Mechanism of glycoform specificity and in vivo protection by an anti-afucosylated IgG nanobody

Gupta, Aaron; Kao, Kevin S.; Yamin, Rachel; Oren, Deena A.; Goldgur, Yehuda; Du, Jonathan; Lollar, Pete; Sundberg, Eric J.; Ravetch, Jeffrey V.

doi:10.1038/s41467-023-38453-1

Title: Mechanism of glycoform specificity and in vivo protection by an anti-afucosylated IgG nanobody

Journal Article · 17 May 2023 · Nature Communications

DOI: https://doi.org/10.1038/s41467-023-38453-1 · OSTI ID:1974279

Gupta, Aaron; Kao, Kevin S.; Yamin, Rachel;

; Goldgur, Yehuda; Du, Jonathan; Lollar, Pete;

;

Abstract Immunoglobulin G (IgG) antibodies contain a complex N -glycan embedded in the hydrophobic pocket between its heavy chain protomers. This glycan contributes to the structural organization of the Fc domain and determines its specificity for Fcγ receptors, thereby dictating distinct cellular responses. The variable construction of this glycan structure leads to highly-related, but non-equivalent glycoproteins known as glycoforms. We previously reported synthetic nanobodies that distinguish IgG glycoforms. Here, we present the structure of one such nanobody, X0, in complex with the Fc fragment of afucosylated IgG1. Upon binding, the elongated CDR3 loop of X0 undergoes a conformational shift to access the buried N -glycan and acts as a ‘glycan sensor’, forming hydrogen bonds with the afucosylated IgG N -glycan that would otherwise be sterically hindered by the presence of a core fucose residue. Based on this structure, we designed X0 fusion constructs that disrupt pathogenic afucosylated IgG1-FcγRIIIa interactions and rescue mice in a model of dengue virus infection.

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Research Organization:: Brookhaven National Laboratory (BNL), Upton, NY (United States). National Synchrotron Light Source II (NSLS-II)

Sponsoring Organization:: Bill and Melinda Gates Foundation; National Institute of Allergy and Infectious Diseases; National Institute of General Medical Sciences; National Institute of General Medical Sciences (NIGMS); National Institutes of Health (NIH); USDOE; USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0012704

OSTI ID:: 1974279

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 14; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (64)

Application of Lectin Microarrays for Biomarker Discovery Dang, Kai; Zhang, Wenjuan; Jiang, Shanfeng ChemistryOpen, Vol. 9, Issue 3 https://doi.org/10.1002/open.201900326	journal	March 2020
Calculating Sedimentation Coefficient Distributions by Direct Modeling of Sedimentation Velocity Concentration Profiles Dam, Julie; Schuck, Peter Methods in Enzymology https://doi.org/10.1016/S0076-6879(04)84012-6	book	January 2004
Analytical Ultracentrifugation: Sedimentation Velocity and Sedimentation Equilibrium Cole, James L.; Lary, Jeffrey W.; Moody, Thomas P. Biophysical Tools for Biologists, Volume One: In Vitro Techniques, p. 143-179 https://doi.org/10.1016/S0091-679X(07)84006-4	book	January 2008
Benralizumab, an anti-interleukin-5 receptor α monoclonal antibody, as add-on treatment for patients with severe, uncontrolled, eosinophilic asthma (CALIMA): a randomised, double-blind, placebo-controlled phase 3 trial FitzGerald, J. Mark; Bleecker, Eugene R.; Nair, Parameswaran The Lancet, Vol. 388, Issue 10056 https://doi.org/10.1016/S0140-6736(16)31322-8	journal	October 2016
Engineered Sialylation of Pathogenic Antibodies In Vivo Attenuates Autoimmune Disease Pagan, Jose D.; Kitaoka, Maya; Anthony, Robert M. Cell, Vol. 172, Issue 3 https://doi.org/10.1016/j.cell.2017.11.041	journal	January 2018
Fc Glycan-Mediated Regulation of Placental Antibody Transfer Jennewein, Madeleine F.; Goldfarb, Ilona; Dolatshahi, Sepideh Cell, Vol. 178, Issue 1 https://doi.org/10.1016/j.cell.2019.05.044	journal	June 2019
Tools for mammalian glycoscience research Griffin, Matthew E.; Hsieh-Wilson, Linda C. Cell, Vol. 185, Issue 15 https://doi.org/10.1016/j.cell.2022.06.016	journal	July 2022
Enhanced Infection of Liver Sinusoidal Endothelial Cells in a Mouse Model of Antibody-Induced Severe Dengue Disease Zellweger, Raphaël M.; Prestwood, Tyler R.; Shresta, Sujan Cell Host & Microbe, Vol. 7, Issue 2 https://doi.org/10.1016/j.chom.2010.01.004	journal	February 2010
The bovine antibody repertoire Zhao, Yaofeng; Jackson, Stephen M.; Aitken, Robert Developmental & Comparative Immunology, Vol. 30, Issue 1-2 https://doi.org/10.1016/j.dci.2005.06.012	journal	January 2006
The Immunoregulatory Roles of Antibody Glycosylation Jennewein, Madeleine F.; Alter, Galit Trends in Immunology, Vol. 38, Issue 5 https://doi.org/10.1016/j.it.2017.02.004	journal	May 2017
Perspectives on Anti-Glycan Antibodies Gleaned from Development of a Community Resource Database Sterner, Eric; Flanagan, Natalie; Gildersleeve, Jeffrey C. ACS Chemical Biology, Vol. 11, Issue 7 https://doi.org/10.1021/acschembio.6b00244	journal	May 2016
Antibody Fucosylation Lowers the FcγRIIIa/CD16a Affinity by Limiting the Conformations Sampled by the N162-Glycan Falconer, Daniel J.; Subedi, Ganesh P.; Marcella, Aaron M. ACS Chemical Biology, Vol. 13, Issue 8 https://doi.org/10.1021/acschembio.8b00342	journal	July 2018
Revisiting the Role of Glycosylation in the Structure of Human IgG Fc Borrok, M. Jack; Jung, Sang Taek; Kang, Tae Hyun ACS Chemical Biology, Vol. 7, Issue 9 https://doi.org/10.1021/cb300130k	journal	June 2012
The 3.2-Å crystal structure of the human IgG1 Fc fragment–FcγRIII complex Sondermann, Peter; Huber, Robert; Oosthuizen, Vaughan Nature, Vol. 406, Issue 6793 https://doi.org/10.1038/35018508	journal	July 2000
Rapid elicitation of broadly neutralizing antibodies to HIV by immunization in cows Sok, Devin; Le, Khoa M.; Vadnais, Melissa Nature, Vol. 548, Issue 7665 https://doi.org/10.1038/nature23301	journal	July 2017
Type I and type II Fc receptors regulate innate and adaptive immunity Pincetic, Andrew; Bournazos, Stylianos; DiLillo, David J. Nature Immunology, Vol. 15, Issue 8 https://doi.org/10.1038/ni.2939	journal	July 2014
Regulation of autoantibody activity by the IL-23–TH17 axis determines the onset of autoimmune disease Pfeifle, René; Rothe, Tobias; Ipseiz, Natacha Nature Immunology, Vol. 18, Issue 1 https://doi.org/10.1038/ni.3579	journal	November 2016
FcγRIIB in autoimmunity and infection: evolutionary and therapeutic implications Smith, Kenneth G. C.; Clatworthy, Menna R. Nature Reviews Immunology, Vol. 10, Issue 5 https://doi.org/10.1038/nri2762	journal	May 2010
Afucosylated Plasmodium falciparum-specific IgG is induced by infection but not by subunit vaccination Larsen, Mads Delbo; Lopez-Perez, Mary; Dickson, Emmanuel Kakra Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-26118-w	journal	October 2021
Extensive substrate recognition by the streptococcal antibody-degrading enzymes IdeS and EndoS Sudol, Abigail S. L.; Butler, John; Ivory, Dylan P. Nature Communications, Vol. 13, Issue 1 https://doi.org/10.1038/s41467-022-35340-z	journal	December 2022
Improved protein structure prediction using potentials from deep learning Senior, Andrew W.; Evans, Richard; Jumper, John Nature, Vol. 577, Issue 7792 https://doi.org/10.1038/s41586-019-1923-7	journal	January 2020
Sialylation of immunoglobulin E is a determinant of allergic pathogenicity Shade, Kai-Ting C.; Conroy, Michelle E.; Washburn, Nathaniel Nature, Vol. 582, Issue 7811 https://doi.org/10.1038/s41586-020-2311-z	journal	May 2020
Fc-optimized antibodies elicit CD8 immunity to viral respiratory infection Bournazos, Stylianos; Corti, Davide; Virgin, Herbert W. Nature, Vol. 588, Issue 7838 https://doi.org/10.1038/s41586-020-2838-z	journal	October 2020
Highly accurate protein structure prediction with AlphaFold Jumper, John; Evans, Richard; Pritzel, Alexander Nature https://doi.org/10.1038/s41586-021-03819-2	journal	July 2021
Target protein deglycosylation in living cells by a nanobody-fused split O-GlcNAcase Ge, Yun; Ramirez, Daniel H.; Yang, Bo Nature Chemical Biology, Vol. 17, Issue 5 https://doi.org/10.1038/s41589-021-00757-y	journal	March 2021
Proinflammatory IgG Fc structures in patients with severe COVID-19 Chakraborty, Saborni; Gonzalez, Joseph; Edwards, Karlie Nature Immunology, Vol. 22, Issue 1 https://doi.org/10.1038/s41590-020-00828-7	journal	November 2020
Yeast surface display platform for rapid discovery of conformationally selective nanobodies McMahon, Conor; Baier, Alexander S.; Pascolutti, Roberta Nature Structural & Molecular Biology, Vol. 25, Issue 3 https://doi.org/10.1038/s41594-018-0028-6	journal	February 2018
Conformational effects of N-glycan core fucosylation of immunoglobulin G Fc region on its interaction with Fcγ receptor IIIa Sakae, Yoshitake; Satoh, Tadashi; Yagi, Hirokazu Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-13845-8	journal	October 2017
Glycosylation, Hypogammaglobulinemia, and Resistance to Viral Infections Sadat, Mohammed A.; Moir, Susan; Chun, Tae-Wook New England Journal of Medicine, Vol. 370, Issue 17 https://doi.org/10.1056/NEJMoa1302846	journal	April 2014
Obinutuzumab for the First-Line Treatment of Follicular Lymphoma Marcus, Robert; Davies, Andrew; Ando, Kiyoshi New England Journal of Medicine, Vol. 377, Issue 14 https://doi.org/10.1056/NEJMoa1614598	journal	October 2017
Agalactosylated IgG antibodies depend on cellular Fc receptors for in vivo activity Nimmerjahn, Falk; Anthony, Robert M.; Ravetch, Jeffrey V. Proceedings of the National Academy of Sciences, Vol. 104, Issue 20 https://doi.org/10.1073/pnas.0702936104	journal	May 2007
Monoclonal antibody-mediated enhancement of dengue virus infectionin vitroandin vivoand strategies for prevention Goncalvez, Ana P.; Engle, Ronald E.; St. Claire, Marisa Proceedings of the National Academy of Sciences, Vol. 104, Issue 22 https://doi.org/10.1073/pnas.0703498104	journal	May 2007
Aglycosylated immunoglobulin G1 variants productively engage activating Fc receptors Sazinsky, S. L.; Ott, R. G.; Silver, N. W. Proceedings of the National Academy of Sciences, Vol. 105, Issue 51 https://doi.org/10.1073/pnas.0809257105	journal	December 2008
Antibody recognition of a unique tumor-specific glycopeptide antigen Brooks, Cory L.; Schietinger, Andrea; Borisova, Svetlana N. Proceedings of the National Academy of Sciences, Vol. 107, Issue 22 https://doi.org/10.1073/pnas.0915176107	journal	May 2010
Unique carbohydrate-carbohydrate interactions are required for high affinity binding between Fc RIII and antibodies lacking core fucose Ferrara, C.; Grau, S.; Jager, C. Proceedings of the National Academy of Sciences, Vol. 108, Issue 31 https://doi.org/10.1073/pnas.1108455108	journal	July 2011
General mechanism for modulating immunoglobulin effector function Sondermann, P.; Pincetic, A.; Maamary, J. Proceedings of the National Academy of Sciences, Vol. 110, Issue 24 https://doi.org/10.1073/pnas.1307864110	journal	May 2013
Modulating IgG effector function by Fc glycan engineering Li, Tiezheng; DiLillo, David J.; Bournazos, Stylianos Proceedings of the National Academy of Sciences, Vol. 114, Issue 13 https://doi.org/10.1073/pnas.1702173114	journal	March 2017
FcRn, but not FcγRs, drives maternal-fetal transplacental transport of human IgG antibodies Borghi, Sara; Bournazos, Stylianos; Thulin, Natalie K. Proceedings of the National Academy of Sciences, Vol. 117, Issue 23 https://doi.org/10.1073/pnas.2004325117	journal	May 2020
Synthetic nanobodies as angiotensin receptor blockers McMahon, Conor; Staus, Dean P.; Wingler, Laura M. Proceedings of the National Academy of Sciences, Vol. 117, Issue 33 https://doi.org/10.1073/pnas.2009029117	journal	August 2020
Synthetic nanobodies as tools to distinguish IgG Fc glycoforms Kao, Kevin S.; Gupta, Aaron; Zong, Guanghui Proceedings of the National Academy of Sciences, Vol. 119, Issue 48 https://doi.org/10.1073/pnas.2212658119	journal	November 2022
The Carbohydrate at FcγRIIIa Asn-162: AN ELEMENT REQUIRED FOR HIGH AFFINITY BINDING TO NON-FUCOSYLATED IgG GLYCOFORMS Ferrara, Claudia; Stuart, Fiona; Sondermann, Peter Journal of Biological Chemistry, Vol. 281, Issue 8 https://doi.org/10.1074/jbc.M510171200	journal	December 2005
Dengue viruses and mononuclear phagocytes. I. Infection enhancement by non-neutralizing antibody Halstead, Sb; O'Rourke, Ej Journal of Experimental Medicine, Vol. 146, Issue 1 https://doi.org/10.1084/jem.146.1.201	journal	July 1977
A single glycan on IgE is indispensable for initiation of anaphylaxis Shade, Kai-Ting C.; Platzer, Barbara; Washburn, Nathaniel Journal of Experimental Medicine, Vol. 212, Issue 4 https://doi.org/10.1084/jem.20142182	journal	March 2015
Protein glycosylation: nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds Spiro, R. G. Glycobiology, Vol. 12, Issue 4 https://doi.org/10.1093/glycob/12.4.43R	journal	April 2002
In Vivo Enhancement of Dengue Virus Infection in Rhesus Monkeys by Passively Transferred Antibody Halstead, S. B. Journal of Infectious Diseases, Vol. 140, Issue 4 https://doi.org/10.1093/infdis/140.4.527	journal	October 1979
The role of differential IgG glycosylation in the interaction of antibodies with FcγRs in vivo Anthony, Robert M.; Nimmerjahn, Falk Current Opinion in Organ Transplantation, Vol. 16, Issue 1 https://doi.org/10.1097/MOT.0b013e328342538f	journal	February 2011
Characterization of a model of lethal dengue virus 2 infection in C57BL/6 mice deficient in the alpha/beta interferon receptor Orozco, Susana; Schmid, Michael A.; Parameswaran, Poornima Journal of General Virology, Vol. 93, Issue 10 https://doi.org/10.1099/vir.0.045088-0	journal	October 2012
Ublituximab (TG-1101), a novel glycoengineered anti-CD20 antibody, in combination with ibrutinib is safe and highly active in patients with relapsed and/or refractory chronic lymphocytic leukaemia: results of a phase 2 trial Sharman, Jeff P.; Farber, Charles M.; Mahadevan, Daruka British Journal of Haematology, Vol. 176, Issue 3 https://doi.org/10.1111/bjh.14447	journal	December 2016
Recapitulation of IVIG Anti-Inflammatory Activity with a Recombinant IgG Fc Anthony, R. M.; Nimmerjahn, F.; Ashline, D. J. Science, Vol. 320, Issue 5874 https://doi.org/10.1126/science.1154315	journal	April 2008
IgG antibodies to dengue enhanced for FcγRIIIA binding determine disease severity Wang, Taia T.; Sewatanon, Jaturong; Memoli, Matthew J. Science, Vol. 355, Issue 6323 https://doi.org/10.1126/science.aai8128	journal	January 2017
Antibody-dependent enhancement of severe dengue disease in humans Katzelnick, Leah C.; Gresh, Lionel; Halloran, M. Elizabeth Science, Vol. 358, Issue 6365 https://doi.org/10.1126/science.aan6836	journal	November 2017
Antibody fucosylation predicts disease severity in secondary dengue infection Bournazos, Stylianos; Vo, Hoa Thi My; Duong, Veasna Science, Vol. 372, Issue 6546 https://doi.org/10.1126/science.abc7303	journal	June 2021
An ultrapotent synthetic nanobody neutralizes SARS-CoV-2 by stabilizing inactive Spike Schoof, Michael; Faust, Bryan; Saunders, Reuben A. Science https://doi.org/10.1126/science.abe3255	journal	November 2020
Early non-neutralizing, afucosylated antibody responses are associated with COVID-19 severity Chakraborty, Saborni; Gonzalez, Joseph C.; Sievers, Benjamin L. Science Translational Medicine, Vol. 14, Issue 635 https://doi.org/10.1126/scitranslmed.abm7853	journal	March 2022
Defining New Therapeutics Using a More Immunocompetent Mouse Model of Antibody-Enhanced Dengue Virus Infection Pinto, Amelia K.; Brien, James D.; Lam, Chia-Ying Kao mBio, Vol. 6, Issue 5 https://doi.org/10.1128/mBio.01316-15	journal	October 2015
Functional diversification of IgGs through Fc glycosylation Wang, Taia T.; Ravetch, Jeffrey V. Journal of Clinical Investigation, Vol. 129, Issue 9 https://doi.org/10.1172/JCI130029	journal	September 2019
A prominent lack of IgG1-Fc fucosylation of platelet alloantibodies in pregnancy Kapur, Rick; Kustiawan, Iwan; Vestrheim, Anne Blood, Vol. 123, Issue 4 https://doi.org/10.1182/blood-2013-09-527978	journal	January 2014
A Multilaboratory Comparison of Calibration Accuracy and the Performance of External References in Analytical Ultracentrifugation Zhao, Huaying; Ghirlando, Rodolfo; Alfonso, Carlos PLOS ONE, Vol. 10, Issue 5 https://doi.org/10.1371/journal.pone.0126420	journal	May 2015
Lethal Antibody Enhancement of Dengue Disease in Mice Is Prevented by Fc Modification Balsitis, Scott J.; Williams, Katherine L.; Lachica, Ruben PLoS Pathogens, Vol. 6, Issue 2 https://doi.org/10.1371/journal.ppat.1000790	journal	February 2010
Immunologic Basis for Long HCDR3s in Broadly Neutralizing Antibodies Against HIV-1 Yu, Lei; Guan, Yongjun Frontiers in Immunology, Vol. 5 https://doi.org/10.3389/fimmu.2014.00250	journal	June 2014
Decoding the Human Immunoglobulin G-Glycan Repertoire Reveals a Spectrum of Fc-Receptor- and Complement-Mediated-Effector Activities Dekkers, Gillian; Treffers, Louise; Plomp, Rosina Frontiers in Immunology, Vol. 8 https://doi.org/10.3389/fimmu.2017.00877	journal	August 2017
Coevolved Canonical Loops Conformations of Single-Domain Antibodies: A Tale of Three Pockets Playing Musical Chairs Gaudreault, Francis; Corbeil, Christopher R.; Purisima, Enrico O. Frontiers in Immunology, Vol. 13 https://doi.org/10.3389/fimmu.2022.884132	journal	June 2022
Core Fucosylation of IgG B Cell Receptor Is Required for Antigen Recognition and Antibody Production Li, Wenzhe; Yu, Rui; Ma, Biao The Journal of Immunology, Vol. 194, Issue 6 https://doi.org/10.4049/jimmunol.1402678	journal	February 2015
Association of FcγRIIa Polymorphism with Clinical Outcome of Dengue Infection: First Insight from Pakistan Mohsin, Saima Naz; Saleem, Mahjabeen; Ghafoor, Farkhanda The American Journal of Tropical Medicine and Hygiene, Vol. 93, Issue 4 https://doi.org/10.4269/ajtmh.15-0199	journal	October 2015

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Title: Mechanism of glycoform specificity and in vivo protection by an anti-afucosylated IgG nanobody

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