Selecting and screening recombinant antibody libraries

Abstract

During the past decade several display methods and other library screening techniques have been developed for isolating monoclonal antibodies (mAbs) from large collections of recombinant antibody fragments. These technologies are now widely exploited to build human antibodies with high affinity and specificity. Clever antibody library designs and selection concepts are now able to identify mAb leads with virtually any specificity. Innovative strategies enable directed evolution of binding sites with ultra-high affinity, high stability and increased potency, sometimes to a level that cannot be achieved by immunization. Automation of the technology is making it possible to identify hundreds of different antibody leads to a single therapeutic target. With the first antibody of this new generation, adalimumab (Humira, a human IgG1 specific for human tumor necrosis factor (TNF)), already approved for therapy and with many more in clinical trials, these recombinant antibody technologies will provide a solid basis for the discovery of antibody-based biopharmaceuticals, diagnostics and research reagents for decades to come.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Generating binding site diversity in the immune system.

Katie Ris

Figure 2: Creating and selecting recombinant antibody libraries.

Katie Ris

Figure 3: Methods for in vitro selection for binding.

Katie Ris

Figure 4: Binding-site diversity in recombinant antibody libraries.

Katie Ris

References

  1. 1

    Winter, G. & Milstein, C. Man-made antibodies. Nature 349, 293–299 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  2. 2

    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  Google Scholar 

  3. 3

    Ward, E.S., Gussow, D., Griffiths, A.D., Jones, P.T. & Winter, G. Binding activities of a repertoire of single immunoglobulin variable domains secreted from Escherichia coli. Nature 341, 544–546 (1989).

    CAS  PubMed  Google Scholar 

  4. 4

    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 

  5. 5

    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 

  6. 6

    Clackson, T., Hoogenboom, H.R., Griffiths, A.D. & Winter, G. Making antibody fragments using phage display libraries. Nature 352, 624–628 (1991).

    CAS  PubMed  Google Scholar 

  7. 7

    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 

  8. 8

    Burton, D.R. et al. A large array of human monoclonal antibodies to type 1 human immunodeficiency virus from combinatorial libraries of asymptomatic individuals. Proc. Natl. Acad. Sci. USA 88, 10134–10137 (1991).

    CAS  PubMed  Google Scholar 

  9. 9

    Winter, G., Griffiths, A.D., Hawkins, R.E. & Hoogenboom, H.R. Making antibody by phage display technology. Annu. Rev. Immunol. 12, 433–455 (1994).

    CAS  PubMed  Google Scholar 

  10. 10

    Hoogenboom, H.R. Overview of antibody phage-display technology and its applications. Methods Mol. Biol. 178, 1–37 (2002).

    CAS  PubMed  Google Scholar 

  11. 11

    Griffiths, A.D. et al. Isolation of high affinity human antibodies directly from large synthetic repertoires. EMBO J. 13, 3245–3260 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  12. 12

    Vaughan, T.J. et al. Human antibodies with sub-nanomolar affinities isolated from a large non-immunized phage display library. Nat. Biotechnol. 14, 309–314 (1996).

    CAS  PubMed  Google Scholar 

  13. 13

    de Haard, H.J. et al. A large non-immunized human Fab fragment phage library that permits rapid isolation and kinetic analysis of high affinity antibodies. J. Biol. Chem. 274, 18218–18230 (1999).

    CAS  Google Scholar 

  14. 14

    Knappik, A. et al. Fully synthetic human combinatorial antibody libraries (HuCAL) based on modular consensus frameworks and CDRs randomized with trinucleotides. J. Mol. Biol. 296, 57–86 (2000).

    CAS  Google Scholar 

  15. 15

    Hoet, R.M. et al. Generation of high-affinity human antibodies by combining donor-derived and synthetic complementarity-determining-region diversity. Nat. Biotechnol. 23, 344–348 (2005).

    CAS  PubMed  Google Scholar 

  16. 16

    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  Google Scholar 

  17. 17

    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  Google Scholar 

  18. 18

    Lu, D. et al. Tailoring in vitro selection for a picomolar affinity human antibody directed against vascular endothelial growth factor receptor 2 for enhanced neutralizing activity. J. Biol. Chem. 278, 43496–43507 (2003).

    CAS  PubMed  Google Scholar 

  19. 19

    Chames, P., Hufton, S.E., Coulie, P.G., Uchanska-Ziegler, B. & Hoogenboom, H.R. Direct selection of a human antibody fragment directed against the tumor T-cell epitope HLA-A1-MAGE-A1 from a nonimmunized phage-Fab library. Proc. Natl. Acad. Sci. USA 97, 7969–7974 (2000).

    CAS  PubMed  Google Scholar 

  20. 20

    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  Google Scholar 

  21. 21

    Moulard, M. et al. Broadly cross-reactive HIV-1-neutralizing human monoclonal Fab selected for binding to gp120–CD4-CCR5 complexes. Proc. Natl. Acad. Sci. USA 99, 6913–6918 (2002).

    CAS  PubMed  Google Scholar 

  22. 22

    Kramer, R.A. et al. The human antibody repertoire specific for rabies virus glycoprotein as selected from immune libraries. Eur. J. Immunol. 35, 2131–2145 (2005).

    CAS  PubMed  Google Scholar 

  23. 23

    Lipovsek, D. & Pluckthun, A. In-vitro protein evolution by ribosome display and mRNA display. J. Immunol. Methods 290, 51–67 (2004).

    CAS  PubMed  Google Scholar 

  24. 24

    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  Google Scholar 

  25. 25

    Schaffitzel, C. et al. In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei. Proc. Natl. Acad. Sci. USA 98, 8572–8577 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. 26

    Jermutus, L., Honegger, A., Schwesinger, F., Hanes, J. & Pluckthun, A. Tailoring in vitro evolution for protein affinity or stability. Proc. Natl. Acad. Sci. USA 98, 75–80 (2001).

    CAS  PubMed  Google Scholar 

  27. 27

    Hanes, J., Jermutus, L., Weber-Bornhauser, S., Bosshard, H.R. & Pluckthun, A. Ribosome display efficiently selects and evolves high-affinity antibodies in vitro from immune libraries. Proc. Natl. Acad. Sci. USA 95, 14130–14135 (1998).

    CAS  PubMed  Google Scholar 

  28. 28

    Zahnd, C. et al. Directed in vitro evolution and crystallographic analysis of a peptide-binding single chain antibody fragment (scFv) with low picomolar affinity. J. Biol. Chem. 279, 18870–18877 (2004).

    CAS  PubMed  Google Scholar 

  29. 29

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

    CAS  PubMed  PubMed Central  Google Scholar 

  30. 30

    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  Google Scholar 

  31. 31

    Daugherty, P.S., Olsen, M.J., Iverson, B.L. & Georgiou, G. Development of an optimized expression system for the screening of antibody libraries displayed on the Escherichia coli surface. Protein Eng. 12, 613–621 (1999).

    CAS  PubMed  Google Scholar 

  32. 32

    Chen, G. et al. Isolation of high-affinity ligand-binding proteins by periplasmic expression with cytometric screening (PECS). Nat. Biotechnol. 19, 537–542 (2001).

    CAS  PubMed  Google Scholar 

  33. 33

    Harvey, B.R. et al. Anchored periplasmic expression, a versatile technology for the isolation of high-affinity antibodies from Escherichia coli-expressed libraries. Proc. Natl. Acad. Sci. USA 101, 9193–9198 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  34. 34

    Urban, J.H. et al. Selection of functional human antibodies from retroviral display libraries. Nucleic Acids Res. 33, e35 (2005).

    PubMed  PubMed Central  Google Scholar 

  35. 35

    Odegrip, R. et al. CIS display: In vitro selection of peptides from libraries of protein-DNA complexes. Proc. Natl. Acad. Sci. USA 101, 2806–2810 (2004).

    CAS  PubMed  Google Scholar 

  36. 36

    Reiersen, H. et al. Covalent antibody display–an in vitro antibody-DNA library selection system. Nucleic Acids Res. 33, e10 (2005).

    PubMed  PubMed Central  Google Scholar 

  37. 37

    Sepp, A., Tawfik, D.S. & Griffiths, A.D. Microbead display by in vitro compartmentalisation: selection for binding using flow cytometry. FEBS Lett. 532, 455–458 (2002).

    CAS  PubMed  Google Scholar 

  38. 38

    Mossner, E., Koch, H. & Pluckthun, A. Fast selection of antibodies without antigen purification: adaptation of the protein fragment complementation assay to select antigen-antibody pairs. J. Mol. Biol. 308, 115–122 (2001).

    CAS  PubMed  Google Scholar 

  39. 39

    Urech, D.M., Lichtlen, P. & Barberis, A. Cell growth selection system to detect extracellular and transmembrane protein interactions. Biochim. Biophys. Acta 1622, 117–127 (2003).

    CAS  PubMed  Google Scholar 

  40. 40

    Jermutus, L. et al. Ligand binding of a ribosome-displayed protein detected in solution at the single molecule level by fluorescence correlation spectroscopy. Eur. Biophys. J. 31, 179–184 (2002).

    CAS  PubMed  Google Scholar 

  41. 41

    Binz, H.K., Amstutz, P. & Pluckthun, A. The matrix reloaded: specific binding proteins based on nonimmunoglobulin domains. Nat. Biotechnol. 23, in the press (2005).

  42. 42

    Zauderer, M. & Smith, E.S. In vitro methods of producing and identifying immunoglobulin molecules in eukaryotic cells. US patent application 20,020,123,057A1 (2002).

  43. 43

    Cumbers, S.J. et al. Generation and iterative affinity maturation of antibodies in vitro using hypermutating B-cell lines. Nat. Biotechnol. 20, 1129–1134 (2002).

    CAS  PubMed  Google Scholar 

  44. 44

    Weller, S. et al. Hypermutation in human B cells in vivo and in vitro. Ann. NY Acad. Sci. 987, 158–165 (2003).

    CAS  PubMed  Google Scholar 

  45. 45

    Nicolaides, N.C., Grasso, L. & Sass, P.M. Methods for generating genetically altered antibody producing cell lines with improved antibody characteristics. US patent 6,808,894 (2004).

  46. 46

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

    CAS  PubMed  Google Scholar 

  47. 47

    Mutuberria, R., Hoogenboom, H.R., van der Linden, E., de Bruïne, A.P. & Roovers, R.C. Model systems to study the parameters determining the success of phage antibody selections on complex antigens. J. Immunol. Methods 231, 65–81 (1999).

    CAS  PubMed  Google Scholar 

  48. 48

    VanAntwerp, J.J. & Wittrup, K.D. Fine affinity discrimination by yeast surface display and flow cytometry. Biotechnol. Prog. 16, 31–37 (2000).

    CAS  PubMed  Google Scholar 

  49. 49

    Zaccolo, M., Griffiths, A.P., Prospero, T.D., Winter, G. & Gherardi, E. Dimerization of Fab fragments enables ready screening of phage antibodies that affect hepatocyte growth factor/scatter factor activity on target cells. Eur. J. Immunol. 27, 618–623 (1997).

    CAS  PubMed  Google Scholar 

  50. 50

    Larocca, D. et al. Evolving phage vectors for cell targeted gene delivery. Curr. Pharm. Biotechnol. 3, 45–57 (2002).

    CAS  PubMed  Google Scholar 

  51. 51

    Janda, K.D. et al. Direct selection for a catalytic mechanism from combinatorial antibody libraries. Proc. Natl. Acad. Sci. USA 91, 2532–2536 (1994).

    CAS  PubMed  Google Scholar 

  52. 52

    Becerril, B., Poul, M.A. & Marks, J.D. Toward selection of internalizing antibodies from phage libraries. Biochem. Biophys. Res. Commun. 255, 386–393 (1999).

    CAS  PubMed  Google Scholar 

  53. 53

    Feldhaus, M.J. & Siegel, R.W. Yeast display of antibody fragments: a discovery and characterization platform. J. Immunol. Methods 290, 69–80 (2004).

    CAS  PubMed  Google Scholar 

  54. 54

    Bradbury, A. et al. Antibodies in proteomics II: screening, high-throughput characterization and downstream applications. Trends Biotechnol. 21, 312–317 (2003).

    CAS  PubMed  Google Scholar 

  55. 55

    Chambers, R.S. High-throughput antibody production. Curr. Opin. Chem. Biol. 9, 46–50 (2005).

    CAS  PubMed  Google Scholar 

  56. 56

    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 

  57. 57

    Liu, B., Huang, L., Sihlbom, C., Burlingame, A. & Marks, J.D. Towards proteome-wide production of monoclonal antibody by phage display. J. Mol. Biol. 315, 1063–1073 (2002).

    CAS  PubMed  Google Scholar 

  58. 58

    Walter, G., Konthur, Z. & Lehrach, H. High-throughput screening of surface displayed gene products. Comb. Chem. High Throughput Screen. 4, 193–205 (2001).

    CAS  PubMed  Google Scholar 

  59. 59

    Pavlik, P. et al. Predicting antigenic peptides suitable for the selection of phage antibodies. Hum. Antibodies 12, 99–112 (2003).

    CAS  PubMed  Google Scholar 

  60. 60

    Van Beijnum, J.R. et al. Target validation for genomics using peptide-specific phage antibodies: a study of five gene products overexpressed in colorectal cancer. Int. J. Cancer 101, 118–127 (2002).

    CAS  PubMed  Google Scholar 

  61. 61

    Frisch, C. et al. From EST to IHC: human antibody pipeline for target research. J. Immunol. Methods 275, 203–212 (2003).

    CAS  PubMed  Google Scholar 

  62. 62

    Hoet, R. et al. Method and apparatus for washing magnetically responsive particles. US patent application 20,030,170,686A1 (2003).

  63. 63

    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 

  64. 64

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

  65. 65

    Angenendt, P. et al. Seeing better through a MIST: evaluation of monoclonal recombinant antibody fragments on microarrays. Anal. Chem. 76, 2916–2921 (2004).

    CAS  PubMed  Google Scholar 

  66. 66

    Vanhercke, T., Ampe, C., Tirry, L. & Denolf, P. Rescue and in situ selection and evaluation (RISE): a method for high-throughput panning of phage display libraries. J. Biomol. Screen. 10, 108–117 (2005).

    CAS  PubMed  Google Scholar 

  67. 67

    Rungpragayphan, S. et al. High-throughput, cloning-independent protein library construction by combining single-molecule DNA amplification with in vitro expression. J. Mol. Biol. 318, 395–405 (2002).

    CAS  PubMed  Google Scholar 

  68. 68

    Holt, L.J., Bussow, K., Walter, G. & Tomlinson, I.M. By-passing selection: direct screening for antibody-antigen interactions using protein arrays. Nucleic Acids Res. 28, e72 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  69. 69

    Watkins, J.D. et al. Discovery of human antibodies to cell surface antigens by capture lift screening of phage-expressed antibody libraries. Anal. Biochem. 256, 169–177 (1998).

    CAS  PubMed  Google Scholar 

  70. 70

    Pini, A., Ricci, C. & Bracci, L. Phage display and colony filter screening for high-throughput selection of antibody libraries. Comb. Chem. High Throughput Screen. 5, 503–510 (2002).

    CAS  PubMed  Google Scholar 

  71. 71

    Michaud, G.A. et al. Analyzing antibody specificity with whole proteome microarrays. Nat. Biotechnol. 21, 1509–1512 (2003).

    CAS  PubMed  Google Scholar 

  72. 72

    Poetz, O. et al. Protein microarrays for antibody profiling: specificity and affinity determination on a chip. Proteomics 5, 2402–2411 (2005).

    CAS  PubMed  Google Scholar 

  73. 73

    Jostock, T. et al. Rapid generation of functional human IgG antibodies derived from Fab-on-phage display libraries. J. Immunol. Methods 289, 65–80 and corrigendum in 294, 209 (2004).

    CAS  PubMed  Google Scholar 

  74. 74

    Sarantopoulos, S., Kao, C.Y., Den, W. & Sharon, J. A method for linking VL and VH region genes that allows bulk transfer between vectors for use in generating polyclonal IgG libraries. J. Immunol. 152, 5344–5351 (1994).

    CAS  PubMed  Google Scholar 

  75. 75

    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 

  76. 76

    Schoonbroodt, S. et al. Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. Nucleic Acids Res. 33, e81 (2005).

    PubMed  PubMed Central  Google Scholar 

  77. 77

    Marzari, R. et al. Molecular dissection of the tissue transglutaminase autoantibody response in celiac disease. J. Immunol. 166, 4170–4176 (2001).

    CAS  PubMed  Google Scholar 

  78. 78

    Roovers, R.C. et al. Evidence for a bias toward intracellular antigens in the local humoral anti-tumor immune response of a colorectal cancer patient revealed by phage display. Int. J. Cancer 93, 832–840 (2001).

    CAS  PubMed  Google Scholar 

  79. 79

    Haurum, J. & Bregenholt, S. Recombinant polyclonal antibodies: therapeutic antibody technologies come full circle. IDrugs 8, 404–409 (2005).

    CAS  PubMed  Google Scholar 

  80. 80

    Hoogenboom, H.R. & Winter, G. By-passing immunisation. Human antibodies from synthetic repertoires of germline VH gene segments rearranged in vitro. J. Mol. Biol. 227, 381–388 (1992).

    CAS  PubMed  Google Scholar 

  81. 81

    Barbas, C.F., Bain, J.D., Hoekstra, D.M. & Lerner, R. Semisynthetic combinatorial libraries: a chemical solution to the diversity problem. Proc. Natl. Acad. Sci. USA 89, 4457–4461 (1992).

    CAS  PubMed  Google Scholar 

  82. 82

    Sidhu, S.S. et al. Phage-displayed antibody libraries of synthetic heavy chain complementarity determining regions. J. Mol. Biol. 338, 299–310 (2004).

    CAS  PubMed  Google Scholar 

  83. 83

    Silacci, M. et al. Design, construction, and characterization of a large synthetic human antibody phage display library. Proteomics 5, 2340–2350 (2005).

    CAS  PubMed  Google Scholar 

  84. 84

    de Wildt, R.M., Mundy, C.R., Gorick, B.D. & Tomlinson, I.M. Antibody arrays for high-throughput screening of antibody-antigen interactions. Nat. Biotechnol. 18, 989–994 (2000).

    CAS  Google Scholar 

  85. 85

    Loset, G.A. et al. Construction, evaluation and refinement of a large human antibody phage library based on the IgD and IgM variable gene repertoire. J. Immunol. Methods 299, 47–62 (2005).

    CAS  PubMed  Google Scholar 

  86. 86

    Soderlind, E. et al. Recombining germline-derived CDR sequences for creating diverse single-framework antibody libraries. Nat. Biotechnol. 18, 852–856 (2000).

    CAS  PubMed  Google Scholar 

  87. 87

    Hust, M. & Dubel, S. Mating antibody phage display with proteomics. Trends Biotechnol. 22, 8–14 (2004).

    CAS  PubMed  Google Scholar 

  88. 88

    Hoogenboom, H.R. & Chames, P. Natural and designer binding sites made by phage display technology. Immunol. Today 21, 371–378 (2000).

    CAS  Google Scholar 

  89. 89

    Xu, J.L. & Davis, M.M. Diversity in the CDR3 region of V(H) is sufficient for most antibody specificities. Immunity 13, 37–45 (2000).

    CAS  PubMed  Google Scholar 

  90. 90

    Senn, B.M. et al. Combinatorial immunoglobulin light chain variability creates sufficient B cell diversity to mount protective antibody responses against pathogen infections. Eur. J. Immunol. 33, 950–961 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  91. 91

    Lee, M.S. et al. Selection of scFvs specific for HBV DNA polymerase using ribosome display. J. Immunol. Methods 284, 147–157 (2004).

    CAS  PubMed  Google Scholar 

  92. 92

    He, M. et al. Selection of a human anti-progesterone antibody fragment from a transgenic mouse library by ARM ribosome display. J. Immunol. Methods 231, 105–117 (1999).

    CAS  PubMed  Google Scholar 

  93. 93

    Bakker, A. et al. Novel human antibody combination effectively neutralizing natural rabies virus variants and individual in vitro escape mutants. J. Virol. 79, 9062–9068 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  94. 94

    Wu, H. et al. Ultra-potent antibodies against Respiratory Syncytial Virus: effects of binding kinetics and binding valency on viral neutralization. J. Mol. Biol. 350, 126–144 (2005).

    CAS  PubMed  Google Scholar 

  95. 95

    Weiner, L.M. & Carter, P. Tunable antibodies. Nat. Biotechnol. 23, 556–557 (2005).

    CAS  PubMed  Google Scholar 

  96. 96

    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  Google Scholar 

  97. 97

    Ho, M., Kreitman, R.J., Onda, M. & Pastan, I. In vitro antibody evolution targeting germline hot spots to increase activity of an anti-CD22 immunotoxin. J. Biol. Chem. 280, 607–617 (2005).

    CAS  PubMed  Google Scholar 

  98. 98

    Foote, J. & Eisen, H.N. Kinetic and affinity limits on antibodies produced during immune responses. Proc. Natl. Acad. Sci. USA 92, 1254–1256 (1995).

    CAS  PubMed  Google Scholar 

  99. 99

    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 

  100. 100

    Rauchenberger, R. et al. Human combinatorial Fab library yielding specific and functional antibodies against the human fibroblast growth factor receptor 3. J. Biol. Chem. 278, 38194–38205 (2003).

    CAS  PubMed  Google Scholar 

  101. 101

    Midelfort, K.S. et al. Substantial energetic improvement with minimal structural perturbation in a high affinity mutant antibody. J. Mol. Biol. 343, 685–701 (2004).

    CAS  PubMed  Google Scholar 

  102. 102

    Baca, M. & Presta, L.G. SJ, O'Connor, S.J. & Wells, J.A. Antibody humanization using monovalent phage display. J. Biol. Chem. 272, 10678–10684 (1997).

    CAS  PubMed  Google Scholar 

  103. 103

    Wu, H., Nie, Y., Huse, W.D. & Watkins, J.D. Humanization of a murine monoclonal antibody by simultaneous optimization of framework and CDR residues. J. Mol. Biol. 294, 151–162 (1999).

    CAS  PubMed  Google Scholar 

  104. 104

    Dall'acqua, W.F. et al. Antibody humanization by framework shuffling. Methods 36, 43–60 (2005).

    CAS  PubMed  Google Scholar 

  105. 105

    Beiboer, S.H. et al. Guided selection of a pan carcinoma specific antibody reveals similar binding characteristics yet structural divergence between the original murine antibody and its human equivalent. J. Mol. Biol. 296, 833–849 (2000).

    CAS  PubMed  Google Scholar 

  106. 106

    Salfeld, J. et al. Human antibodies that bind human TNFα. US patent 6,090,382 (2000).

  107. 107

    Naundorf, S. et al. In vitro and in vivo activity of MT201, a fully human monoclonal antibody for pancarcinoma treatment. Int. J. Cancer 100, 101–110 (2002).

    CAS  PubMed  Google Scholar 

  108. 108

    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  PubMed  Google Scholar 

  109. 109

    Rader, C., Cheresh, D.A. & Barbas, C.F., III. A phage display approach for rapid antibody humanization: designed combinatorial V gene libraries. Proc. Natl. Acad. Sci. USA 95, 8910–8915 (1998).

    CAS  PubMed  Google Scholar 

  110. 110

    Jung, S., Honegger, A. & Pluckthun, A. Selection for improved protein stability by phage display. J. Mol. Biol. 294, 163–180 (1999).

    CAS  PubMed  Google Scholar 

  111. 111

    Kristensen, P. & Winter, G. Proteolytic selection for protein folding using filamentous bacteriophages. Fold. Des. 3, 321–328 (1998).

    CAS  PubMed  Google Scholar 

  112. 112

    Brockmann, E.C., Cooper, M., Stromsten, N., Vehniainen, M. & Saviranta, P. Selecting for antibody scFv fragments with improved stability using phage display with denaturation under reducing conditions. J. Immunol. Methods 296, 159–170 (2005).

    CAS  PubMed  Google Scholar 

  113. 113

    Jespers, L., Schon, O., Famm, K. & Winter, G. Aggregation-resistant domain antibodies selected on phage by heat denaturation. Nat. Biotechnol. 22, 1161–1165 (2004).

    CAS  PubMed  Google Scholar 

  114. 114

    Shusta, E.V., Raines, R.T., Pluckthun, A. & Wittrup, K.D. Increasing the secretory capacity of Saccharomyces cerevisiae for production of single-chain antibody fragments. Nat. Biotechnol. 16, 773–777 (1998).

    CAS  PubMed  Google Scholar 

  115. 115

    Shusta, E.V., Holler, P.D., Kieke, M.C., Kranz, D.M. & Wittrup, K.D. Directed evolution of a stable scaffold for T-cell receptor engineering. Nat. Biotechnol. 18, 754–759 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  116. 116

    Graff, C.P., Chester, K., Begent, R. & Wittrup, K.D. Directed evolution of an anti-carcinoembryonic antigen scFv with a 4-day monovalent dissociation half-time at 37 degrees C. Protein Eng. Des. Sel. 17, 293–304 (2004).

    CAS  PubMed  Google Scholar 

  117. 117

    Roodveldt, C., Aharoni, A. & Tawfik, D.S. Directed evolution of proteins for heterologous expression and stability. Curr. Opin. Struct. Biol. 15, 50–56 (2005).

    CAS  PubMed  Google Scholar 

  118. 118

    Topping, K.P., Hough, V.C., Monson, J.R. & Greenman, J. Isolation of human colorectal tumour reactive antibodies using phage display technology. Int. J. Oncol. 16, 187–195 (2000).

    CAS  PubMed  Google Scholar 

  119. 119

    Roovers, R.C., van der Linden, E., de Bruïne, A.P., Arends, J.W. & Hoogenboom, H.R. Identification of colon tumour-associated antigens by phage antibody selections on primary colorectal carcinoma. Eur. J. Cancer 37, 542–549 (2001).

    CAS  PubMed  Google Scholar 

  120. 120

    Tur, M.K. et al. A novel approach for immunization, screening and characterization of selected scFv libraries using membrane fractions of tumor cells. Int. J. Mol. Med. 11, 523–527 (2003).

    CAS  PubMed  Google Scholar 

  121. 121

    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 

  122. 122

    Liu, B., Conrad, F., Cooperberg, M.R., Kirpotin, D.B. & Marks, J.D. Mapping tumor epitope space by direct selection of single-chain Fv antibody libraries on prostate cancer cells. Cancer Res. 64, 704–710 (2004).

    CAS  PubMed  Google Scholar 

  123. 123

    Nizak, C. et al. Recombinant antibodies against subcellular fractions used to track endogenous Golgi protein dynamics in vivo. Traffic 4, 739–753 (2003).

    CAS  PubMed  Google Scholar 

  124. 124

    Ridgway, J.B. et al. Identification of a human anti-CD55 single-chain Fv by subtractive panning of a phage library using tumor and nontumor cell lines. Cancer Res. 59, 2718–2723 (1999).

    CAS  PubMed  Google Scholar 

  125. 125

    Geuijen, C.A. et al. A proteomic approach to tumour target identification using phage display, affinity purification and mass spectrometry. Eur. J. Cancer 41, 178–187 (2005).

    CAS  PubMed  Google Scholar 

  126. 126

    Bakker, A.B. et al. C-type lectin-like molecule-1: a novel myeloid cell surface marker associated with acute myeloid leukemia. Cancer Res. 64, 8443–8450 (2004).

    CAS  PubMed  Google Scholar 

  127. 127

    Visintin, M., Meli, G.A., Cannistraci, I. & Cattaneo, A. Intracellular antibodies for proteomics. J. Immunol. Methods 290, 135–153 (2004).

    CAS  PubMed  Google Scholar 

  128. 128

    Martineau, P., Jones, P. & Winter, G. Expression of an antibody fragment at high levels in the bacterial cytoplasm. J. Mol. Biol. 280, 117–127 (1998).

    CAS  PubMed  Google Scholar 

  129. 129

    Gargano, N. & Cattaneo, A. Rescue of a neutralizing anti-viral antibody fragment from an intracellular polyclonal repertoire expressed in mammalian cells. FEBS Lett. 414, 537–540 (1997).

    CAS  PubMed  Google Scholar 

  130. 130

    Gennari, F. et al. Direct phage to intrabody screening (DPIS): demonstration by isolation of cytosolic intrabodies against the TES1 site of Epstein Barr virus latent membrane protein 1 (LMP1) that block NF-kappaB transactivation. J. Mol. Biol. 335, 193–207 (2004).

    CAS  PubMed  Google Scholar 

  131. 131

    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  Google Scholar 

  132. 132

    auf der Maur, 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).

    CAS  Google Scholar 

  133. 133

    Tanaka, T., Lobato, M.N. & Rabbitts, T.H. Single domain intracellular antibodies: a minimal fragment for direct in vivo selection of antigen-specific intrabodies. J. Mol. Biol. 331, 1109–1120 (2003).

    CAS  PubMed  Google Scholar 

  134. 134

    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 

  135. 135

    Pendley, C., Schantz, A. & Wagner, C. Immunogenicity of therapeutic monoclonal antibodies. Curr. Opin. Mol. Ther. 5, 172–179 (2003).

    CAS  PubMed  Google Scholar 

  136. 136

    Zemlin, M. et al. Expressed murine and human CDR-H3 intervals of equal length exhibit distinct repertoires that differ in their amino acid composition and predicted range of structures. J. Mol. Biol. 334, 733–749 (2003).

    CAS  PubMed  Google Scholar 

  137. 137

    Harris, R.J., Shire, S.J. & Winter, C. Commercial manufacturing scale formulation and analytical characterization of therapeutic recombinant antibodies. Drug Dev. Res. 61, 137–154 (2004).

    CAS  Google Scholar 

  138. 138

    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  Google Scholar 

  139. 139

    Fellouse, F.A. et al. Molecular recognition by a binary code. J. Mol. Biol. 348, 1153–1162 (2005).

    CAS  PubMed  Google Scholar 

  140. 140

    Rao, B.M., Lauffenburger, D.A. & Wittrup, K.D. Integrating cell-level kinetic modeling into the design of engineered protein therapeutics. Nat. Biotechnol. 23, 191–194 (2005).

    CAS  PubMed  Google Scholar 

  141. 141

    De Genst, E., Areskoug, D., Decanniere, K., Muyldermans, S. & Andersson, K. Kinetic and affinity predictions of a protein-protein interaction using multivariate experimental design. J. Biol. Chem. 277, 29897–29907 (2002).

    CAS  PubMed  Google Scholar 

  142. 142

    Bond, C.J., Wiesmann, C., Marsters, J.C. Jr. & Sidhu, S.S. A structure-based database of antibody variable domain diversity. J. Mol. Biol. 348, 699–709 (2005).

    CAS  PubMed  Google Scholar 

  143. 143

    Almagro, J.C. Identification of differences in the specificity-determining residues of antibodies that recognize antigens of different size: implications for the rational design of antibody repertoires. J. Mol. Recognit. 17, 132–143 (2004).

    CAS  PubMed  Google Scholar 

  144. 144

    Kirkham, P.M., Neri, D. & Winter, G. Towards the design of an antibody that recognises a given protein epitope. J. Mol. Biol. 285, 909–915 (1999).

    CAS  PubMed  Google Scholar 

  145. 145

    Calarese, D.A. et al. Antibody domain exchange is an immunological solution to carbohydrate cluster recognition. Science 300, 2065–2071 (2003).

    CAS  PubMed  Google Scholar 

  146. 146

    Darbha, R. et al. Crystal structure of the broadly cross-reactive HIV-1-neutralizing Fab X5 and fine mapping of its epitope. Biochemistry 43, 1410–1417 (2004).

    CAS  PubMed  Google Scholar 

  147. 147

    Jespers, L., Bonnert, T.P. & Winter, G. Selection of optical biosensors from chemisynthetic antibody libraries. Protein Eng. Des. Sel. 17, 709–713 (2004).

    CAS  PubMed  Google Scholar 

  148. 148

    Ehrlich, P. On autoimmunity with special references to cell life. Proc. R. Soc. 66, 424–448 (1900).

    CAS  Google Scholar 

  149. 149

    Salvatore, G., Beers, R., Margulies, I., Kreitman, R.J. & Pastan, I. Improved cytotoxic activity toward cell lines and fresh leukemia cells of a mutant anti-CD22 immunotoxin obtained by antibody phage display. Clin. Cancer Res. 8, 995–1002 (2002).

    CAS  Google Scholar 

  150. 150

    Chames, P. et al. TCR-like human antibodies expressed on human CTLs mediate antibody affinity-dependent cytolytic activity. J. Immunol. 169, 1110–1118 (2002).

    CAS  PubMed  Google Scholar 

  151. 151

    Chen, Y. et al. Selection and analysis of an optimized anti-VEGF antibody: crystal structure of an affinity-matured Fab in complex with antigen. J. Mol. Biol. 293, 865–881 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  152. 152

    Colby, D.W. et al. Potent inhibition of huntingtin aggregation and cytotoxicity by a disulfide bond-free single-domain intracellular antibody. Proc. Natl. Acad. Sci. USA 101, 17616–17621 (2004).

    CAS  PubMed  Google Scholar 

  153. 153

    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 

  154. 154

    Azriel-Rosenfeld, R., Valensi, M. & Benhar, I. A human synthetic combinatorial library of arrayable single-chain antibodies based on shuffling in vivo formed CDRs into general framework regions. J. Mol. Biol. 335, 177–192 (2004).

    CAS  PubMed  Google Scholar 

  155. 155

    Yau, K.Y. et al. Affinity maturation of a V(H)H by mutational hotspot randomization. J. Immunol. Methods 297, 213–224 (2005).

    CAS  PubMed  Google Scholar 

  156. 156

    De Pascalis, R. et al. In vitro affinity maturation of a specificity-determining region-grafted humanized anticarcinoma antibody: isolation and characterization of minimally immunogenic high-affinity variants. Clin. Cancer Res. 9, 5521–5531 (2003).

    CAS  PubMed  Google Scholar 

  157. 157

    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 

  158. 158

    Hoogenboom, H.R.J.M. & Somers, V. Hybridization control of sequence variation. US patent application 20,040,005,709A1 (2004).

  159. 159

    Sblattero, D. & Bradbury, A. Exploiting recombination in single bacteria to make large phage antibody libraries. Nat. Biotechnol. 18, 75–80 (2000).

    CAS  Google Scholar 

  160. 160

    Lutz, R. & Bujard, H. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1–I2 regulatory elements. Nucleic Acids Res. 25, 1203–1210 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  161. 161

    Hoet, R., Ladner, R.C. & Frans, N. Methods and compositions for controlling valency of phage display. US patent application 20,040,180,422A1 (2004).

  162. 162

    McGuinness, B.T. et al. Phage diabody repertoires for selection of large numbers of bispecific antibody fragments. Nat. Biotechnol. 14, 1149–1154 (1996).

    CAS  PubMed  Google Scholar 

  163. 163

    Lee, C.V., Sidhu, S.S. & Fuh, G. Bivalent antibody phage display mimics natural immunoglobulin. J. Immunol. Methods 284, 119–132 (2004).

    CAS  PubMed  Google Scholar 

  164. 164

    Poul, M.A. & Marks, J.D. Targeted gene delivery to mammalian cells by filamentous bacteriophage. J. Mol. Biol. 288, 203–211 (1999).

    CAS  PubMed  Google Scholar 

  165. 165

    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).

    CAS  PubMed  Google Scholar 

  166. 166

    de Wildt, R.M., Tomlinson, I.M., Ong, J.L. & Holliger, P. Isolation of receptor-ligand pairs by capture of long-lived multivalent interaction complexes. Proc. Natl. Acad. Sci. USA 99, 8530–8535 (2002).

    CAS  PubMed  Google Scholar 

  167. 167

    Mattheakis, L.C., Bhatt, R.R. & Dower, W.J. An in vitro polysome display system for identifying ligands from very large peptide libraries. Proc. Natl. Acad. Sci. USA 91, 9022–9026 (1994).

    CAS  PubMed  Google Scholar 

  168. 168

    He, M. & Taussig, M.J. Antibody-ribosome-mRNA (ARM) complexes as efficient selection particles for in vitro display and evolution of antibody combining sites. Nucleic Acids Res. 25, 5132–5134 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  169. 169

    Hanes, J. & Pluckthun, A. In vitro selection and evolution of functional proteins by using ribosome display. Proc. Natl. Acad. Sci. USA 94, 4937–4942 (1997).

    CAS  Google Scholar 

  170. 170

    Wilson, D.S., Keefe, A.D. & Szostak, J.W. The use of mRNA display to select high-affinity protein-binding peptides. Proc. Natl. Acad. Sci. USA 98, 3750–3755 (2001).

    CAS  Google Scholar 

  171. 171

    Xu, L. et al. Directed evolution of high-affinity antibody mimics using mRNA display. Chem. Biol. 9, 933–942 (2002).

    CAS  PubMed  Google Scholar 

  172. 172

    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 

  173. 173

    Yeung, Y.A. & Wittrup, K.D. Quantitative screening of yeast surface-displayed polypeptide libraries by magnetic bead capture. Biotechnol. Prog. 18, 212–220 (2002).

    CAS  PubMed  Google Scholar 

  174. 174

    van den Beucken, T. et al. Affinity maturation of Fab antibody fragments by fluorescent-activated cell sorting of yeast-displayed libraries. FEBS Lett. 546, 288–294 (2003).

    CAS  PubMed  Google Scholar 

  175. 175

    Hufton, S.E. & Hoogenboom, H.R.J.M. Multi-chain eukaryotic display vectors and uses thereof. US patent application 20,030,186,374A1 (2003).

  176. 176

    Blaise, L. et al. Construction and diversification of yeast cell surface displayed libraries by yeast mating: application to the affinity maturation of Fab antibody fragments. Gene 342, 211–218 (2004).

    CAS  PubMed  Google Scholar 

  177. 177

    Swers, J.S., Kellogg, B.A. & Wittrup, K.D. Shuffled antibody libraries created by in vivo homologous recombination and yeast surface display. Nucleic Acids Res. 32, e36 (2004).

    PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

I thank many colleagues including Jane Osbourn and Lutz Jermutus, Clive Wood, Zhenping Zhu, Patrick Bauerle, Herren Wu, David Chen and Lex Bakker for sharing unpublished results and am grateful to Mark Alfenito for reviewing the manuscript.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Hennie R Hoogenboom.

Ethics declarations

Competing interests

The author declares no competing financial interests.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Hoogenboom, H. Selecting and screening recombinant antibody libraries. Nat Biotechnol 23, 1105–1116 (2005). https://doi.org/10.1038/nbt1126

Download citation

Further reading

Search

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing