Abstract
The particular interest in VH antibody fragments stems from the fact that they can rival their “naturally occurring” single-domain antibody (sdAb) counterparts (camelid VHHs and shark VNARs) with regard to such desirable characteristics as stability, solubility, expression, and ability to penetrate cryptic epitopes and outperform them in terms of less immunogenicity, a much valued property in human immunotherapy applications. However, human VHs are typically prone to aggregation. Various approaches for developing non-aggregating human VHs with binding specificities have relied on a combination of recombinant DNA technology and phage-display technology. VH gene libraries are constructed synthetically by randomizing the CDRs of a single VH scaffold fused to a gene encoding a phage coat protein. Recombinant phage expressing the resulting VH libraries in fusion with the pIII protein is propagated in Escherichia coli. Monoclonal phage displaying VHs with specificities for target antigens are isolated from the libraries by a process called panning. The exertion of stability pressure in addition to binding pressure during panning ensures that the isolated VH binders are also non-aggregating. The genes encoding the desired VHs selected from the libraries are packaged within the phage particles, linking genotype and phenotype, hence making possible the identification of the selected VHs through identifying its physically linked genotype. Here, we describe the application of recombinant DNA and phage-display technologies for the construction of a phage-displayed human VH library, the panning of the library against a protein, and the expression, purification, and characterization of non-aggregating VHs isolated by panning.
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References
Ward, E. S., Gussow, D., Griffiths, A. D., Jones, P. T., and Winter, G. (1989) Binding activities of a repertoire of single immunoglobulin variable domains secreted from Escherichia coli. Nature 341, 544–546.
Arbabi-Ghahroudi, M., Desmyter, A., Wyns, L., Hamers, R., and Muyldermans, S. (1997) Selection and identification of single domain antibody fragments from camel heavy-chain antibodies. FEBS Lett. 414, 521–526.
Hamers-Casterman C., Atarhouch, T., Muyldermans, S., Robinson, G., Hamers, C., Songa, E. B., Bendahman, N., and Hamers, R. (1993) Naturally occurring antibodies devoid of light chains. Nature 363, 446–448.
Dooley, H. and Flajnik, M. F. (2006) Antibody repertoire development in cartilaginous fish. Dev. Comp. Immunol. 30, 43–56.
Greenberg, A. S., Avila, D., Hughes, M., Hughes, A., McKinney, E. C., and Flajnik, M. F. (1995) A new antigen receptor gene family that undergoes rearrangement and extensive somatic diversification in sharks. Nature 374, 168–173.
Roux, K. H., Greenberg, A. S., Greene, L., Strelets, L., Avila, D., McKinney, E. C., and Flajnik, M. F. (1998) Structural analysis of the nurse shark (new) antigen receptor (NAR): molecular convergence of NAR and unusual mammalian immunoglobulins. Proc. Natl. Acad. Sci. USA 95, 11804–11809.
Dooley, H., Flajnik, M. F., and Porter, A. J. (2003) Selection and characterization of naturally occurring single-domain (IgNAR) antibody fragments from immunized sharks by phage display. Mol. Immunol. 40, 25–33.
Liu, J. L., Anderson, G. P., Delehanty, J. B., Baumann, R., Hayhurst, A., and Goldman, E. R. (2007) Selection of cholera toxin specific IgNAR single-domain antibodies from a naive shark library. Mol. Immunol. 44, 1775–1783.
Nuttall, S. D., Krishnan, U. V., Hattarki, M., De Gori, R., Irving, R. A., and Hudson, P. J. (2001) Isolation of the new antigen receptor from Wobbegong sharks, and use as a scaffold for the display of protein loop libraries. Mol. Immunol. 38, 313–326.
Nuttall, S. D., Krishnan, U. V., Doughty, L., Nathanielsz, A., Ally, N., Pike, R. N., Hudson, P. J., Kortt, A. A., and Irving, R. A. (2002) A naturally occurring NAR variable domain binds the Kgp protease from Porphyromonas gingivalis. FEBS Lett. 516, 80–86.
Revets, H., De Baetselier, P., and Muyldermans, S. (2005) Nanobodies as novel agents for cancer therapy. Expert Opin. Biol. Ther. 5, 111–124.
Davies, J. and Riechmann, L. (1994) ‘Camelising’ human antibody fragments: NMR studies on VH domains. FEBS Lett. 339, 285–290.
Davies, J. and Riechmann, L. (1995) Antibody VH domains as small recognition units. Biotechnology NY 13, 475–479.
Tanha, J., Xu, P., Chen, Z. G., Ni, F., Kaplan, H., Narang, S. A., and MacKenzie, C. R. (2001) Optimal design features of camelized human single-domain antibody libraries. J. Biol. Chem. 276, 24774–24780.
Reiter, Y., Schuck, P., Boyd, L. F., and Plaksin, D. (1999) An antibody single-domain phage display library of a native heavy chain variable region: isolation of functional single-domain VH molecules with a unique interface. J. Mol. Biol. 290, 685–698.
Tanha, J., Dubuc, G., Hirama, T., Narang, S. A., and MacKenzie, C. R. (2002) Selection by phage display of llama conventional VH fragments with heavy chain antibody VHH properties. J. Immunol. Methods 263, 97–109.
Vranken, W., Tolkatchev, D., Xu, P., Tanha, J., Chen, Z., Narang, S., and Ni, F. (2002) Solution structure of a llama single-domain antibody with hydrophobic residues typical of the VH/VL interface. Biochemistry 41, 8570–8579.
Christ, D., Famm, K., and Winter, G. (2007) Repertoires of aggregation-resistant human antibody domains. Protein Eng. Des. Sel. 20, 413–416.
De Bernardis, F., Liu, H., O'Mahony, R., La Valle, R., Bartollino, S., Sandini, S., Grant, S., Brewis, N., Tomlinson, I., Basset, R. C., Holton, J., Roitt, I. M., and Cassone, A. (2007) Human domain antibodies against virulence traits of Candida albicans inhibit fungus adherence to vaginal epithelium and protect against experimental vaginal candidiasis. J. Infect. Dis. 195, 149–157.
Jespers, L., Schon, O., James, L. C., Veprintsev, D., and Winter, G. (2004) Crystal structure of HEL4, a soluble, refoldable human VH single domain with a germ-line scaffold. J. Mol. Biol. 337, 893–903.
Jespers, L., Schon, O., Famm, K., and Winter, G. (2004) Aggregation-resistant domain antibodies selected on phage by heat denaturation. Nat. Biotechnol. 22, 1161–1165.
To, R., Hirama, T., Arbabi-Ghahroudi, M., MacKenzie, R., Wang, P., Xu, P., Ni, F., and Tanha, J. (2005) Isolation of monomeric human VHs by a phage selection. J. Biol. Chem. 280, 41395–41403.
Colby, D. W., Garg, P., Holden, T., Chao, G., Webster, J. M., Messer, A., Ingram, V. M., and Wittrup, K. D. (2004) Development of a human light chain variable domain (VL) intracellular antibody specific for the amino terminus of huntingtin via yeast surface display. J. Mol. Biol. 342, 901–912.
Colby, D. W., Chu, Y., Cassady, J. P., Duennwald, M., Zazulak, H., Webster, J. M., Messer, A., Lindquist, S., Ingram, V. M., and Wittrup, K. D. (2004) Potent inhibition of huntingtin aggregation and cytotoxicity by a disulfide bond-free single-domain intracellular antibody. Proc. Natl. Acad. Sci. USA 101, 17616–17621.
Holt, L. J., Herring, C., Jespers, L. S., Woolven, B. P., and Tomlinson, I. M. (2003) Domain antibodies: proteins for therapy. Trends Biotechnol. 21, 484–490.
Paz, K., Brennan, L. A., Iacolina, M., Doody, J., Hadari, Y. R., and Zhu, Z. (2005) Human single-domain neutralizing intrabodies directed against Etk kinase: a novel approach to impair cellular transformation. Mol. Cancer Ther. 4, 1801–1809.
Kopsidas, G., Roberts, A. S., Coia, G., Streltsov, V. A., and Nuttall, S. D. (2006) In vitro improvement of a shark IgNAR antibody by Qβ replicase mutation and ribosome display mimics in vivo affinity maturation. Immunol. Lett. 107, 163–168.
Kopsidas, G., Carman, R. K., Stutt, E. L., Raicevic, A., Roberts, A. S., Siomos, M. A., Dobric, N., Pontes-Braz, L., and Coia, G. (2007) RNA mutagenesis yields highly diverse mRNA libraries for in vitro protein evolution. BMC. Biotechnol. 7, 18.
Nguyen, V. K., Desmyter, A., and Muyldermans, S. (2001) Functional heavy-chain antibodies in Camelidae. Adv. Immunol. 79, 261–296.
Tanaka, T., Lobato, M. N., and Rabbitts, T. H. (2003) Single domain intracellular antibodies: a minimal fragment for direct in vivo selection of antigen-specific intrabodies. J. Mol. Biol. 331, 1109–1120.
Arbabi-Ghahroudi, M., Tanha, J., and MacKenzie, R. (2005) Prokaryotic expression of antibodies. Cancer Metastasis Rev. 24, 501–519.
Constantine, K. L., Goldfarb, V., Wittekind, M., Anthony, J., Ng, S. C., and Mueller, L. (1992) Sequential 1H and 15N NMR assignments and secondary structure of a recombinant anti-digoxin antibody VL domain. Biochemistry 31, 5033–5043.
Constantine, K. L., Goldfarb, V., Wittekind, M., Friedrichs, M. S., Anthony, J., Ng, S. C., and Mueller, L. (1993) Aliphatic 1H and 13C resonance assignments for the 26-10 antibody VL domain derived from heteronuclear multidimensional NMR spectroscopy. J. Biomol. NMR 3, 41–54.
Goldman, E. R., Anderson, G. P., Liu, J. L., Delehanty, J. B., Sherwood, L. J., Osborn, L. E., Cummins, L. B., and Hayhurst, A. (2006) Facile generation of heat-stable antiviral and antitoxin single domain antibodies from a semisynthetic llama library. Anal. Chem. 78, 8245–8255.
Harmsen, M. M. and de Haard, H. J. (2007) Properties, production, and applications of camelid single-domain antibody fragments. Appl. Microbiol. Biotechnol. 77, 13–22.
Cwirla, S. E., Peters, E. A., Barrett, R. W., and Dower, W. J. (1990) Peptides on phage: a vast library of peptides for identifying ligands. Proc. Natl. Acad. Sci. USA 87, 6378–6382.
Scott, J. K. and Smith, G. P. (1990) Searching for peptide ligands with an epitope library. Science 249, 386–390.
Smith, G. P. (1985) Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 228, 1315–1317.
Barbas, C. F., III, Kang, A. S., Lerner, R. A., and Benkovic, S. J. (1991) Assembly of combinatorial antibody libraries on phage surfaces: the gene III site. Proc. Natl. Acad. Sci. USA 88, 7978–7982.
Bradbury, A. and Cattaneo, A. (1995) The use of phage display in neurobiology. Trends Neurosci. 18, 243–249.
Bradbury, A. (2003). scFvs and beyond. Drug Discov. Today 8, 737–739.
Breitling, F., Dubel, S., Seehaus, T., Klewinghaus, I., and Little, M. (1991) A surface expression vector for antibody screening. Gene 104, 147–153.
Clackson, T., Hoogenboom, H. R., Griffiths, A. D., and Winter, G. (1991) Making antibody fragments using phage display libraries. Nature 352, 624–628.
Davies, J. and Riechmann, L. (1996) Single antibody domains as small recognition units: design and in vitro antigen selection of camelized, human VH domains with improved protein stability. Protein Eng. 9, 531–537.
Hoogenboom, H. R., Griffiths, A. D., Johnson, K. S., Chiswell, D. J., Hudson, P., and Winter, G. (1991) Multi-subunit proteins on the surface of filamentous phage: methodologies for displaying antibody (Fab) heavy and light chains. Nucleic Acids Res. 19, 4133–4137.
Hoogenboom, H. R., de Bruine, A. P., Hufton, S. E., Hoet, R. M., Arends, J. W., and Roovers, R. C. (1998) Antibody phage display technology and its applications. Immunotechnology 4, 1–20.
Lowman, H. B. (1997) Bacteriophage display and discovery of peptide leads for drug development. Annu. Rev. Biophys. Biomol. Struct. 26, 401–424.
Marks, J. D., Hoogenboom, H. R., Bonnert, T. P., McCafferty, J., Griffiths, A. D., and Winter, G. (1991) By-passing immunization. Human antibodies from V-gene libraries displayed on phage. J. Mol. Biol. 222, 581–597.
McCafferty, J., Griffiths, A. D., Winter, G., and Chiswell, D. J. (1990) Phage antibodies: filamentous phage displaying antibody variable domains. Nature 348, 552–554.
Marks, J. D. and Bradbury, A. (2004) Selection of human antibodies from phage display libraries. Methods Mol. Biol. 248, 161–176.
Sblattero, D. and Bradbury, A. (2000) Exploiting recombination in single bacteria to make large phage antibody libraries. Nat. Biotechnol. 18, 75–80.
Winter, G., Griffiths, A. D., Hawkins, R. E., and Hoogenboom, H. R. (1994) Making antibodies by phage display technology. Annu. Rev. Immunol. 12, 433–455.
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. (1994) Isolation of high affinity human antibodies directly from large synthetic repertoires. EMBO J. 13, 3245–3260.
Sidhu, S. S., Li, B., Chen, Y., Fellouse, F. A., Eigenbrot, C., and Fuh, G. (2004) Phage-displayed antibody libraries of synthetic heavy chain complementarity determining regions. J. Mol. Biol. 338, 299–310.
Baek, H., Suk, K. H., Kim, Y. H., and Cha, S. (2002) An improved helper phage system for efficient isolation of specific antibody molecules in phage display. Nucleic Acids Res. 30, e18.
Chames, P. and Baty, D. (2000) Antibody engineering and its applications in tumor targeting and intracellular immunization. FEMS Microbiol. Lett. 189, 1–8.
Arap, M. A. (2005) Phage display technology: applications and innovations. Genet. Mol. Biol. 28, 1–9.
Conrad, U. and Scheller, J. (2005) Considerations on antibody-phage display methodology. Comb. Chem. High Throughput Screen. 8, 117–126.
Duenas, M., Malmborg, A. C., Casalvilla, R., Ohlin, M., and Borrebaeck, C. A. (1996) Selection of phage displayed antibodies based on kinetic constants. Mol. Immunol. 33, 279–285.
Harrison, J. L., Williams, S. C., Winter, G., and Nissim, A. (1996) Screening of phage antibody libraries. Methods Enzymol. 267, 83–109.
Hawkins, R. E., Russell, S. J., and Winter, G. (1992) Selection of phage antibodies by binding affinity mimicking affinity maturation. J. Mol. Biol. 226, 889–896.
Mancini, N., Carletti, S., Perotti, M., Canducci, F., Mammarella, M., Sampaolo, M., and Burioni, R. (2004) Phage display for the production of human monoclonal antibodies against human pathogens. New Microbiol. 27, 315–328.
Davies, J. and Riechmann, L. (1995) Antibody VH domains as small recognition units. Biotechnology NY 13, 475–479.
Tanha, J., Nguyen, T. D., Ng, A., Ryan, S., Ni, F., and MacKenzie, R. (2006) Improving solubility and refolding efficiency of human VHs by a novel mutational approach. Protein Eng. Des. Sel. 19, 503–509.
Rondot, S., Koch, J., Breitling, F., and Dubel, S. (2001) A helper phage to improve single-chain antibody presentation in phage display. Nat. Biotechnol. 19, 75–78.
Sambrook, J., Fritsch, E. F., and Maniatis, T. (ed.) (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
Desmyter, A., Transue, T. R., Arbabi-Ghahroudi, M., Thi, M. H., Poortmans, F., Hamers, R., Muyldermans, S., and Wyns, L. (1996) Crystal structure of a camel single-domain VH antibody fragment in complex with lysozyme. Nat. Struct. Biol. 3, 803–811.
Holliger, P. and Hudson, P. J. (2005) Engineered antibody fragments and the rise of single domains. Nat. Biotechnol. 23, 1126–1136.
Stanfield, R. L., Dooley, H., Flajnik, M. F., and Wilson, I. A. (2004) Crystal structure of a shark single-domain antibody V region in complex with lysozyme. Science 305, 1770–1773.
Stijlemans, B., Conrath, K., Cortez-Retamozo, V., Van Xong, H., Wyns, L., Senter, P., Revets, H., De Baetselier, P., Muyldermans, S., and Magez, S. (2004) Efficient targeting of conserved cryptic epitopes of infectious agents by single domain antibodies. African trypanosomes as paradigm. J. Biol. Chem. 279, 1256–1261.
Ho, S. N., Hunt, H. D., Horton, R. M., Pullen, J. K., and Pease, L. R. (1989) Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77, 51–59.
Tung, W. L. and Chow, K. C. (1995) A modified medium for efficient electrotransformation of E. coli. Trends Genet. 11, 128–129.
Tanha, J., Muruganandam, A., and Stanimirovic, D. (2003) Phage display technology for identifying specific antigens on brain endothelial cells. Methods Mol. Med. 89, 435–450.
Anand, N. N., Dubuc, G., Phipps, J., MacKenzie, C. R., Sadowska, J., Young, N. M., Bundle, D. R., and Narang, S. A. (1991) Synthesis and expression in Escherichia coli of cistronic DNA encoding an antibody fragment specific for a Salmonella serotype B O-antigen. Gene 100, 39–44.
MacKenzie, C. R., Sharma, V., Brummell, D., Bilous, D., Dubuc, G., Sadowska, J., Young, N. M., Bundle, D. R., and Narang, S. A. (1994) Effect of Cλ-Cκ domain switching on Fab activity and yield in Escherichia coli: synthesis and expression of genes encoding two anti-carbohydrate Fabs. Biotechnology NY 12, 390–395.
Laemmli, U. K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680–685.
Pace, C. N., Vajdos, F., Fee, L., Grimsley, G., and Gray, T. (1995) How to measure and predict the molar absorption coefficient of a protein. Protein Sci. 4, 2411–2423.
Ewert, S., Cambillau, C., Conrath, K., and Plűckthun, A. (2002) Biophysical properties of camelid VHH domains compared to those of human VH3 domains. Biochemistry 41, 3628–3636.
Ewert, S., Huber, T., Honegger, A., and Plűckthun, A. (2003) Biophysical properties of human antibody variable domains. J. Mol. Biol. 325, 531–553.
Zhang, J., Tanha, J., Hirama, T., Khieu, N. H., To, R., Tong-Sevinc, H., Stone, E., Brisson, J. R., and MacKenzie, C. R. (2004) Pentamerization of single-domain antibodies from phage libraries: A novel strategy for the rapid generation of high-avidity antibody reagents. J. Mol. Biol. 335, 49–56.
Christ, D., Famm, K., and Winter, G. (2006) Tapping diversity lost in transformations – in vitro amplification of ligation reactions. Nucleic Acids Res. 34, e108.
Kabat, E. A., Wu, T. T., Perry, H. M., Gottesman, K. S. and Foeller, C. (ed.) (1991). Sequences of Proteins of Immunological Interest. US Department of Health and Human Services, US Public Health Service, Bethesda, MD.
Stone, E., Hirama, T., Tanha, J., Tong-Sevinc, H., Li, S., MacKenzie, C. R., and Zhang, J. (2007). The assembly of single domain antibodies into bispecific decavalent molecules. J. Immunol. Methods 318, 88–94.
Acknowledgments
The assistance of Rebecca To, Nathalie Gaudette, and Hong Tong-Sevinc with library construction, panning, protein expression, and purification is gratefully acknowledged. We thank Shakeeba Waseh for performing size-exclusion chromatography experiments. Requests for pMED1 vector should be addressed to Mehdi Arbabi-Ghahroudi.
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Arbabi-Ghahroudi, M., MacKenzie, R., Tanha, J. (2009). Selection of Non-aggregating VH Binders from Synthetic VH Phage-Display Libraries. In: Dimitrov, A. (eds) Therapeutic Antibodies. Methods in Molecular Biology™, vol 525. Humana Press. https://doi.org/10.1007/978-1-59745-554-1_10
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