Multi-compartmental diversification of neutralizing antibody lineages dissected in SARS-CoV-2 spike-immunized macaques.
Animals
Spike Glycoprotein, Coronavirus
/ immunology
Macaca mulatta
Antibodies, Neutralizing
/ immunology
SARS-CoV-2
/ immunology
B-Lymphocytes
/ immunology
Antibodies, Viral
/ immunology
Phylogeny
Antibodies, Monoclonal
/ immunology
Epitopes
/ immunology
COVID-19
/ immunology
Humans
COVID-19 Vaccines
/ immunology
Receptors, Antigen, B-Cell
/ immunology
Somatic Hypermutation, Immunoglobulin
Immunization
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
27 Jul 2024
27 Jul 2024
Historique:
received:
15
02
2024
accepted:
03
07
2024
medline:
28
7
2024
pubmed:
28
7
2024
entrez:
27
7
2024
Statut:
epublish
Résumé
The continued evolution of SARS-CoV-2 underscores the need to understand qualitative aspects of the humoral immune response elicited by spike immunization. Here, we combine monoclonal antibody (mAb) isolation with deep B cell receptor (BCR) repertoire sequencing of rhesus macaques immunized with prefusion-stabilized spike glycoprotein. Longitudinal tracing of spike-sorted B cell lineages in multiple immune compartments demonstrates increasing somatic hypermutation and broad dissemination of vaccine-elicited B cells in draining and non-draining lymphoid compartments, including the bone marrow, spleen and, most notably, periaortic lymph nodes. Phylogenetic analysis of spike-specific monoclonal antibody lineages identified through deep repertoire sequencing delineates extensive intra-clonal diversification that shaped neutralizing activity. Structural analysis of the spike in complex with a broadly neutralizing mAb provides a molecular basis for the observed differences in neutralization breadth between clonally related antibodies. Our findings highlight that immunization leads to extensive intra-clonal B cell evolution where members of the same lineage can both retain the original epitope specificity and evolve to recognize additional spike variants not previously encountered.
Identifiants
pubmed: 39068149
doi: 10.1038/s41467-024-50286-0
pii: 10.1038/s41467-024-50286-0
doi:
Substances chimiques
Spike Glycoprotein, Coronavirus
0
Antibodies, Neutralizing
0
Antibodies, Viral
0
spike protein, SARS-CoV-2
0
Antibodies, Monoclonal
0
Epitopes
0
COVID-19 Vaccines
0
Receptors, Antigen, B-Cell
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
6338Subventions
Organisme : Svenska Forskningsrådet Formas (Swedish Research Council Formas)
ID : 2018-05973
Organisme : Svenska Forskningsrådet Formas (Swedish Research Council Formas)
ID : 2018-02381
Organisme : Svenska Forskningsrådet Formas (Swedish Research Council Formas)
ID : 2017-00968
Organisme : Svenska Forskningsrådet Formas (Swedish Research Council Formas)
ID : 2017-6702
Organisme : Svenska Forskningsrådet Formas (Swedish Research Council Formas)
ID : 2018-3808
Organisme : Svenska Forskningsrådet Formas (Swedish Research Council Formas)
ID : 2022-06725
Organisme : Svenska Forskningsrådet Formas (Swedish Research Council Formas)
ID : 2017-00968
Organisme : Svenska Forskningsrådet Formas (Swedish Research Council Formas)
ID : 2017-6702
Organisme : Svenska Forskningsrådet Formas (Swedish Research Council Formas)
ID : 2018-3808
Organisme : EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
ID : 101003653
Organisme : EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
ID : 101003653
Organisme : Science for Life Laboratory (SciLifeLab)
ID : VC-2022-0028
Organisme : Science for Life Laboratory (SciLifeLab)
ID : VC-2022-0028
Organisme : Familjen Erling-Perssons Stiftelse (Erling-Persson Family Foundation)
ID : 20210125
Organisme : Familjen Erling-Perssons Stiftelse (Erling-Persson Family Foundation)
ID : 20210125
Informations de copyright
© 2024. The Author(s).
Références
Karlsson Hedestam, G. B. et al. The challenges of eliciting neutralizing antibodies to HIV-1 and to influenza virus. Nat. Rev. Microbiol. 6, 143–155 (2008).
pubmed: 18197170
doi: 10.1038/nrmicro1819
Bq, O. et al. Enhanced neutralization resistance of SARS-CoV-2 Enhanced neutralization resistance of SARS-CoV-2 Omicron subvariants. Cell Host Microbe https://doi.org/10.1016/j.chom.2022.11.012 (2022).
Tuekprakhon, A. et al. Antibody escape of SARS-CoV-2 Omicron BA.4 and BA.5 from vaccine and BA.1 serum. Cell 185, 2422–2433.e13 (2022).
pubmed: 35772405
pmcid: 9181312
doi: 10.1016/j.cell.2022.06.005
Hachmann, N. P. et al. Neutralization escape by SARS-CoV-2 omicron subvariants BA.2.12.1, BA.4, and BA.5. N. Engl. J. Med. 387, 86–88 (2022).
pubmed: 35731894
doi: 10.1056/NEJMc2206576
Shrestha, L. B., Foster, C., Rawlinson, W., Tedla, N. & Bull, R. A. Evolution of the SARS-CoV-2 omicron variants BA.1 to BA.5: implications for immune escape and transmission. Rev. Med. Virol. 32, e2381 (2022).
pubmed: 35856385
pmcid: 9349777
doi: 10.1002/rmv.2381
Cao, Y. et al. Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75. Cell Host Microbe 30, 1527–1539.e5 (2022).
pubmed: 36270286
pmcid: 9531665
doi: 10.1016/j.chom.2022.09.018
Sheward, D. J. et al. Sensitivity of the SARS-CoV-2 BA.2.86 variant to prevailing neutralising antibody responses. Lancet Infect. Dis. 23, e462–e463 (2023).
pubmed: 37776877
doi: 10.1016/S1473-3099(23)00588-1
Sheward, D. J. et al. Evasion of neutralising antibodies by omicron sublineage BA.2.75. Lancet Infect. Dis. 22, 1421–1422 (2022).
pubmed: 36058228
pmcid: 9436366
doi: 10.1016/S1473-3099(22)00524-2
Sheward, D. J. et al. Omicron sublineage BA.2.75.2 exhibits extensive escape from neutralising antibodies. Lancet Infect. Dis. 22, 1538–1540 (2022).
pubmed: 36244347
pmcid: 9560757
doi: 10.1016/S1473-3099(22)00663-6
Roemer, C. et al. SARS-CoV-2 evolution in the Omicron era. Nat. Microbiol. 8, 1952–1959 (2023).
pubmed: 37845314
doi: 10.1038/s41564-023-01504-w
Tas, J. M. J. et al. Visualizing antibody affinity maturation in germinal centers. Science 351, 1048–1054 (2016).
pubmed: 26912368
pmcid: 4938154
doi: 10.1126/science.aad3439
Victora, G. D. et al. Germinal center dynamics revealed by multiphoton microscopy with a photoactivatable fluorescent reporter. Cell 143, 592–605 (2010).
pubmed: 21074050
pmcid: 3035939
doi: 10.1016/j.cell.2010.10.032
Sheward, D. J. et al. Structural basis of Omicron neutralization by affinity-matured public antibodies. bioRxiv https://doi.org/10.1101/2022.01.03.474825 (2022).
Korenkov, M. et al. Somatic hypermutation introduces bystander mutations that prepare SARS-CoV-2 antibodies for emerging variants. Immunity https://doi.org/10.1016/j.immuni.2023.11.004 (2023).
Chernyshev, M. et al. Vaccination of SARS-CoV-2-infected individuals expands a broad range of clonally diverse affinity-matured B cell lineages. Nat. Commun. 14, 2249 (2023).
pubmed: 37076511
pmcid: 10115384
doi: 10.1038/s41467-023-37972-1
Phad, G. E. et al. Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses. J. Exp. Med. 217, e20191155 (2020).
pubmed: 31704807
doi: 10.1084/jem.20191155
Sacks, D. et al. Somatic hypermutation to counter a globally rare viral immunotype drove off-track antibodies in the CAP256-VRC26 HIV-1 V2-directed bNAb lineage. PLoS Pathog. 15, 1–20 (2019).
doi: 10.1371/journal.ppat.1008005
Bhiman, J. N. et al. Viral variants that initiate and drive maturation of V1V2-directed HIV-1 broadly neutralizing antibodies. Nat. Med. 21, 1332–1336 (2015).
pubmed: 26457756
pmcid: 4637988
doi: 10.1038/nm.3963
Sok, D. et al. The effects of somatic hypermutation on neutralization and binding in the PGT121 family of broadly neutralizing HIV antibodies. PLoS Pathog. 9, e1003754 (2013).
pubmed: 24278016
pmcid: 3836729
doi: 10.1371/journal.ppat.1003754
Turner, J. S. et al. SARS-CoV-2 infection induces long-lived bone marrow plasma cells in humans. Nature 595, 421–425 (2021).
pubmed: 34030176
doi: 10.1038/s41586-021-03647-4
Schulz, A. R. et al. SARS-CoV-2 specific plasma cells acquire long-lived phenotypes in human bone marrow. EBioMedicine 95, 104735 (2023).
pubmed: 37556944
pmcid: 10432952
doi: 10.1016/j.ebiom.2023.104735
Prabhakaran, M. et al. Adjuvanted SARS- 2 spike protein vaccination elicits long-lived plasma cells in nonhuman primates. Sci. Transl. Med. 16, 5960 (2024).
Mandolesi, M. et al. SARS-CoV-2 protein subunit vaccination of mice and rhesus macaques elicits potent and durable neutralizing antibody responses. Cell Rep. Med. 2, 100252 (2021).
pubmed: 33842900
pmcid: 8020888
doi: 10.1016/j.xcrm.2021.100252
Corcoran, M. M. et al. Production of individualized v gene databases reveals high levels of immunoglobulin genetic diversity. Nat. Commun. 7, 13642 (2016).
pubmed: 27995928
pmcid: 5187446
doi: 10.1038/ncomms13642
Chernyshev, M., Kaduk, M., Corcoran, M. & Karlsson Hedestam, G. B. VDJ gene usage in IgM repertoires of rhesus and cynomolgus macaques. Front. Immunol. 12, 815680 (2022).
pubmed: 35087534
pmcid: 8786739
doi: 10.3389/fimmu.2021.815680
Gangavarapu, K. et al. Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations. Nat. Methods 20, 512–522 (2023).
pubmed: 36823332
pmcid: 10399614
doi: 10.1038/s41592-023-01769-3
Li, D. et al. Breadth of SARS-CoV-2 neutralization and protection induced by a nanoparticle vaccine. Nat. Commun. 13, 6309 (2022).
Rappaport, A. R. et al. Low-dose self-amplifying mRNA COVID-19 vaccine drives strong protective immunity in non-human primates against SARS-CoV-2 infection. Nat. Commun. 13, 1–10 (2022).
doi: 10.1038/s41467-022-31005-z
Corbett, K. S. et al. Evaluation of the mRNA-1273 vaccine against SARS-CoV-2 in Nonhuman Primates. N. Engl. J. Med. 383, 1544–1555 (2020).
pubmed: 32722908
doi: 10.1056/NEJMoa2024671
King, H. A. D. et al. Efficacy and breadth of adjuvanted SARS-CoV-2 receptor-binding domain nanoparticle vaccine in macaques. Proc. Natl Acad. Sci. USA 118, 1–11 (2021).
doi: 10.1073/pnas.2106433118
van Doremalen, N. et al. ChAdOx1 nCoV-19 vaccine prevents SARS-CoV-2 pneumonia in rhesus macaques. Nature 586, 578–582 (2020).
pubmed: 32731258
pmcid: 8436420
doi: 10.1038/s41586-020-2608-y
Waickman, A. T. et al. mRNA-1273 vaccination protects against SARS-CoV-2-elicited lung inflammation in nonhuman primates. JCI Insight 7, e160039 (2022).
Guebre-Xabier, M. et al. NVX-CoV2373 vaccine protects cynomolgus macaque upper and lower airways against SARS-CoV-2 challenge. Vaccine 38, 7892–7896 (2020).
pubmed: 33139139
pmcid: 7584426
doi: 10.1016/j.vaccine.2020.10.064
Yadav, P. D. et al. Immunogenicity and protective efficacy of inactivated SARS-CoV-2 vaccine candidate, BBV152 in rhesus macaques. Nat. Commun. 12, 1–11 (2021).
doi: 10.1038/s41467-021-21639-w
Francica, J. R. et al. Protective antibodies elicited by SARS-CoV-2 spike protein vaccination are boosted in the lung after challenge in nonhuman primates. Sci. Transl. Med. 13, 1–18 (2021).
doi: 10.1126/scitranslmed.abi4547
Joyce, M. G. et al. A SARS-CoV-2 ferritin nanoparticle vaccine elicits protective immune responses in nonhuman primates. Sci. Transl. Med. 14, 1–16 (2022).
doi: 10.1126/scitranslmed.abi5735
Corbett, K. S. et al. Protection against SARS-CoV-2 Beta variant in mRNA-1273 vaccine–boosted nonhuman primates. Science (1979) 374, 1343–1353 (2021).
Liu, J. et al. CD8 T cells contribute to vaccine protection against SARS-CoV-2 in macaques. Sci. Immunol. 7, eabq7647 (2022).
Garrido, C. et al. SARS-CoV-2 vaccines elicit durable immune responses in infant rhesus macaques. Sci. Immunol. 6, 1–17 (2021).
doi: 10.1126/sciimmunol.abj3684
Corbett, K. S. et al. mRNA-1273 protects against SARS-CoV-2 beta infection in nonhuman primates. Nat. Immunol. 22, 1306–1315 (2021).
pubmed: 34417590
pmcid: 8488000
doi: 10.1038/s41590-021-01021-0
Yu, J. et al. DNA vaccine protection against SARS-CoV-2 in rhesus macaques. Science (1979) 369, 806–811 (2020).
Vázquez Bernat, N. et al. Rhesus and cynomolgus macaque immunoglobulin heavy-chain genotyping yields comprehensive databases of germline VDJ alleles. Immunity 54, 355-366.e4 (2021).
He, W. T. et al. Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques. Sci. Transl. Med. 14, eabl9605 (2022).
Feng, Y. et al. Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine. Sci. Transl. Med. 15, eadg7404 (2023).
Sankhala, R. S. et al. Diverse array of neutralizing antibodies elicited upon Spike Ferritin Nanoparticle vaccination in rhesus macaques. Nat. Commun. 15, 1–19 (2024).
doi: 10.1038/s41467-023-44265-0
Galson, J. D. et al. B-cell repertoire dynamics after sequential hepatitis B vaccination and evidence for cross-reactive B-cell activation. Genome Med. 8, 1–13 (2016).
Ehrhardt, S. A. et al. Polyclonal and convergent antibody response to Ebola virus vaccine rVSV-ZEBOV. Nat. Med. 25, 1589–1600 (2019).
pubmed: 31591605
doi: 10.1038/s41591-019-0602-4
Zhang, Y. et al. Analysis of B cell receptor repertoires reveals key signatures of the systemic B cell response after SARS-CoV-2 infection. J. Virol. 96, e0160021 (2022).
Sundling, C. et al. Single-cell and deep sequencing of IgG-switched macaque B cells reveal a diverse Ig repertoire following Immunization. J. Immunol. 192, 3637–3644 (2014).
pubmed: 24623130
doi: 10.4049/jimmunol.1303334
Scharf, L. et al. Longitudinal single-cell analysis of SARS-CoV-2-reactive B cells uncovers persistence of early-formed, antigen-specific clones. JCI Insight 8, e165299 (2023).
Muecksch, F. et al. Affinity maturation of SARS-CoV-2 neutralizing antibodies confers potency, breadth, and resilience to viral escape mutations. Immunity 54, 1853–1868.e7 (2021).
pubmed: 34331873
pmcid: 8323339
doi: 10.1016/j.immuni.2021.07.008
Gaebler, C. et al. Evolution of antibody immunity to SARS-CoV-2. Nature 591, 639–644 (2021).
pubmed: 33461210
pmcid: 8221082
doi: 10.1038/s41586-021-03207-w
Luo, K. et al. Tissue memory B cell repertoire analysis after ALVAC/AIDSVAX B/E gp120 immunization of rhesus macaques. J. Clin. Investig. 1, 1–17 (2016).
Lindsay, K. E. et al. Visualization of early events in mRNA vaccine delivery in non-human primates via PET–CT and near-infrared imaging. Nat. Biomed. Eng. 3, 371–380 (2019).
pubmed: 30936432
doi: 10.1038/s41551-019-0378-3
Wu, G. C., Cheung, N. K. V., Georgiou, G., Marcotte, E. M. & Ippolito, G. C. Temporal stability and molecular persistence of the bone marrow plasma cell antibody repertoire. Nat. Commun. 7, 1–9 (2016).
doi: 10.1038/ncomms13838
Robinson, M. J. et al. Intrinsically determined turnover underlies broad heterogeneity in plasma-cell lifespan. Immunity 56, 1596–1612.e4 (2023).
pubmed: 37164016
doi: 10.1016/j.immuni.2023.04.015
Robinson, M. J. et al. Long-lived plasma cells accumulate in the bone marrow at a constant rate from early in an immune response. Sci. Immunol. 7, eabm8389 (2022).
Benet, Z., Jing, Z. & Fooksman, D. R. Plasma cell dynamics in the bone marrow niche. Cell Rep. 34, 108733 (2021).
pubmed: 33567286
pmcid: 8023250
doi: 10.1016/j.celrep.2021.108733
Song, G. et al. Cross-reactive serum and memory B-cell responses to spike protein in SARS-CoV-2 and endemic coronavirus infection. Nat. Commun. 12, 1–10 (2021).
Ng, K. W. et al. Preexisting and de novo humoral immunity to SARS-CoV-2 in humans. Science (1979) 370, 1339–1343 (2020).
Park, Y. J. et al. Imprinted antibody responses against SARS-CoV-2 Omicron sublineages. Science (1979) 378, 619–627 (2022).
Quandt, J. et al. Omicron BA.1 breakthrough infection drives cross-variant neutralization and memory B cell formation against conserved epitopes. Sci. Immunol. 7, 1–13 (2022).
doi: 10.1126/sciimmunol.abq2427
Weber, T. et al. Enhanced SARS-CoV-2 humoral immunity following breakthrough infection builds upon the preexisting memory B cell pool. Sci. Immunol. 8, 1–14 (2023).
doi: 10.1126/sciimmunol.adk5845
Longo, N. S. & Lipsky, P. E. Why do B cells mutate their immunoglobulin receptors? Trends Immunol. 27, 374–380 (2006).
pubmed: 16809065
doi: 10.1016/j.it.2006.06.007
Sheward, D. J. et al. Beta RBD boost broadens antibody-mediated protection against SARS-CoV-2 variants in animal models. Cell Rep. Med. 2, 100450 (2021).
Brochu, H. N. et al. Systematic profiling of full-length ig and tcr repertoire diversity in rhesus macaque through long read transcriptome sequencing. J. Immunol. 204, 3434–3444 (2020).
pubmed: 32376650
pmcid: 7276939
doi: 10.4049/jimmunol.1901256
Bernat, N. V. et al. High-quality library preparation for NGS-based immunoglobulin germline gene inference and repertoire expression analysis. Front Immunol 10, 660 (2019).
Kumar, V. et al. Long-read amplicon denoising. Nucleic Acids Res. 47, e104 (2019).
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
pubmed: 23329690
pmcid: 3603318
doi: 10.1093/molbev/mst010
Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2 - approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
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).
pubmed: 17996249
doi: 10.1016/j.jim.2007.09.017
Tegunov, D. & Cramer, P. Real-time cryo-electron microscopy data preprocessing with Warp. Nat. Methods 16, 1146–1152 (2019).
pubmed: 31591575
pmcid: 6858868
doi: 10.1038/s41592-019-0580-y
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. CryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
pubmed: 28165473
doi: 10.1038/nmeth.4169
Custódio, T. F. et al. Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2. Nat. Commun. 11, 5588 (2020).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
pubmed: 34265844
pmcid: 8371605
doi: 10.1038/s41586-021-03819-2
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).
pubmed: 20383002
pmcid: 2852313
doi: 10.1107/S0907444910007493
Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D Struct. Biol. 75, 861–877 (2019).
pubmed: 31588918
pmcid: 6778852
doi: 10.1107/S2059798319011471
Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018).
pubmed: 28710774
doi: 10.1002/pro.3235
Schrödinger, L. L. C. The {PyMOL} Molecular Graphics System, Version ~1.8 (2015).