Effective high-throughput isolation of fully human antibodies targeting infectious pathogens

Lutz Gieselmann, Christoph Kreer, Meryem Seda Ercanoglu, Nathalie Lehnen, Matthias Zehner, Philipp Schommers, Julian Potthoff, Henning Gruell, Florian Klein

Published: 2021-05-24 DOI: 10.1038/s41596-021-00554-w

high-throughput

antibody isolation

infectious pathogens

neutralizing antibodies

openPrimeR

AI 解读

Supplementary information

Supplementary Information

Supplementary Tables 1–9.

Reporting Summary

Generation of mouse–human chimeric embryos

Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting

Generation of CRISPR–Cas9-mediated genetic knockout human intestinal tissue–derived enteroid lines by lentivirus transduction and single-cell cloning

A puromycin-dependent activity-based sensing probe for histochemical staining of hydrogen peroxide in cells and animal tissues

Decoding personal biotic and abiotic airborne exposome

A clinically relevant model of focal embolic cerebral ischemia by thrombus and thrombolysis in rhesus monkeys

Bioengineering human intestinal mucosal grafts using patient-derived organoids, fibroblasts and scaffolds

Biomimetic tail-to-head terpene cyclizations using the resorcin[4]arene capsule catalyst

Neuroscience robotics for controlled induction and real-time assessment of hallucinations

Scanorama: integrating large and diverse single-cell transcriptomic datasets

Single-cell RNA sequencing (scRNA-seq)（单细胞RNA测序）

Data integration（数据集成）

Heterogeneity（异质性）

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References

Supplementary information

Mire, C. E. et al. Human-monoclonal-antibody therapy protects nonhuman primates against advanced Lassa fever. Nat. Med. 23, 1146–1149 (2017).
Grilo, A. L. & Mantalaris, A. The increasingly human and profitable monoclonal antibody market. Trends Biotechnol 37, 9–16 (2019).
Kaplon, H., Muralidharan, M., Schneider, Z. & Reichert, J. M. Antibodies to watch in 2020. MAbs 12, 1703531 (2020).
Corti, D. et al. Cross-neutralization of four paramyxoviruses by a human monoclonal antibody. Nature 501, 439–443 (2013).
Smith, S. A. et al. Isolation and characterization of broad and ultrapotent human monoclonal antibodies with therapeutic activity against Chikungunya virus. Cell Host Microbe 18, 86–95 (2015).
Stettler, K. et al. Specificity, cross-reactivity, and function of antibodies elicited by Zika virus infection. Science 353, 823–826 (2016).
Mendoza, P. et al. Combination therapy with anti-HIV-1 antibodies maintains viral suppression. Nature 561, 479–484 (2018).
Bournazos, S. et al. Broadly neutralizing anti-HIV-1 antibodies require Fc effector functions for in vivo activity. Cell 158, 1243–1253 (2014).
van Erp, E. A., Luytjes, W., Ferwerda, G. & van Kasteren, P. B. Fc-mediated antibody effector functions during respiratory syncytial virus infection and disease. Front. Immunol. 10, 548 (2019).
Asokan, M. et al. Fc-mediated effector function contributes to the in vivo antiviral effect of an HIV neutralizing antibody. Proc. Natl Acad. Sci. USA 117, 18754–18763 (2020).
Keizer, R. J., Huitema, A. D. R., Schellens, J. H. M. & Beijnen, J. H. Clinical pharmacokinetics of therapeutic monoclonal antibodies. Clin. Pharmacokinet. 49, 493–507 (2010).
Ryman, J. T. & Meibohm, B. Pharmacokinetics of monoclonal antibodies. CPT Pharmacometrics Syst. Pharmacol. 6, 576–588 (2017).
Cohen, Y. Z. et al. Safety, pharmacokinetics, and immunogenicity of the combination of the broadly neutralizing anti-HIV-1 antibodies 3BNC117 and 10-1074 in healthy adults: A randomized, phase 1 study. PLoS ONE 14, e0219142 (2019).
Pelegrin, M., Naranjo-Gomez, M. & Piechaczyk, M. Antiviral monoclonal antibodies: can they be more than simple neutralizing agents? Trends Microbiol. 23, 653–665 (2015).
Panda, S. & Ding, J. L. Natural antibodies bridge innate and adaptive immunity. J. Immunol. 194, 13–20 (2015).
Zuniga, E. I., Macal, M., Lewis, G. M. & Harker, J. A. Innate and adaptive immune regulation during chronic viral infections. Annu. Rev. Virol. 2, 573–597 (2015).
Küppers, R., Zhao, M., Hansmann, M. L. & Rajewsky, K. Tracing B cell development in human germinal centres by molecular analysis of single cells picked from histological sections. EMBO J. 12, 4955–4967 (1993).
Wardemann, H. et al. Predominant autoantibody production by early human B cell precursors. Science 301, 1374–1377 (2003).
Smith, K. et al. Rapid generation of fully human monoclonal antibodies specific to a vaccinating antigen. Nat. Protoc. 4, 372–384 (2009).
von Boehmer, L. et al. Sequencing and cloning of antigen-specific antibodies from mouse memory B cells. Nat. Protoc. 11, 1908–1923 (2016).
Mascola, J. R. et al. Protection of macaques against pathogenic simian/human immunodeficiency virus 89.6PD by passive transfer of neutralizing antibodies. J. Virol. 73, 4009–4018 (1999).
Mascola, J. R. et al. Protection of macaques against vaginal transmission of a pathogenic HIV-1/SIV chimeric virus by passive infusion of neutralizing antibodies. Nat. Med. 6, 207–210 (2000).
Balazs, A. B. et al. Antibody-based protection against HIV infection by vectored immunoprophylaxis. Nature 481, 81–84 (2011).
Schepens, B. et al. Nanobodies® specific for respiratory syncytial virus fusion protein protect against infection by inhibition of fusion. J. Infect. Dis. 204, 1692–1701 (2011).
Detalle, L. et al. Generation and characterization of ALX-0171, a potent novel therapeutic nanobody for the treatment of respiratory syncytial virus infection. Antimicrob. Agents Chemother. 60, 6–13 (2016).
Paules, C. I. et al. The hemagglutinin A stem antibody MEDI8852 prevents and controls disease and limits transmission of pandemic influenza viruses. J. Infect. Dis. 216, 356–365 (2017).
Van Heeke, G. et al. Nanobodies® as inhaled biotherapeutics for lung diseases. Pharmacol. Ther. 169, 47–56 (2017).
Walker, L. M. & Burton, D. R. Passive immunotherapy of viral infections: ‘super-antibodies’ enter the fray. Nat. Rev. Immunol. 18, 297–308 (2018).
Graham, B. S., Gilman, M. S. A. & McLellan, J. S. Structure-based vaccine antigen design. Annu. Rev. Med. 70, 91–104 (2019).
Kreer, C., Gruell, H., Mora, T., Walczak, A. M. & Klein, F. Exploiting B cell receptor analyses to inform on HIV-1 vaccination strategies. Vaccines 8, 13 (2020).
Gaebler, C. et al. Isolation of HIV-1-reactive antibodies using cell surface-expressed gp160Δc(BaL.). J. Immunol. Methods 397, 47–54 (2013).
Corti, D. et al. Prophylactic and postexposure efficacy of a potent human monoclonal antibody against MERS coronavirus. Proc. Natl Acad. Sci. USA 112, 10473–10478 (2015).
Xiao, X. et al. A novel antibody discovery platform identifies anti-influenza A broadly neutralizing antibodies from human memory B cells. MAbs 8, 916–927 (2016).
Ehrhardt, S. A. et al. Polyclonal and convergent antibody response to Ebola virus vaccine rVSV-ZEBOV. Nat. Med. 25, 1589–1600 (2019).
Schoofs, T. et al. Broad and potent neutralizing antibodies recognize the silent face of the HIV envelope. Immunity 50, 1513–1529.e9 (2019).
Schommers, P. et al. Restriction of HIV-1 escape by a highly broad and potent neutralizing antibody. Cell 180, 471–489.e22 (2020).
Kreer, C. et al. Longitudinal isolation of potent near-germline SARS-CoV-2-neutralizing antibodies from COVID-19 patients. Cell 182, 843–854.e12 (2020).
Rogers, T. F. et al. Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model. Science 369, 956–963 (2020).
Babcook, J. S., Leslie, K. B., Olsen, O. A., Salmon, R. A. & Schrader, J. W. A novel strategy for generating monoclonal antibodies from single, isolated lymphocytes producing antibodies of defined specificities. Proc. Natl Acad. Sci. USA 93, 7843–7848 (1996).
Harding, F. A., Stickler, M. M., Razo, J. & DuBridge, R. B. The immunogenicity of humanized and fully human antibodies: residual immunogenicity resides in the CDR regions. MAbs 2, 256–265 (2010).
Laffleur, B., Pascal, V., Sirac, C. & Cogné, M. Production of human or humanized antibodies in mice. Methods Mol. Biol. 901, 149–159 (2012).
Tiller, T. et al. Efficient generation of monoclonal antibodies from single human B cells by single cell RT-PCR and expression vector cloning. J. Immunol. Methods 329, 112–124 (2008).
Joyce, M. G. et al. Vaccine-induced antibodies that neutralize group 1 and group 2 influenza A viruses. Cell 166, 609–623 (2016).
Robbiani, D. F. et al. Recurrent potent human neutralizing antibodies to Zika virus in Brazil and Mexico. Cell 169, 597–609.e11 (2017).
Theobald, S. J. et al. Repertoire characterization and validation of gB-specific human IgGs directly cloned from humanized mice vaccinated with dendritic cells and protected against HCMV. PLoS Pathog. 16, e1008560 (2020).
Döring, M., Kreer, C., Lehnen, N., Klein, F. & Pfeifer, N. Modeling the amplification of immunoglobulins through machine learning on sequence-specific features. Sci. Rep. 9, 10748 (2019).
Kreer, C. et al. openPrimeR for multiplex amplification of highly diverse templates. J. Immunol. Methods 480, 112752 (2020).
Scheid, J. F. et al. Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding. Science 333, 1633–1637 (2011).
Liao, H.-X. et al. High-throughput isolation of immunoglobulin genes from single human B cells and expression as monoclonal antibodies. J. Virol. Methods 158, 171–179 (2009).
Sanders, R. W. et al. A next-generation cleaved, soluble HIV-1 Env trimer, BG505 SOSIP.664 gp140, expresses multiple epitopes for broadly neutralizing but not non-neutralizing antibodies. PLoS Pathog. 9, e1003618 (2013).
Lan, J. et al. Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor. Nature 581, 215–220 (2020).
Pallesen, J. et al. Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen. Proc. Natl Acad. Sci. USA 114, E7348–E7357 (2017).
Scherer, E. M. et al. Characteristics of memory B cells elicited by a highly efficacious HPV vaccine in subjects with no pre-existing immunity. PLoS Pathog. 10, e1004461 (2014).
Bornholdt, Z. A. et al. Isolation of potent neutralizing antibodies from a survivor of the 2014 Ebola virus outbreak. Science 351, 1078–1083 (2016).
Gilman, M. S. A. et al. Rapid profiling of RSV antibody repertoires from the memory B cells of naturally infected adult donors. Sci. Immunol. 1, eaaj1879 (2016).
Andrews, S. F. et al. Preferential induction of cross-group influenza A hemagglutinin stem-specific memory B cells after H7N9 immunization in humans. Sci. Immunol. 2, eaan2676 (2017).
Dussupt, V. et al. Potent Zika and dengue cross-neutralizing antibodies induced by Zika vaccination in a dengue-experienced donor. Nat. Med. 26, 228–235 (2020).
Ma, K. et al. Multiple functions of B cells in the pathogenesis of systemic lupus erythematosus. Int. J. Mol. Sci. 20, 6021 (2019).
Tipton, C. M., Hom, J. R., Fucile, C. F., Rosenberg, A. F. & Sanz, I. Understanding B-cell activation and autoantibody repertoire selection in systemic lupus erythematosus: a B-cell immunomics approach. Immunol. Rev. 284, 120–131 (2018).
Marston, B., Palanichamy, A. & Anolik, J. H. B cells in the pathogenesis and treatment of rheumatoid arthritis. Curr. Opin. Rheumatol. 22, 307–315 (2010).
Sharonov, G. V., Serebrovskaya, E. O., Yuzhakova, D. V., Britanova, O. V. & Chudakov, D. M. B cells, plasma cells and antibody repertoires in the tumour microenvironment. Nat. Rev. Immunol. 20, 294–307 (2020).
Scheid, J. F. et al. A method for identification of HIV gp140 binding memory B cells in human blood. J. Immunol. Methods 343, 65–67 (2009).
Huse, W. D. et al. Generation of a large combinatorial library of the immunoglobulin repertoire in phage lambda. Science 246, 1275–1281 (1989).
Boder, E. T. & Wittrup, K. D. Yeast surface display for screening combinatorial polypeptide libraries. Nat. Biotechnol. 15, 553–557 (1997).
Wiesner, M. et al. Conditional immortalization of human B cells by CD40 ligation. PLoS ONE 3, e1464 (2008).
Huang, J. et al. Identification of a CD4-binding-site antibody to HIV that evolved near-pan neutralization breadth. Immunity 45, 1108–1121 (2016).
Wec, A. Z. et al. Antibodies from a human survivor define sites of vulnerability for broad protection against ebolaviruses. Cell 169, 878–890.e15 (2017).
McCafferty, J., Griffiths, A. D., Winter, G. & Chiswell, D. J. Phage antibodies: filamentous phage displaying antibody variable domains. Nature 348, 552–554 (1990).
Kwakkenbos, M. J., van Helden, P. M., Beaumont, T. & Spits, H. Stable long-term cultures of self-renewing B cells and their applications. Immunol. Rev. 270, 65–77 (2016).
Doria-Rose, N. A. et al. New member of the V1V2-directed CAP256-VRC26 lineage that shows increased breadth and exceptional potency. J. Virol. 90, 76–91 (2016).
Kwakkenbos, M. J. et al. Generation of stable monoclonal antibody-producing B cell receptor-positive human memory B cells by genetic programming. Nat. Med. 16, 123–128 (2010).
Corti, D. et al. A neutralizing antibody selected from plasma cells that binds to group 1 and group 2 influenza A hemagglutinins. Science 333, 850–856 (2011).
Kwong, P. D. & Mascola, J. R. Human antibodies that neutralize HIV-1: identification, structures, and B cell ontogenies. Immunity 37, 412–425 (2012).
Sok, D. et al. Rapid elicitation of broadly neutralizing antibodies to HIV by immunization in cows. Nature 548, 108–111 (2017).
Zhao, X. et al. Immunization-elicited broadly protective antibody reveals Ebolavirus fusion loop as a site of vulnerability. Cell 169, 891–904.e15 (2017).
Ye, J., Ma, N., Madden, T. L. & Ostell, J. M. IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res. 41, W34–W40 (2013).
Lefranc, M. P. et al. IMGT, the international ImMunoGeneTics database. Nucleic Acids Res. 27, 209–212 (1999).
Hsieh, C.-L. et al. Structure-based design of prefusion-stabilized SARS-CoV-2 spikes. Science 369, 1501–1505 (2020).
Giudicelli, V., Chaume, D. & Lefranc, M.-P. IMGT/V-QUEST, an integrated software program for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis. Nucleic Acids Res. 32, W435–W440 (2004).

Effective high-throughput isolation of fully human antibodies targeting infectious pathogens

Supplementary information

Supplementary Information

Reporting Summary

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