, 367–373 (2008).

    CAS  PubMed  Google Scholar 

  178. Roth, A. et al. Anti-CD166 single chain antibody-mediated intracellular delivery of liposomal drugs to prostate cancer cells. Mol. Cancer Ther. 6, 2737–2746 (2007).

    CAS  PubMed  Google Scholar 

  179. Liu, B. et al. Recombinant full-length human IgG1s targeting hormone-refractory prostate cancer. J. Mol. Med. 85, 1113–1123 (2007).

    CAS  PubMed  Google Scholar 

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Acknowledgements

A.R.M.B. is grateful to the US National Institutes of Health (P50GM085273 and R01-HG004852-01A1), US Department of Energy (GTL program) and the US Department of Defense, Defense Threat Reduction Agency for funding. S.D. gratefully acknowledges funding by the EU 7th framework programme (Projects: Affinomics and AffinityProteome). J.M. is pleased to acknowledge funding by the Wellcome Trust.

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

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