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Yom A, Chiang A, Lewis NE. Boltzmann Model Predicts Glycan Structures from Lectin Binding. Anal Chem 2024; 96:8332-8341. [PMID: 38720429 PMCID: PMC11162346 DOI: 10.1021/acs.analchem.3c04992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2024]
Abstract
Glycans are complex oligosaccharides that are involved in many diseases and biological processes. Unfortunately, current methods for determining glycan composition and structure (glycan sequencing) are laborious and require a high level of expertise. Here, we assess the feasibility of sequencing glycans based on their lectin binding fingerprints. By training a Boltzmann model on lectin binding data, we predict the approximate structures of 88 ± 7% of N-glycans and 87 ± 13% of O-glycans in our test set. We show that our model generalizes well to the pharmaceutically relevant case of Chinese hamster ovary (CHO) cell glycans. We also analyze the motif specificity of a wide array of lectins and identify the most and least predictive lectins and glycan features. These results could help streamline glycoprotein research and be of use to anyone using lectins for glycobiology.
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Affiliation(s)
- Aria Yom
- Department of Physics, University of California, San Diego, California 92093, United States
| | - Austin Chiang
- Department of Pediatrics, University of California, San Diego, California 92093, United States
- Immunology Center of Georgia, Augusta University, Augusta, Georgia 30912, United States
- Department of Medicine, Augusta University, Augusta, Georgia 30912, United States
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, California 92093, United States
- Department of Bioengineering, University of California, San Diego, California 92093, United States
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2
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Yom A, Chiang A, Lewis NE. A Boltzmann model predicts glycan structures from lectin binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.03.543532. [PMID: 37333412 PMCID: PMC10274649 DOI: 10.1101/2023.06.03.543532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Glycans are complex oligosaccharides involved in many diseases and biological processes. Unfortunately, current methods for determining glycan composition and structure (glycan sequencing) are laborious and require a high level of expertise. Here, we assess the feasibility of sequencing glycans based on their lectin binding fingerprints. By training a Boltzmann model on lectin binding data, we predict the approximate structures of 88 ± 7% of N-glycans and 87 ± 13% of O-glycans in our test set. We show that our model generalizes well to the pharmaceutically relevant case of Chinese Hamster Ovary (CHO) cell glycans. We also analyze the motif specificity of a wide array of lectins and identify the most and least predictive lectins and glycan features. These results could help streamline glycoprotein research and be of use to anyone using lectins for glycobiology.
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Affiliation(s)
- Aria Yom
- Department of Physics, University of California, San Diego. CA 92093, USA
| | - Austin Chiang
- Department of Pediatrics, University of California, San Diego. CA 92093, USA
- Immunology Center of Georgia, Augusta University, Augusta, GA 30912, USA
- Department of Medicine, Augusta University, Augusta, GA 30912, USA
| | - Nathan E Lewis
- Department of Bioengineering, University of California, San Diego. CA 92093, USA
- Department of Pediatrics, University of California, San Diego. CA 92093, USA
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3
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Knorr DA, Blanchard L, Leidner RS, Jensen SM, Meng R, Jones A, Ballesteros-Merino C, Bell RB, Baez M, Marino A, Sprott D, Bifulco CB, Piening B, Dahan R, Osorio JC, Fox BA, Ravetch JV. FcγRIIB Is an Immune Checkpoint Limiting the Activity of Treg-Targeting Antibodies in the Tumor Microenvironment. Cancer Immunol Res 2024; 12:322-333. [PMID: 38147316 PMCID: PMC10911703 DOI: 10.1158/2326-6066.cir-23-0389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 10/10/2023] [Accepted: 12/21/2023] [Indexed: 12/27/2023]
Abstract
Preclinical murine data indicate that fragment crystallizable (Fc)-dependent depletion of intratumoral regulatory T cells (Treg) is a major mechanism of action of anti-CTLA-4. However, the two main antibodies administered to patients (ipilimumab and tremelimumab) do not recapitulate these effects. Here, we investigate the underlying mechanisms responsible for the limited Treg depletion observed with these therapies. Using an immunocompetent murine model humanized for CTLA-4 and Fcγ receptors (FcγR), we show that ipilimumab and tremelimumab exhibit limited Treg depletion in tumors. Immune profiling of the tumor microenvironment (TME) in both humanized mice and humans revealed high expression of the inhibitory Fc receptor, FcγRIIB, which limits antibody-dependent cellular cytotoxicity/phagocytosis. Blocking FcγRIIB in humanized mice rescued the Treg-depleting capacity and antitumor activity of ipilimumab. Furthermore, Fc engineering of antibodies targeting Treg-associated targets (CTLA-4 or CCR8) to minimize FcγRIIB binding significantly enhanced Treg depletion, resulting in increased antitumor activity across various tumor models. Our results define the inhibitory FcγRIIB as an immune checkpoint limiting antibody-mediated Treg depletion in the TME, and demonstrate Fc engineering as an effective strategy to overcome this limitation and improve the efficacy of Treg-targeting antibodies.
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Affiliation(s)
- David A. Knorr
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lucas Blanchard
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, New York
| | - Rom S. Leidner
- Earle A. Chiles Research Institute (a division of Providence Cancer Institute), Portland, Oregon
| | - Shawn M. Jensen
- Earle A. Chiles Research Institute (a division of Providence Cancer Institute), Portland, Oregon
| | - Ryan Meng
- Earle A. Chiles Research Institute (a division of Providence Cancer Institute), Portland, Oregon
| | - Andrew Jones
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, New York
| | | | - Richard B. Bell
- Earle A. Chiles Research Institute (a division of Providence Cancer Institute), Portland, Oregon
| | - Maria Baez
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, New York
| | - Alessandra Marino
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, New York
| | - David Sprott
- Earle A. Chiles Research Institute (a division of Providence Cancer Institute), Portland, Oregon
| | - Carlo B. Bifulco
- Earle A. Chiles Research Institute (a division of Providence Cancer Institute), Portland, Oregon
| | - Brian Piening
- Earle A. Chiles Research Institute (a division of Providence Cancer Institute), Portland, Oregon
| | - Rony Dahan
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Juan C. Osorio
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bernard A. Fox
- Earle A. Chiles Research Institute (a division of Providence Cancer Institute), Portland, Oregon
| | - Jeffrey V. Ravetch
- Laboratory of Molecular Genetics and Immunology, Rockefeller University, New York, New York
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Tong M, Liu P, Li C, Zhang Z, Sun W, Dong P, Fan N, Wang X, Liu J, Lv C, Cao Z, Wang Y. Interaction of Asn297-Linked Glycan Ligands with the Fc Fragment of the Immunoglobulin Class G1: A Molecular Dynamics Simulation Study. J Chem Inf Model 2024; 64:785-798. [PMID: 38262973 DOI: 10.1021/acs.jcim.3c01584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
The allosteric modulation of the homodimeric H10-03-6 protein to glycan ligands L1 and L2, and the STAB19 protein to glycan ligands L3 and L4, respectively, has been studied by molecular dynamics simulations and free energy calculations. The results revealed that the STAB19 protein has a significantly higher affinity for L3 (-11.38 ± 2.32 kcal/mol) than that for L4 (-5.51 ± 1.92 kcal/mol). However, the combination of the H10-03-6 protein with glycan L2 (1.23 ± 6.19 kcal/mol) is energetically unfavorable compared with that of L1 (-13.96 ± 0.35 kcal/mol). Further, the binding of glycan ligands L3 and L4 to STAB19 would result in the significant closure of the two CH2 domains of the STAB19 conformation with the decrease of the centroid distances between the two CH2 domains compared with the H10-03-6/L1/L2 complex. The CH2 domain closure of STAB19 relates directly to the formation of new hydrogen bonds and hydrophobic interactions between the residues Ser239, Val240, Asp265, Glu293, Asn297, Thr299, Ser337, Asp376, Thr393, Pro395, and Pro396 in STAB19 and glycan ligands L3 and L4, which suggests that these key residues would contribute to the specific regulation of STAB19 to L3 and L4. In addition, the distance analysis revealed that the EF loop in the H10-03-6/L1/L2 model presents a high flexibility and partial disorder compared with the stabilized STAB19/L3/L4 complex. These results will be helpful in understanding the specific regulation through the asymmetric structural characteristics in the CH2 and CH3 domains of the H10-03-6 and STAB19 proteins.
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Affiliation(s)
- Mingqiong Tong
- Shandong Engineering Research Center of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou 253023, China
| | - Peng Liu
- Faculty of Electrical Engineering, Universiti Teknologi Malaysia, UTM, Johor Bahru, Johor Darul Takzim 81310, Malaysia
- The Office of Academic Affairs, Dezhou University, Dezhou 253023, China
| | - Chaoqun Li
- Hebei Key Laboratory of Heterocyclic Compounds, College of Chemistry, Chemical Engineering and Materials, Handan University, Handan, Hebei 056005, China
| | - Zhongyu Zhang
- Shandong Engineering Research Center of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou 253023, China
| | - Wan Sun
- Shandong Engineering Research Center of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou 253023, China
| | - Pingxuan Dong
- Shandong Engineering Research Center of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou 253023, China
| | - Na Fan
- Shandong Engineering Research Center of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou 253023, China
| | - Xiaoyue Wang
- Shandong Engineering Research Center of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou 253023, China
| | - Jing Liu
- Shandong Engineering Research Center of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou 253023, China
| | - Chao Lv
- College of Chemistry and Chemical Engineering, Dezhou University, Dezhou 253023, China
| | - Zanxia Cao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Yan Wang
- College of Chemistry, Beijing Normal University, 19# Xinjiekouwai Street, Beijing 100875, China
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Kanto N, Ohkawa Y, Kitano M, Maeda K, Shiida M, Ono T, Ota F, Kizuka Y, Kunimasa K, Nishino K, Mukai M, Seike M, Azuma A, Harada Y, Fukuda T, Gu J, Taniguchi N. A highly specific antibody against the core fucose of the N-glycan in IgG identifies the pulmonary diseases and its regulation by CCL2. J Biol Chem 2023; 299:105365. [PMID: 37865317 PMCID: PMC10663832 DOI: 10.1016/j.jbc.2023.105365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 10/01/2023] [Accepted: 10/09/2023] [Indexed: 10/23/2023] Open
Abstract
Glycan structure is often modulated in disease or predisease states, suggesting that such changes might serve as biomarkers. Here, we generated a monoclonal antibody (mAb) against the core fucose of the N-glycan in human IgG. Notably, this mAb can be used in Western blotting and ELISA. ELISA using this mAb revealed a low level of the core fucose of the N-glycan in IgG, suggesting that the level of acore fucosylated (noncore fucosylated) IgG was increased in the sera of the patients with lung cancer, chronic obstructive pulmonary disease, and interstitial pneumonia compared to healthy subjects. In a coculture analysis using human lung adenocarcinoma A549 cells and antibody-secreting B cells, the downregulation of the FUT8 (α1,6 fucosyltransferase) gene and a low level of core fucose of the N-glycan in IgG in antibody-secreting B cells were observed after coculture. A dramatic alteration in gene expression profiles for cytokines, chemokines, and their receptors were also observed after coculturing, and we found that the identified C-C motif chemokine 2 was partially involved in the downregulation of the FUT8 gene and the low level of core fucose of the N-glycan in IgG in antibody-secreting B cells. We also developed a latex turbidimetric immunoassay using this mAb. These results suggest that communication with C-C motif chemokine 2 between lung cells and antibody-secreting B cells downregulate the level of core fucose of the N-glycan in IgG, i.e., the increased level of acore fucosylated (noncore fucosylated) IgG, which would be a novel biomarker for the diagnosis of patients with pulmonary diseases.
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Affiliation(s)
- Noriko Kanto
- Depertment of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, Osaka, Japan
| | - Yuki Ohkawa
- Depertment of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, Osaka, Japan
| | - Masato Kitano
- Depertment of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, Osaka, Japan; Department of Molecular Biochemistry and Clinical Investigation, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Kento Maeda
- Depertment of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, Osaka, Japan
| | - Masafumi Shiida
- Research and Development Division, Minaris Medical Co, Ltd, Shizuoka, Japan
| | - Tatsuya Ono
- Research and Development Division, Minaris Medical Co, Ltd, Shizuoka, Japan
| | - Fumi Ota
- Disease Glycomics Team, Global Research Cluster, RIKEN, Saitama, Japan
| | - Yasuhiko Kizuka
- Institute for Glyco-core Research, Gifu University, Gifu, Japan
| | - Kei Kunimasa
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Kazumi Nishino
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Mikio Mukai
- Deparetment of Medical Check-up, Osaka International Cancer Institute, Osaka, Japan
| | - Masahiro Seike
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Arata Azuma
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Yoichiro Harada
- Depertment of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, Osaka, Japan
| | - Tomohiko Fukuda
- Division of Regulatory Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
| | - Jianguo Gu
- Division of Regulatory Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, Sendai, Miyagi, Japan
| | - Naoyuki Taniguchi
- Depertment of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, Osaka, Japan.
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Edgar JE, Trezise S, Anthony RM, Krammer F, Palese P, Ravetch JV, Bournazos S. Antibodies elicited in humans upon chimeric hemagglutinin-based influenza virus vaccination confer FcγR-dependent protection in vivo. Proc Natl Acad Sci U S A 2023; 120:e2314905120. [PMID: 37871218 PMCID: PMC10622865 DOI: 10.1073/pnas.2314905120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 09/19/2023] [Indexed: 10/25/2023] Open
Abstract
Antibody responses against highly conserved epitopes on the stalk domain of influenza virus hemagglutinin (HA) confer broad protection; however, such responses are limited. To effectively induce stalk-specific immunity against conserved HA epitopes, sequential immunization strategies have been developed based on chimeric HA (cHA) constructs featuring different head domains but the same stalk regions. Immunogenicity studies in small animal models, as well as in humans, revealed that cHA immunogens elicit stalk-specific IgG responses with broad specificity against heterologous influenza virus strains. However, the mechanisms by which these antibodies confer in vivo protection and the contribution of their Fc effector function remain unclear. To characterize the role of Fc-FcγR (Fcγ receptor) interactions to the in vivo protective activity of IgG antibodies elicited in participants in a phase I trial of a cHA vaccine candidate, we performed passive transfer studies of vaccine-elicited IgG antibodies in mice humanized for all classes of FcγRs, as well as in mice deficient for FcγRs. IgG antibodies elicited upon cHA vaccination completely protected FcγR humanized mice against lethal influenza virus challenge, while no protection was evident in FcγR-deficient mice, suggesting a major role for FcγR pathways in the protective function of vaccine-elicited IgG antibodies. These findings have important implications for influenza vaccine development, guiding the design of vaccination approaches with the capacity to elicit IgG responses with optimal Fc effector function.
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Affiliation(s)
- Julia E. Edgar
- Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, NY10065
| | - Stephanie Trezise
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA02129
| | - Robert M. Anthony
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA02129
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY10029
- Center for Vaccine Research and Pandemic Preparedness, Icahn School of Medicine at Mount Sinai, New York, NY10029
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY10029
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY10029
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY10029
| | - Jeffrey V. Ravetch
- Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, NY10065
| | - Stylianos Bournazos
- Laboratory of Molecular Genetics and Immunology, The Rockefeller University, New York, NY10065
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Ionescu RE. Ultrasensitive Electrochemical Immunosensors Using Nanobodies as Biocompatible Sniffer Tools of Agricultural Contaminants and Human Disease Biomarkers. MICROMACHINES 2023; 14:1486. [PMID: 37630022 PMCID: PMC10456424 DOI: 10.3390/mi14081486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023]
Abstract
Nanobodies (Nbs) are known as camelid single-domain fragments or variable heavy chain antibodies (VHH) that in vitro recognize the antigens (Ag) similar to full-size antibodies (Abs) and in vivo allow immunoreactions with biomolecule cavities inaccessible to conventional Abs. Currently, Nbs are widely used for clinical treatments due to their remarkably improved performance, ease of production, thermal robustness, superior physical and chemical properties. Interestingly, Nbs are also very promising bioreceptors for future rapid and portable immunoassays, compared to those using unstable full-size antibodies. For all these reasons, Nbs are excellent candidates in ecological risk assessments and advanced medicine, enabling the development of ultrasensitive biosensing platforms. In this review, immobilization strategies of Nbs on conductive supports for enhanced electrochemical immune detection of food contaminants (Fcont) and human biomarkers (Hbio) are discussed. In the case of Fcont, the direct competitive immunoassay detection using coating antigen solid surface is the most commonly used approach for efficient Nbs capture which was characterized with cyclic voltammetry (CV) and differential pulse voltammetry (DPV) when the signal decays for increasing concentrations of free antigen prepared in aqueous solutions. In contrast, for the Hbio investigations on thiolated gold electrodes, increases in amperometric and electrochemical impedance spectroscopy (EIS) signals were recorded, with increases in the antigen concentrations prepared in PBS or spiked real human samples.
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Affiliation(s)
- Rodica Elena Ionescu
- Light, Nanomaterials and Nanotechnology (L2n) Laboratory, CNRS EMR 7004, University of Technology of Troyes, 12 Rue Marie Curie CS 42060, 10004 Troyes, France
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Gupta A, Kao KS, Yamin R, Oren DA, Goldgur Y, Du J, Lollar P, Sundberg EJ, Ravetch JV. Mechanism of glycoform specificity and in vivo protection by an anti-afucosylated IgG nanobody. Nat Commun 2023; 14:2853. [PMID: 37202422 PMCID: PMC10195009 DOI: 10.1038/s41467-023-38453-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/03/2023] [Indexed: 05/20/2023] Open
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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Affiliation(s)
- Aaron Gupta
- Laboratory of Molecular Genetics & Immunology, The Rockefeller University, New York, NY, USA
| | - Kevin S Kao
- Laboratory of Molecular Genetics & Immunology, The Rockefeller University, New York, NY, USA
| | - Rachel Yamin
- Laboratory of Molecular Genetics & Immunology, The Rockefeller University, New York, NY, USA
| | - Deena A Oren
- Structural Biology Resource Center, The Rockefeller University, New York, NY, USA
| | - Yehuda Goldgur
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jonathan Du
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Pete Lollar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric J Sundberg
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Jeffrey V Ravetch
- Laboratory of Molecular Genetics & Immunology, The Rockefeller University, New York, NY, USA.
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Gupta A, Kao K, Yamin R, Oren DA, Goldgur Y, Du J, Lollar P, Sundberg EJ, Ravetch JV. Mechanism of glycoform specificity and protection against antibody dependent enhancement by an anti-afucosylated IgG nanobody. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.23.525277. [PMID: 36747840 PMCID: PMC9900767 DOI: 10.1101/2023.01.23.525277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Immunoglobulin G (IgG) antibodies contain a single, complex N -glycan on each IgG heavy chain protomer embedded in the hydrophobic pocket between its Cγ2 domains. The presence of this glycan contributes to the structural organization of the Fc domain and determines its specificity for Fcγ receptors, thereby determining distinct cellular responses. On the Fc, the variable construction of this glycan structure leads to a family of highly-related, but non-equivalent glycoproteins known as glycoforms. We previously reported the development of synthetic nanobodies that distinguish IgG glycoforms without cross-reactivity to off-target glycoproteins or free glycans. Here, we present the X-ray crystal structure of one such nanobody, X0, in complex with its specific binding partner, the Fc fragment of afucosylated IgG1. Two X0 nanobodies bind a single afucosylated Fc homodimer at the upper Cγ2 domain, making both protein-protein and protein-carbohydrate contacts and overlapping the binding site for Fcγ receptors. 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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