Immune repertoire mining for rapid affinity optimization of mouse monoclonal antibodies

References

• Kohler G, Milstein C. Continuous cultures of fused cells secreting antibody of predefined specificity. Nature. 1975;256:495–97.
   PubMed Web of Science ®Google Scholar
• Tiller T, Busse CE, Wardemann H. Cloning and expression of murine Ig genes from single B cells. J Immunol Methods. 2009;350:183–93. doi:10.1016/j.jim.2009.08.009.
   PubMed Web of Science ®Google Scholar
• Hershberg U, Luning Prak ET. The analysis of clonal expansions in normal and autoimmune B cell repertoires. Phil Trans R Soc B. 2015;370:20140239.
   Google Scholar
• Levin AM, Weiss GA. Optimizing the affinity and specificity of proteins with molecular display. Mol Biosyst. 2006;2:49–57. doi:10.1039/b511782h.
   PubMed Web of Science ®Google Scholar
• Parola C, Neumeier D, Reddy ST. Integrating high-throughput screening and sequencing for monoclonal antibody discovery and engineering. Immunology. 2018;153:31–41. doi:10.1111/imm.12838.
   PubMed Web of Science ®Google Scholar
• Zhu J, Ofek G, Yang Y, Zhang B, Louder MK, Lu G, McKee K, Pancera M, Skinner J, Zhang Z, et al. Mining the antibodyome for HIV-1-neutralizing antibodies with next-generation sequencing and phylogenetic pairing of heavy/light chains. Proc Natl Acad Sci USA. 2013;110:6470–75. doi:10.1073/pnas.1219320110.
   PubMed Web of Science ®Google Scholar
• Sok D, Laserson U, Laserson J, Liu Y, Vigneault F, Julien JP, Briney B, Ramos A, Saye KF, Le K, et al. The effects of somatic hypermutation on neutralization and binding in the PGT121 family of broadly neutralizing HIV antibodies. PLoS Pathog. 2013;9:e1003754. doi:10.1371/journal.ppat.1003754.
   PubMed Web of Science ®Google Scholar
• Rudicell RS, Kwon YD, Ko SY, Pegu A, Louder MK, Georgiev IS, Wu X, Zhu J, Boyington JC, Chen X, et al. Enhanced potency of a broadly neutralizing HIV-1 antibody in vitro improves protection against lentiviral infection in vivo. J Virol. 2014;88:12669–82. doi:10.1128/JVI.02213-14.
   PubMed Web of Science ®Google Scholar
• Yu L, Guan Y. Immunologic basis for long HCDR3s in broadly neutralizing antibodies against HIV-1. Front Immunol. 2014;5:250. doi:10.3389/fimmu.2014.00250.
   PubMed Web of Science ®Google Scholar
• Burton DR, Hangartner L. Broadly neutralizing antibodies to HIV and their role in vaccine design. Annu Rev Immunol. 2016;34:635–59. doi:10.1146/annurev-immunol-041015-055515.
   PubMed Web of Science ®Google Scholar
• Breden F, Lepik C, Longo NS, Montero M, Lipsky PE, Scott JK. Comparison of antibody repertoires produced by HIV-1 infection, other chronic and acute infections, and systemic autoimmune disease. PLoS One. 2011;6:e16857. doi:10.1371/journal.pone.0016857.
   PubMed Web of Science ®Google Scholar
• Zemlin M, Klinger M, Link J, Zemlin C, Bauer K, Engler JA, Schroeder HW, Kirkham PM. 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.
   PubMed Web of Science ®Google Scholar
• Schroeder HW Jr. Similarity and divergence in the development and expression of the mouse and human antibody repertoires. Dev Comp Immunol. 2006;30:119–35. doi:10.1016/j.dci.2005.06.006.
   PubMed Web of Science ®Google Scholar
• Kabat EA, Wu TT, Perry HM, Gottesman KS, Foeller C. Sequences of proteins of immunological interest. Bethesda (MD): NIH Publication; 1991.
   Google Scholar
• Lefranc MP, Ehrenmann F, Ginestoux C, Giudicelli V, Duroux P. Use of IMGT((R)) databases and tools for antibody engineering and humanization. Methods Mol Biol. 2012;907:3–37. doi:10.1007/978-1-61779-974-7_1.
   PubMedGoogle Scholar
• Foote J, Winter G. Antibody framework residues affecting the conformation of the hypervariable loops. J Mol Biol. 1992;224:487–99.
   PubMed Web of Science ®Google Scholar
• Presta LG, Lahr SJ, Shields RL, Porter JP, Gorman CM, Fendly BM, Jardieu PM. Humanization of an antibody directed against IgE. J Immunol. 1993;151:2623–32.
   PubMed Web of Science ®Google Scholar
• Padlan EA. Anatomy of the antibody molecule. Mol Immunol. 1994;31:169–217.
   PubMed Web of Science ®Google Scholar
• Bujotzek A, Dunbar J, Lipsmeier F, Schafer W, Antes I, Deane CM, Georges G. Prediction of VH-VL domain orientation for antibody variable domain modeling. Proteins. 2015;83:681–95. doi:10.1002/prot.24756.
   PubMed Web of Science ®Google Scholar
• North B, Lehmann A, Dunbrack RL Jr. A new clustering of antibody CDR loop conformations. J Mol Biol. 2011;406:228–56. doi:10.1016/j.jmb.2010.10.030.
   PubMed Web of Science ®Google Scholar
• Bengoa-Vergniory N, Roberts RF, Wade-Martins R, Alegre-Abarrategui J. Alpha-synuclein oligomers: a new hope. Acta Neuropathol. 2017;134:819–38. doi:10.1007/s00401-017-1755-1.
   PubMed Web of Science ®Google Scholar
• Polson AG, Zheng B, Elkins K, Chang W, Du C, Dowd P, Yen L, Tan C, Hongo J-A, Koeppen H, et al. Expression pattern of the human FcRH/IRTA receptors in normal tissue and in B-chronic lymphocytic leukemia. Int Immunol. 2006;18:1363–73. doi:10.1093/intimm/dxl069.
   PubMed Web of Science ®Google Scholar
• Hotzel I, Theil FP, Bernstein LJ, Prabhu S, Deng R, Quintana L, Lutman J, Sibia R, Chan P, Bumbaca D, et al. A strategy for risk mitigation of antibodies with fast clearance. MAbs. 2012;4:753–60. doi:10.4161/mabs.22189.
   PubMed Web of Science ®Google Scholar
• Hazen M, Bhakta S, Vij R, Randle S, Kallop D, Chiang V, Hötzel I, Jaiswal BS, Ervin KE, Li B, et al. An improved and robust DNA immunization method to develop antibodies against extracellular loops of multi-transmembrane proteins. MAbs. 2014;6:95–107. doi:10.4161/mabs.26761.
   PubMed Web of Science ®Google Scholar
• Chen Y, Kim SH, Shang Y, Guillory J, Stinson J, Zhang Q, Hötzel I, Hoi KH. Barcoded sequencing workflow for high throughput digitization of hybridoma antibody variable domain sequences. J Immunol Methods. 2018;455:88–94. doi:10.1016/j.jim.2018.01.004.
   PubMed Web of Science ®Google Scholar
• Lefranc MP. IMGT, the international ImMunoGeneTics database: a high-quality information system for comparative immunogenetics and immunology. Dev Comp Immunol. 2002;26:697–705.
   PubMed Web of Science ®Google Scholar
• Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33:1870–74. doi:10.1093/molbev/msw054.
   PubMed Web of Science ®Google Scholar
• Bos AB, Luan P, Duque JN, Reilly D, Harms PD, Wong AW. Optimization and automation of an end-to-end high throughput microscale transient protein production process. Biotechnol Bioeng. 2015;112:1832–42. doi:10.1002/bit.25601.
   PubMed Web of Science ®Google Scholar
• Luan P, Lee S, Arena TA, Paluch M, Kansopon J, Viajar S, Begum Z, Chiang N, Nakamura G, Hass PE, et al. Automated high throughput microscale antibody purification workflows for accelerating antibody discovery. MAbs. 2018;10:624–35. doi:10.1080/19420862.2018.1445450.
   PubMed Web of Science ®Google Scholar
• Vij R, Lin Z, Chiang N, Vernes JM, Storek KM, Park S, Chan J, Meng YG, Comps-Agrar L, Luan P, et al. A targeted boost-and-sort immunization strategy using Escherichia coli BamA identifies rare growth inhibitory antibodies. Sci Rep. 2018;8:7136. doi:10.1038/s41598-018-25609-z.
   PubMed Web of Science ®Google Scholar