Abstract
Antibodies that bind their respective targets with high affinity and specificity have proven to be essential reagents for biological research. Antibody phage display has become the leading tool for the rapid isolation of single-chain variable fragment (scFv) antibodies in vitro for research applications, but there is usually a gap between scFv isolation and its application in an array format suitable for high-throughput proteomics. In this chapter, we present our antibody phage display system where antibody isolation and scFv immobilization are facilitated by the design of the phagemid vector used as platform. In our system, the scFvs are fused at their C-termini to a cellulose-binding domain (CBD) and can be immobilized onto cellulose-based filters. This made it possible to develop a unique filter lift screen that allowed the efficient screen for multiple binding specificities, and to directly apply library-derived scFvs in an antibody spotted microarray.
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Hale, G., Therapeutic antibodies-delivering the promise? Adv. Drug Deliv. Rev. 2006, 58, 633–639
Baker, M., Upping the ante on antibodies, Nat. Biotechnol. 2005, 23, 1065–1072
Wingren, C.; Borrebaeck, C. A., High-throughput proteomics using antibody microarrays, Expert Rev. Proteomics 2004, 1, 355–364
Hoogenboom, H. R., Selecting and screening recombinant antibody libraries, Nat. Biotechnol. 2005, 23, 1105–1116
Bradbury, A. R.; Velappan, N.; Verzillo, V.; Ovecka, M.; Marzari, R.; Sblattero, D.; Chasteen, L.; Siegel, R.; Pavlik, P., Antibodies in proteomics, Methods Mol. Biol. 2004, 248, 519–546
DeRisi, J. L.; Iyer, V. R.; Brown, P. O., Exploring the metabolic and genetic control of gene expression on a genomic scale, Science 1997, 278, 680–686
Anderson, L.; Seilhamer, J., A comparison of selected mrna and protein abundances in human liver, Electrophoresis 1997, 18, 533–537
Gygi, S. P.; Rochon, Y.; Franza, B. R.; Aebersold, R., Correlation between protein and mRNA abundance in yeast, Mol. Cell Biol. 1999, 19, 1720–1730
Martzen, M. R.; McCraith, S. M.; Spinelli, S. L.; Torres, F. M.; Fields, S.; Grayhack, E. J.; Phizicky, E. M., A biochemical genomics approach for identifying genes by the activity of their products, Science 1999, 286, 1153–1155
Ross-Macdonald, P.; Coelho, P. S.; Roemer, T.; Agarwal, S.; Kumar, A.; Jansen, R.; Cheung, K. H.; Sheehan, A.; Symoniatis, D.; Umansky, L.; Heidtman, M.; Nelson, F. K.; Iwasaki, H.; Hager, K.; Gerstein, M.; Miller, P.; Roeder, G. S.; Snyder, M., Large-scale analysis of the yeast genome by transposon tagging and gene disruption, Nature 1999, 402, 413–418
Carr, K. M.; Rosenblatt, K.; Petricoin, E. F.; Liotta, L. A., Genomic and proteomic approaches for studying human cancer: Prospects for true patient-tailored therapy, Hum. Genomics 2004, 1, 134–140
McCafferty, J.; Griffiths, A. D.; Winter, G.; Chiswell, D. J., Phage antibodies: Filamentous phage displaying antibody variable domains, Nature 1990, 348, 552–554
Marks, J. D.; Hoogenboom, H. R.; Bonnert, T. P.; McCafferty, J.; Griffiths, A. D.; Winter, G., By-passing immunization. Human antibodies from v-gene libraries displayed on phage, J. Mol. Biol. 1991, 222, 581–597
Barbas, C. F. d., Recent advances in phage display, Curr. Opin. Biotechnol. 1993, 4, 526–530
Benhar, I., Biotechnological applications of phage and cell display, Biotechnol. Adv. 2001, 19, 1–33
Bird, R. E.; Hardman, K. D.; Jacobson, J. W.; Johnson, S.; Kaufman, B. M.; Lee, S. M.; Lee, T.; Pope, S. H.; Riordan, G. S.; Whitlow, M., Single-chain antigen-binding proteins, Science 1988, 242, 423–426
Huston, J. S.; Levinson, D.; Mudgett-Hunter, M.; Tai, M. S.; Novotny, J.; Margolies, M. N.; Ridge, R. J.; Bruccoleri, R. E.; Haber, E.; Crea, R.; et al., Protein engineering of antibody binding sites: Recovery of specific activity in an anti-digoxin single-chain fv analogue produced in Escherichia coli, Proc. Natl. Acad. Sci. (USA) 1988, 85, 5879–5883
Vaughan, T. J.; Williams, A. J.; Pritchard, K.; Osbourn, J. K.; Pope, A. R.; Earnshaw, J. C.; McCafferty, J.; Hodits, R. A.; Wilton, J.; Johnson, K. S., Human antibodies with sub-nanomolar affinities isolated from a large non-immunized phage display library, Nat. Biotechnol. 1996, 14, 309–314
de Haard, H. J.; van Neer, N.; Reurs, A.; Hufton, S. E.; Roovers, R. C.; Henderikx, P.; de Bruine, A. P.; Arends, J. W.; Hoogenboom, H. R., A large non-immunized human fab fragment phage library that permits rapid isolation and kinetic analysis of high affinity antibodies, J. Biol. Chem. 1999, 274, 18218–18230
Knappik, A.; Ge, L.; Honegger, A.; Pack, P.; Fischer, M.; Wellnhofer, G.; Hoess, A.; Wolle, J.; Plückthun, A.; Virnekas, B., Fully synthetic human combinatorial antibody libraries (hucal) based on modular consensus frameworks and cdrs randomized with trinucleotides, J. Mol. Biol. 2000, 296, 57–86
Soderlind, E.; Strandberg, L.; Jirholt, P.; Kobayashi, N.; Alexeiva, V.; Aberg, A. M.; Nilsson, A.; Jansson, B.; Ohlin, M.; Wingren, C.; Danielsson, L.; Carlsson, R.; Borrebaeck, C. A., Recombining germline-derived cdr sequences for creating diverse single-framework antibody libraries, Nat. Biotechnol. 2000, 18, 852–856
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. 2004, 335, 177–192
Coomber, D. W., Panning of antibody phage-display libraries. Standard protocols, Methods Mol. Biol. 2002, 178, 133–145
Barbas, C. F.; Burton, D. R.; Scott, J. K.; Silverman, G. J., Phage display: A laboratory manual; Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY, 2001, pp 736
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. 2000, 28, E72
Radosevic, K.; Voerman, J. S.; Hemmes, A.; Muskens, F.; Speleman, L.; de Weers, M.; Rosmalen, J. G.; Knegt, P.; van Ewijk, W., Colony lift assay using cell-coated filters: A fast and efficient method to screen phage libraries for cell-binding clones, J. Immunol. Methods 2003, 272, 219–233
Watkins, J. D.; Beuerlein, G.; Wu, H.; McFadden, P. R.; Pancook, J. D.; Huse, W. D., Discovery of human antibodies to cell surface antigens by capture lift screening of phage-expressed antibody libraries, Anal. Biochem. 1998, 256, 169–177
Wingren, C.; Steinhauer, C.; Ingvarsson, J.; Persson, E.; Larsson, K.; Borrebaeck, C. A., Microarrays based on affinity-tagged single-chain fv antibodies: Sensitive detection of analyte in complex proteomes, Proteomics 2005, 5, 1281–1291
Kwon, Y.; Han, Z.; Karatan, E.; Mrksich, M.; Kay, B. K., Antibody arrays prepared by cutinase-mediated immobilization on self-assembled monolayers, Anal. Chem. 2004, 76, 5713–5720
Rodenburg, C. M.; Mernaugh, R.; Bilbao, G.; Khazaeli, M. B., Production of a single chain anti-cea antibody from the hybridoma cell line t84.66 using a modified colony-lift selection procedure to detect antigen-positive scfv bacterial clones, Hybridoma 1998, 17, 1–8
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. 2000, 18, 989–994
Giovannoni, L.; Viti, F.; Zardi, L.; Neri, D., Isolation of anti-angiogenesis antibodies from a large combinatorial repertoire by colony filter screening, Nucleic Acids Res. 2001, 29, E27
Skerra, A.; Dreher, M. L.; Winter, G., Filter screening of antibody fab fragments secreted from individual bacterial colonies: Specific detection of antigen binding with a two-membrane system, Anal. Biochem. 1991, 196, 151–155
Berdichevsky, Y.; Ben-Zeev, E.; Lamed, R.; Benhar, I., Phage display of a cellulose binding domain from clostridium thermocellum and its application as a tool for antibody engineering, J. Immunol. Methods 1999, 228, 151–162
Hayashi, N.; Kipriyanov, S.; Fuchs, P.; Welschof, M.; Dorsam, H.; Little, M., A single expression system for the display, purification and conjugation of single-chain antibodies, Gene 1995, 160, 129–130
Berdichevsky, Y.; Lamed, R.; Frenkel, D.; Gophna, U.; Bayer, E. A.; Yaron, S.; Shoham, Y.; Benhar, I., Matrix-assisted refolding of single-chain fv- cellulose binding domain fusion proteins, Protein Expr. Purif. 1999, 17, 249–259
Ofir, K.; Berdichevsky, Y.; Benhar, I.; Azriel-Rosenfeld, R.; Lamed, R.; Barak, Y.; Bayer, E. A.; Morag, E., Versatile protein microarray based on carbohydrate-binding modules, Proteomics 2005, 5, 1806–1814
Maynard, J.; Georgiou, G., Antibody engineering, Annu. Rev. Biomed. Eng. 2000, 2, 339–376
Jiang, X.; Suzuki, H.; Hanai, Y.; Wada, F.; Hitomi, K.; Yamane, T.; Nakano, H., A novel strategy for generation of monoclonal antibodies from single b cells using rt-pcr technique and in vitro expression, Biotechnol. Prog. 2006, 22, 979–988
Coronella, J. A.; Telleman, P.; Truong, T. D.; Ylera, F.; Junghans, R. P., Amplification of igg vh and vl (fab) from single human plasma cells and b cells, Nucleic Acids Res. 2000, 28, E85
Wang, X.; Stollar, B. D., Human immunoglobulin variable region gene analysis by single cell RT-PCR, J. Immunol. Methods 2000, 244, 217–225
Nissim, A.; Hoogenboom, H. R.; Tomlinson, I. M.; Flynn, G.; Midgley, C.; Lane, D.; Winter, G., Antibody fragments from a ‘single pot’ phage display library as immunochemical reagents, Embo J. 1994, 13, 692–698
Jirholt, P.; Ohlin, M.; Borrebaeck, C. A. K.; Soderlind, E., Exploiting sequence space: Shuffling in vivo formed complementarity determining regions into a master framework, Gene 1998, 215, 471–476
Borrebaeck, C. A.; Ohlin, M., Antibody evolution beyond nature, Nat. Biotechnol. 2002, 20, 1189–1190
Carlsson, R.; Soderlind, E., N-coder concept: Unique types of antibodies for diagnostic use and therapy, Expert Rev. Mol. Diagn. 2001, 1, 102–108
Rothlisberger, D.; Pos, K. M.; Plückthun, A., An antibody library for stabilizing and crystallizing membrane proteins – selecting binders to the citrate carrier cits, FEBS Lett. 2004, 564, 340–348
Tomlinson, I. M.; Walter, G.; Marks, J. D.; Llewelyn, M. B.; Winter, G., The repertoire of human germline vh sequences reveals about fifty groups of vh segments with different hypervariable loops, J. Mol. Biol. 1992, 227, 776–798
Pini, A.; Viti, F.; Santucci, A.; Carnemolla, B.; Zardi, L.; Neri, P.; Neri, D., 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. 1998, 273, 21769–21776.
Kobayashi, N.; Soderlind, E.; Borrebaeck, C. A., Analysis of assembly of synthetic antibody fragments: Expression of functional scfv with predefined specificity, Biotechniques 1997, 23, 500–503
Cox, J. P.; Tomlinson, I. M.; Winter, G., A directory of human germ-line v kappa segments reveals a strong bias in their usage, Eur. J. Immunol. 1994, 24, 827–836
Griffiths, A. D.; Williams, S. C.; Hartley, O.; Tomlinson, I. M.; Waterhouse, P.; Crosby, W. L.; Kontermann, R. E.; Jones, P. T.; Low, N. M.; Allison, T. J.; et al., Isolation of high affinity human antibodies directly from large synthetic repertoires, Embo J. 1994, 13, 3245–3260
Ohlin, M.; Borrebaeck, C. A., Characteristics of human antibody repertoires following active immune responses in vivo, Mol. Immunol. 1996, 33, 583–592
Huang, S. C.; Jiang, R.; Glas, A. M.; Milner, E. C., Non-stochastic utilization of ig v region genes in unselected human peripheral b cells, Mol. Immunol. 1996, 33, 553–560
Benhar, I.; Tamarkin, A.; Marash, L.; Berdichevsky, Y.; Yaron, S.; Shoham, Y.; Lamed, R.; Bayer, E. A., Phage display of cellulose binding domains for biotechnological application, In Glycosyl hydrolases for biomass conversion; M. E. Himmel; J. O. Baker and J. N. Saddler, Ed.; American Chemical Society: Washington, DC, 2001; Vol. 769; 168–189
Benhar, I.; Reiter, Y., Phage display of single-chain antibodies (scfvs), In Current protocols in immunology; J. E. Coligan. Ed.; Wiley, New York, NY, 2002; 10.19B.11–10.19B.39
Feldhaus, M. J.; Siegel, R. W.; Opresko, L. K.; Coleman, J. R.; Feldhaus, J. M.; Yeung, Y. A.; Cochran, J. R.; Heinzelman, P.; Colby, D.; Swers, J.; Graff, C.; Wiley, H. S.; Wittrup, K. D., Flow-cytometric isolation of human antibodies from a nonimmune saccharomyces cerevisiae surface display library, Nat. Biotechnol. 2003, 21, 163–170
Sheets, M. D.; Amersdorfer, P.; Finnern, R.; Sargent, P.; Lindqvist, E.; Schier, R.; Hemingsen, G.; Wong, C.; Gerhart, J. C.; Marks, J. D., Efficient construction of a large nonimmune phage antibody library: The production of high-affinity human single-chain antibodies to protein antigens, Proc Natl Acad Sci U S A 1998, 95, 6157–6162
Steukers, M.; Schaus, J. M.; van Gool, R.; Hoyoux, A.; Richalet, P.; Sexton, D. J.; Nixon, A. E.; Vanhove, M., Rapid kinetic-based screening of human fab fragments, J. Immunol. Methods 2006, 310, 126–135
Soderlind, E.; Carlsson, R.; Borrebaeck, C. A.; Ohlin, M., The immune diversity in a test tube-non-immunised antibody libraries and functional variability in defined protein scaffolds, Comb. Chem. High Throughput Screen. 2001, 4, 409–416
Shimizu, T.; Oda, M.; Azuma, T., Estimation of the relative affinity of b cell receptor by flow cytometry, J. Immunol. Methods 2003, 276, 33–44
Olsson, P.; Bera, T. K.; Essand, M.; Kumar, V.; Duray, P.; Vincent, J.; Lee, B.; Pastan, I., Gdep, a new gene differentially expressed in normal prostate and prostate cancer, Prostate 2001, 48, 231–241
Holt, L. J.; Enever, C.; de Wildt, R. M.; Tomlinson, I. M., The use of recombinant antibodies in proteomics, Curr. Opin. Biotechnol. 2000, 11, 445–449
Ward, E. S., Antibody engineering using Escherichia coli as host, Adv. Pharmacol. 1993, 24, 1–20
Adams, G. P.; Schier, R., Generating improved single-chain fv molecules for tumor targeting, J. Immunol. Methods 1999, 231, 249–260
Worn, A.; Plückthun, A., Stability engineering of antibody single-chain fv fragments, J. Mol. Biol. 2001, 305, 989–1010
Cohen, P. A., Intrabodies. Targeting scfv expression to eukaryotic intracellular compartments, Methods Mol. Biol. 2002, 178, 367–378
Bilbao, G.; Contreras, J. L.; Curiel, D. T., Genetically engineered intracellular single-chain antibodies in gene therapy, Mol. Biotechnol. 2002, 22, 191–211
Leath, C. A., III; Douglas, J. T.; Curiel, D. T.; Alvarez, R. D., Single-chain antibodies: A therapeutic modality for cancer gene therapy (review), Int. J. Oncol. 2004, 24, 765–771
Huhalov, A.; Chester, K. A., Engineered single chain antibody fragments for radioimmunotherapy, Q. J. Nucl. Med. Mol. Imaging 2004, 48, 279–288
Holliger, P.; Hudson, P. J., Engineered antibody fragments and the rise of single domains, Nat. Biotechnol. 2005, 23, 1126–1136
Kreutzberger, J., Protein microarrays: A chance to study microorganisms? Appl. Microbiol. Biotechnol. 2006, 70, 383–390
Denkberg, G.; Lev, A.; Eisenbach, L.; Benhar, I.; Reiter, Y., Selective targeting of melanoma and apcs using a recombinant antibody with tcr-like specificity directed toward a melanoma differentiation antigen, J. Immunol. 2003, 171, 2197–2207
Artzy Schnirman, A.; Zahavi, E.; Yeger, H.; Rosenfeld, R.; Benhar, I.; Reiter, Y.; Sivan, U., Antibody molecules discriminate between crystalline facets of a gallium arsenide semiconductor, Nano Lett. 2006, 6, 1870–1874
Machlenkin, A.; Azriel-Rosenfeld, R.; Volovitz, I.; Vadai, E.; Lev, A.; Paz, A.; Goldberger, O.; Reiter, Y.; Tzehoval, E.; Benhar, I.; Eisenbach, L., Preventive and therapeutic vaccination with pap-3, a novel human prostate cancer peptide, inhibits carcinoma development in HLA transgenic mice, Cancer Immunol. Immunother. 2007, 56, 217–226
Azriel-Rosenfeld, R. Ph.D. Thesis, Tel-Aviv University, 2005
Valensi, M. M.Sc. Thesis, Tel-Aviv University, 2005
Machlenkin, A.; Azriel-Rosenfeld, R.; Volovitz, I.; Vadai, E.; Lev, A.; Paz, A.; Goldberger, O.; Reiter, Y.; Tzehoval, E.; Benhar, I.; Eisenbach, L., Preventive and therapeutic vaccination with pap-3, a novel human prostate cancer peptide, inhibits carcinoma development in hla transgenic mice, Cancer Immunol. Immunother. 2007, 56, 217–226
Machlenkin, A.; Paz, A.; Bar Haim, E.; Goldberger, O.; Finkel, E.; Tirosh, B.; Volovitz, I.; Vadai, E.; Lugassy, G.; Cytron, S.; Lemonnier, F.; Tzehoval, E.; Eisenbach, L., Human ctl epitopes prostatic acid phosphatase-3 and six-transmembrane epithelial antigen of prostate-3 as candidates for prostate cancer immunotherapy, Cancer Res. 2005, 65, 6435–6442
Pascolo, S.; Bervas, N.; Ure, J. M.; Smith, A. G.; Lemonnier, F. A.; Perarnau, B., Hla-a2.1-restricted education and cytolytic activity of cd8(+) t lymphocytes from beta2 microglobulin (beta2m) hla-a2.1 monochain transgenic h-2db beta2m double knockout mice, J. Exp. Med. 1997, 185, 2043–2051
Gilbert, I.; Schiffmann, S.; Rubenwolf, S.; Jensen, K.; Mai, T.; Albrecht, C.; Lankenau, A.; Beste, G.; Blank, K.; Gaub, H. E.; Clausen-Schaumann, H., Double chip protein arrays using recombinant single-chain fv antibody fragments, Proteomics 2004, 4, 1417–1420
Borrebaeck, C. A.; Ekstrom, S.; Hager, A. C.; Nilsson, J.; Laurell, T.; Marko-Varga, G., Protein chips based on recombinant antibody fragments: A highly sensitive approach as detected by mass spectrometry, Biotechniques 2001, 30, 1126–1132
Angenendt, P.; Wilde, J.; Kijanka, G.; Baars, S.; Cahill, D. J.; Kreutzberger, J.; Lehrach, H.; Konthur, Z.; Glokler, J., Seeing better through a mist: Evaluation of monoclonal recombinant antibody fragments on microarrays, Anal. Chem. 2004, 76, 2916–2921
Acknowledgments and Notes
The work reported in this chapter was supported in part by a research grant from the Israel Science Foundation, administered by the Israel National Academy for Sciences and Humanities (Jerusalem, Israel). The n-CoDeR® technology is covered by IP rights held by BioInvent, Sweden (http://www.bioinvent.com).
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Benhar, I. (2009). Combinatorial Libraries of Arrayable Single-Chain Antibodies. In: Potyrailo, R.A., Mirsky, V.M. (eds) Combinatorial Methods for Chemical and Biological Sensors. Integrated Analytical Systems. Springer, New York, NY. https://doi.org/10.1007/978-0-387-73713-3_9
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