9,450
Views
151
CrossRef citations to date
0
Altmetric
Report

A fully synthetic human Fab antibody library based on fixed VH/VL framework pairings with favorable biophysical properties

, , , , , , , , , , , , , , , & show all
Pages 445-470 | Received 12 Dec 2012, Accepted 06 Mar 2013, Published online: 09 Apr 2013

References

  • Carter PJ. Potent antibody therapeutics by design. Nat Rev Immunol 2006; 6:343 - 57; http://dx.doi.org/10.1038/nri1837; PMID: 16622479
  • Traggiai E, Becker S, Subbarao K, Kolesnikova L, Uematsu Y, Gismondo MR, et al. An efficient method to make human monoclonal antibodies from memory B cells: potent neutralization of SARS coronavirus. Nat Med 2004; 10:871 - 5; http://dx.doi.org/10.1038/nm1080; PMID: 15247913
  • Olsson L, Kaplan HS. Human-human hybridomas producing monoclonal antibodies of predefined antigenic specificity. Proc Natl Acad Sci U S A 1980; 77:5429 - 31; http://dx.doi.org/10.1073/pnas.77.9.5429; PMID: 6159646
  • Meijer PJ, Andersen PS, Haahr Hansen M, Steinaa L, Jensen A, Lantto J, et al. Isolation of human antibody repertoires with preservation of the natural heavy and light chain pairing. J Mol Biol 2006; 358:764 - 72; http://dx.doi.org/10.1016/j.jmb.2006.02.040; PMID: 16563430
  • Tiller T, Meffre E, Yurasov S, Tsuiji M, Nussenzweig MC, Wardemann H. Efficient generation of monoclonal antibodies from single human B cells by single cell RT-PCR and expression vector cloning. J Immunol Methods 2008; 329:112 - 24; http://dx.doi.org/10.1016/j.jim.2007.09.017; PMID: 17996249
  • Tiller T. Single B cell antibody technologies. N Biotechnol 2011; 28:453 - 7; http://dx.doi.org/10.1016/j.nbt.2011.03.014; PMID: 21473940
  • Köhler G, Milstein C. Continuous cultures of fused cells secreting antibody of predefined specificity. Nature 1975; 256:495 - 7; http://dx.doi.org/10.1038/256495a0; PMID: 1172191
  • Lonberg N. Human monoclonal antibodies from transgenic mice. Handb Exp Pharmacol 2008; 69 - 97; http://dx.doi.org/10.1007/978-3-540-73259-4_4; PMID: 18071942
  • Hanes J, Plückthun A. In vitro selection and evolution of functional proteins by using ribosome display. Proc Natl Acad Sci U S A 1997; 94:4937 - 42; http://dx.doi.org/10.1073/pnas.94.10.4937; PMID: 9144168
  • He M, Taussig MJ. Antibody-ribosome-mRNA (ARM) complexes as efficient selection particles for in vitro display and evolution of antibody combining sites. Nucleic Acids Res 1997; 25:5132 - 4; http://dx.doi.org/10.1093/nar/25.24.5132; PMID: 9396828
  • Boder ET, Wittrup KD. Yeast surface display for screening combinatorial polypeptide libraries. Nat Biotechnol 1997; 15:553 - 7; http://dx.doi.org/10.1038/nbt0697-553; PMID: 9181578
  • McCafferty J, Griffiths AD, Winter G, Chiswell DJ. Phage antibodies: filamentous phage displaying antibody variable domains. Nature 1990; 348:552 - 4; http://dx.doi.org/10.1038/348552a0; PMID: 2247164
  • Smith GP. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science 1985; 228:1315 - 7; http://dx.doi.org/10.1126/science.4001944; PMID: 4001944
  • Winter G, Griffiths AD, Hawkins RE, Hoogenboom HR. Making antibodies by phage display technology. Annu Rev Immunol 1994; 12:433 - 55; http://dx.doi.org/10.1146/annurev.iy.12.040194.002245; PMID: 8011287
  • Marks JD, Hoogenboom HR, Bonnert TP, McCafferty J, Griffiths AD, Winter G. By-passing immunization. Human antibodies from V-gene libraries displayed on phage. J Mol Biol 1991; 222:581 - 97; http://dx.doi.org/10.1016/0022-2836(91)90498-U; PMID: 1748994
  • Vaughan TJ, Williams AJ, Pritchard K, Osbourn JK, Pope AR, Earnshaw JC, et al. Human antibodies with sub-nanomolar affinities isolated from a large non-immunized phage display library. Nat Biotechnol 1996; 14:309 - 14; http://dx.doi.org/10.1038/nbt0396-309; PMID: 9630891
  • Huse WD, Sastry L, Iverson SA, Kang AS, Alting-Mees M, Burton DR, et al. Generation of a large combinatorial library of the immunoglobulin repertoire in phage lambda. Science 1989; 246:1275 - 81; http://dx.doi.org/10.1126/science.2531466; PMID: 2531466
  • Hoet RM, Cohen EH, Kent RB, Rookey K, Schoonbroodt S, Hogan S, et al. Generation of high-affinity human antibodies by combining donor-derived and synthetic complementarity-determining-region diversity. Nat Biotechnol 2005; 23:344 - 8; http://dx.doi.org/10.1038/nbt1067; PMID: 15723048
  • Knappik A, Ge L, Honegger A, Pack P, Fischer M, Wellnhofer G, et al. Fully synthetic human combinatorial antibody libraries (HuCAL) based on modular consensus frameworks and CDRs randomized with trinucleotides. J Mol Biol 2000; 296:57 - 86; http://dx.doi.org/10.1006/jmbi.1999.3444; PMID: 10656818
  • Prassler J, Thiel S, Pracht C, Polzer A, Peters S, Bauer M, et al. HuCAL PLATINUM, a synthetic Fab library optimized for sequence diversity and superior performance in mammalian expression systems. J Mol Biol 2011; 413:261 - 78; http://dx.doi.org/10.1016/j.jmb.2011.08.012; PMID: 21856311
  • Rothe C, Urlinger S, Löhning C, Prassler J, Stark Y, Jäger U, et al. The human combinatorial antibody library HuCAL GOLD combines diversification of all six CDRs according to the natural immune system with a novel display method for efficient selection of high-affinity antibodies. J Mol Biol 2008; 376:1182 - 200; http://dx.doi.org/10.1016/j.jmb.2007.12.018; PMID: 18191144
  • Ponsel D, Neugebauer J, Ladetzki-Baehs K, Tissot K. High affinity, developability and functional size: the holy grail of combinatorial antibody library generation. Molecules 2011; 16:3675 - 700; http://dx.doi.org/10.3390/molecules16053675; PMID: 21540796
  • Hoogenboom HR. Selecting and screening recombinant antibody libraries. Nat Biotechnol 2005; 23:1105 - 16; http://dx.doi.org/10.1038/nbt1126; PMID: 16151404
  • Hudson PJ. Recombinant antibody fragments. Curr Opin Biotechnol 1998; 9:395 - 402; http://dx.doi.org/10.1016/S0958-1669(98)80014-1; PMID: 9720265
  • Söderlind E, Strandberg L, Jirholt P, Kobayashi N, Alexeiva V, Aberg AM, et al. Recombining germline-derived CDR sequences for creating diverse single-framework antibody libraries. Nat Biotechnol 2000; 18:852 - 6; http://dx.doi.org/10.1038/78458; PMID: 10932154
  • Jenkins N, Murphy L, Tyther R. Post-translational modifications of recombinant proteins: significance for biopharmaceuticals. Mol Biotechnol 2008; 39:113 - 8; http://dx.doi.org/10.1007/s12033-008-9049-4; PMID: 18327554
  • Raab D, Graf M, Notka F, Schödl T, Wagner R. The GeneOptimizer Algorithm: using a sliding window approach to cope with the vast sequence space in multiparameter DNA sequence optimization. Syst Synth Biol 2010; 4:215 - 25; http://dx.doi.org/10.1007/s11693-010-9062-3; PMID: 21189842
  • Virnekäs B, Ge L, Plückthun A, Schneider KC, Wellnhofer G, Moroney SE. Trinucleotide phosphoramidites: ideal reagents for the synthesis of mixed oligonucleotides for random mutagenesis. Nucleic Acids Res 1994; 22:5600 - 7; http://dx.doi.org/10.1093/nar/22.25.5600; PMID: 7838712
  • Van den Brulle J, Fischer M, Langmann T, Horn G, Waldmann T, Arnold S, et al. A novel solid phase technology for high-throughput gene synthesis. Biotechniques 2008; 45:340 - 3; http://dx.doi.org/10.2144/000112953; PMID: 18778261
  • Mietzner B, Tsuiji M, Scheid J, Velinzon K, Tiller T, Abraham K, et al. Autoreactive IgG memory antibodies in patients with systemic lupus erythematosus arise from nonreactive and polyreactive precursors. Proc Natl Acad Sci U S A 2008; 105:9727 - 32; http://dx.doi.org/10.1073/pnas.0803644105; PMID: 18621685
  • Tiller T, Tsuiji M, Yurasov S, Velinzon K, Nussenzweig MC, Wardemann H. Autoreactivity in human IgG+ memory B cells. Immunity 2007; 26:205 - 13; http://dx.doi.org/10.1016/j.immuni.2007.01.009; PMID: 17306569
  • Tsuiji M, Yurasov S, Velinzon K, Thomas S, Nussenzweig MC, Wardemann H. A checkpoint for autoreactivity in human IgM+ memory B cell development. J Exp Med 2006; 203:393 - 400; http://dx.doi.org/10.1084/jem.20052033; PMID: 16446381
  • Wardemann H, Yurasov S, Schaefer A, Young JW, Meffre E, Nussenzweig MC. Predominant autoantibody production by early human B cell precursors. Science 2003; 301:1374 - 7; http://dx.doi.org/10.1126/science.1086907; PMID: 12920303
  • Yurasov S, Hammersen J, Tiller T, Tsuiji M, Wardemann H. B-cell tolerance checkpoints in healthy humans and patients with systemic lupus erythematosus. Ann N.Y. Acad.Sci 2005; 1062:165 - 74; http://dx.doi.org/10.1196/annals.1358.019
  • Yurasov S, Tiller T, Tsuiji M, Velinzon K, Pascual V, Wardemann H, et al. Persistent expression of autoantibodies in SLE patients in remission. J Exp Med 2006; 203:2255 - 61; http://dx.doi.org/10.1084/jem.20061446; PMID: 16966430
  • Brezinschek HP, Foster SJ, Brezinschek RI, Dörner T, Domiati-Saad R, Lipsky PE. Analysis of the human VH gene repertoire. Differential effects of selection and somatic hypermutation on human peripheral CD5(+)/IgM+ and CD5(-)/IgM+ B cells. J Clin Invest 1997; 99:2488 - 501; http://dx.doi.org/10.1172/JCI119433; PMID: 9153293
  • Demaison C, David D, Letourneur F, Thèze J, Saragosti S, Zouali M. Analysis of human VH gene repertoire expression in peripheral CD19+ B cells. Immunogenetics 1995; 42:342 - 52; http://dx.doi.org/10.1007/BF00179395; PMID: 7590967
  • Foster SJ, Brezinschek HP, Brezinschek RI, Lipsky PE. Molecular mechanisms and selective influences that shape the kappa gene repertoire of IgM+ B cells. J Clin Invest 1997; 99:1614 - 27; http://dx.doi.org/10.1172/JCI119324; PMID: 9120005
  • de Wildt RM, Hoet RM, van Venrooij WJ, Tomlinson IM, Winter G. Analysis of heavy and light chain pairings indicates that receptor editing shapes the human antibody repertoire. J Mol Biol 1999; 285:895 - 901; http://dx.doi.org/10.1006/jmbi.1998.2396; PMID: 9887257
  • Chothia C, Lesk AM, Gherardi E, Tomlinson IM, Walter G, Marks JD, et al. Structural repertoire of the human VH segments. J Mol Biol 1992; 227:799 - 817; http://dx.doi.org/10.1016/0022-2836(92)90224-8; PMID: 1404389
  • Lloyd C, Lowe D, Edwards B, Welsh F, Dilks T, Hardman 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 2009; 22:159 - 68; http://dx.doi.org/10.1093/protein/gzn058; PMID: 18974080
  • Bhat NM, Bieber MM, Stevenson FK, Teng NN. Rapid cytotoxicity of human B lymphocytes induced by VH4-34 (VH4.21) gene-encoded monoclonal antibodies. Clin Exp Immunol 1996; 105:183 - 90; http://dx.doi.org/10.1046/j.1365-2249.1996.d01-733.x; PMID: 8697629
  • Glanville J, Zhai W, Berka J, Telman D, Huerta G, Mehta GR, et al. Precise determination of the diversity of a combinatorial antibody library gives insight into the human immunoglobulin repertoire. Proc Natl Acad Sci U S A 2009; 106:20216 - 21; http://dx.doi.org/10.1073/pnas.0909775106; PMID: 19875695
  • Tomlinson IM, Cox JP, Gherardi E, Lesk AM, Chothia C. The structural repertoire of the human V kappa domain. EMBO J 1995; 14:4628 - 38; PMID: 7556106
  • Williams SC, Frippiat JP, Tomlinson IM, Ignatovich O, Lefranc MP, Winter G. Sequence and evolution of the human germline V lambda repertoire. J Mol Biol 1996; 264:220 - 32; http://dx.doi.org/10.1006/jmbi.1996.0636; PMID: 8951372
  • Dunn-Walters D, Boursier L, Spencer J. Effect of somatic hypermutation on potential N-glycosylation sites in human immunoglobulin heavy chain variable regions. Mol Immunol 2000; 37:107 - 13; http://dx.doi.org/10.1016/S0161-5890(00)00038-9; PMID: 10865109
  • Carter P, Presta L, Gorman CM, Ridgway JB, Henner D, Wong WL, et al. Humanization of an anti-p185HER2 antibody for human cancer therapy. Proc Natl Acad Sci U S A 1992; 89:4285 - 9; http://dx.doi.org/10.1073/pnas.89.10.4285; PMID: 1350088
  • Ewert S, Huber T, Honegger A, Plückthun A. Biophysical properties of human antibody variable domains. J Mol Biol 2003; 325:531 - 53; http://dx.doi.org/10.1016/S0022-2836(02)01237-8; PMID: 12498801
  • Steidl S, Ratsch O, Brocks B, Dürr M, Thomassen-Wolf E. In vitro affinity maturation of human GM-CSF antibodies by targeted CDR-diversification. Mol Immunol 2008; 46:135 - 44; http://dx.doi.org/10.1016/j.molimm.2008.07.013; PMID: 18722015
  • Cummings MD, Farnum MA, Nelen MI. Universal screening methods and applications of ThermoFluor. J Biomol Screen 2006; 11:854 - 63; http://dx.doi.org/10.1177/1087057106292746; PMID: 16943390
  • Ericsson UB, Hallberg BM, Detitta GT, Dekker N, Nordlund P. Thermofluor-based high-throughput stability optimization of proteins for structural studies. Anal Biochem 2006; 357:289 - 98; http://dx.doi.org/10.1016/j.ab.2006.07.027; PMID: 16962548
  • He F, Hogan S, Latypov RF, Narhi LO, Razinkov VI. High throughput thermostability screening of monoclonal antibody formulations. J Pharm Sci 2010; 99:1707 - 20; PMID: 19780136
  • Zemlin M, Klinger M, Link J, Zemlin C, Bauer K, Engler JA, 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 2003; 334:733 - 49; http://dx.doi.org/10.1016/j.jmb.2003.10.007; PMID: 14636599
  • Krebs B, Rauchenberger R, Reiffert S, Rothe C, Tesar M, Thomassen E, et al. High-throughput generation and engineering of recombinant human antibodies. J Immunol Methods 2001; 254:67 - 84; http://dx.doi.org/10.1016/S0022-1759(01)00398-2; PMID: 11406154
  • Rauchenberger R, Borges E, Thomassen-Wolf E, Rom E, Adar R, Yaniv Y, et al. Human combinatorial Fab library yielding specific and functional antibodies against the human fibroblast growth factor receptor 3. J Biol Chem 2003; 278:38194 - 205; http://dx.doi.org/10.1074/jbc.M303164200; PMID: 12842902
  • McGee P. Building better antibody therapeutics. Drug Discovery & Development 2007; 10:26 - 8
  • Jayaram N, Bhowmick P, Martin AC. Germline VH/VL pairing in antibodies. Protein Eng Des Sel 2012; 25:523 - 9; http://dx.doi.org/10.1093/protein/gzs043; PMID: 22802295
  • Schaefer JV, Plückthun A. Transfer of engineered biophysical properties between different antibody formats and expression systems. Protein Eng Des Sel 2012; 25:485 - 506; http://dx.doi.org/10.1093/protein/gzs039; PMID: 22763265
  • Ejima D, Tsumoto K, Fukada H, Yumioka R, Nagase K, Arakawa T, et al. Effects of acid exposure on the conformation, stability, and aggregation of monoclonal antibodies. Proteins 2007; 66:954 - 62; http://dx.doi.org/10.1002/prot.21243; PMID: 17154421
  • Low D, O’Leary R, Pujar NS. Future of antibody purification. J Chromatogr B Analyt Technol Biomed Life Sci 2007; 848:48 - 63; http://dx.doi.org/10.1016/j.jchromb.2006.10.033; PMID: 17134947
  • Ahrer K, Buchacher A, Iberer G, Jungbauer A. Thermodynamic stability and formation of aggregates of human immunoglobulin G characterised by differential scanning calorimetry and dynamic light scattering. J Biochem Biophys Methods 2006; 66:73 - 86; http://dx.doi.org/10.1016/j.jbbm.2005.12.003; PMID: 16458360
  • Brezinschek HP, Foster SJ, Dörner T, Brezinschek RI, Lipsky PE. Pairing of variable heavy and variable kappa chains in individual naive and memory B cells. J Immunol 1998; 160:4762 - 7; PMID: 9590222
  • Luo J, Obmolova G, Huang A, Strake B, Teplyakov A, Malia T, et al. Coevolution of antibody stability and Vκ CDR-L3 canonical structure. J Mol Biol 2010; 402:708 - 19; http://dx.doi.org/10.1016/j.jmb.2010.08.009; PMID: 20727359
  • Walsh G, Jefferis R. Post-translational modifications in the context of therapeutic proteins. Nat Biotechnol 2006; 24:1241 - 52; http://dx.doi.org/10.1038/nbt1252; PMID: 17033665
  • Zheng Y, Tesar DB, Benincosa L, Birnböck H, Boswell CA, Bumbaca D, et al. Minipig as a potential translatable model for monoclonal antibody pharmacokinetics after intravenous and subcutaneous administration. MAbs 2012; 4:243 - 55; http://dx.doi.org/10.4161/mabs.4.2.19387; PMID: 22453096
  • Igawa T, Ishii S, Tachibana T, Maeda A, Higuchi Y, Shimaoka S, et al. Antibody recycling by engineered pH-dependent antigen binding improves the duration of antigen neutralization. Nat Biotechnol 2010; 28:1203 - 7; http://dx.doi.org/10.1038/nbt.1691; PMID: 20953198
  • Ravn U, Gueneau F, Baerlocher L, Osteras M, Desmurs M, Malinge P, et al. By-passing in vitro screening--next generation sequencing technologies applied to antibody display and in silico candidate selection. Nucleic Acids Res 2010; 38:e193; http://dx.doi.org/10.1093/nar/gkq789; PMID: 20846958
  • Venet S, Ravn U, Buatois V, Gueneau F, Calloud S, Kosco-Vilbois M, et al. Transferring the characteristics of naturally occurring and biased antibody repertoires to human antibody libraries by trapping CDRH3 sequences. PLoS One 2012; 7:e43471; http://dx.doi.org/10.1371/journal.pone.0043471; PMID: 22937053
  • Kuroda D, Shirai H, Kobori M, Nakamura H. Systematic classification of CDR-L3 in antibodies: implications of the light chain subtypes and the VL-VH interface. Proteins 2009; 75:139 - 46; http://dx.doi.org/10.1002/prot.22230; PMID: 18798566
  • Retter I, Althaus HH, Münch R, Müller W. VBASE2, an integrative V gene database. Nucleic Acids Res 2005; 33:Database issue D671 - 4; http://dx.doi.org/10.1093/nar/gki088; PMID: 15608286
  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389 - 402; http://dx.doi.org/10.1093/nar/25.17.3389; PMID: 9254694
  • Honegger A, Plückthun A. Yet another numbering scheme for immunoglobulin variable domains: an automatic modeling and analysis tool. J Mol Biol 2001; 309:657 - 70; http://dx.doi.org/10.1006/jmbi.2001.4662; PMID: 11397087
  • Hieter PA, Maizel JV Jr., Leder P. Evolution of human immunoglobulin kappa J region genes. J Biol Chem 1982; 257:1516 - 22; PMID: 6276389
  • Kawasaki K, Minoshima S, Nakato E, Shibuya K, Shintani A, Schmeits JL, et al. One-megabase sequence analysis of the human immunoglobulin lambda gene locus. Genome Res 1997; 7:250 - 61; http://dx.doi.org/10.1101/gr.7.3.250; PMID: 9074928
  • Ravetch JV, Siebenlist U, Korsmeyer S, Waldmann T, Leder P. Structure of the human immunoglobulin mu locus: characterization of embryonic and rearranged J and D genes. Cell 1981; 27:583 - 91; http://dx.doi.org/10.1016/0092-8674(81)90400-1; PMID: 6101209
  • Stubenrauch K, Wessels U, Lenz H. Evaluation of an immunoassay for human-specific quantitation of therapeutic antibodies in serum samples from non-human primates. J Pharm Biomed Anal 2009; 49:1003 - 8; http://dx.doi.org/10.1016/j.jpba.2009.01.030; PMID: 19250787
  • Cho MS, Yee H, Chan S. Establishment of a human somatic hybrid cell line for recombinant protein production. J Biomed Sci 2002; 9:631 - 8; http://dx.doi.org/10.1007/BF02254991; PMID: 12432229

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.