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Mesonzhnik N, Belushenko A, Novikova P, Kukharenko A, Afonin M. Enhanced N-Glycan Profiling of Therapeutic Monoclonal Antibodies through the Application of Upper-Hinge Middle-Up Level LC-HRMS Analysis. Antibodies (Basel) 2024; 13:66. [PMID: 39189237 PMCID: PMC11348383 DOI: 10.3390/antib13030066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 07/29/2024] [Accepted: 07/31/2024] [Indexed: 08/28/2024] Open
Abstract
Therapeutic monoclonal antibodies (mAbs) are crucial in modern medicine due to their effectiveness in treating various diseases. However, the structural complexity of mAbs, particularly their glycosylation patterns, presents challenges for quality control and biosimilarity assessment. This study explores the use of upper-hinge middle-up (UHMU)-level ultra-high-performance liquid chromatography-high-resolution mass spectrometry (LC-HRMS) analysis to improve N-glycan profiling of mAbs. Two specific enzymes, known as IgG degradation enzymes (IGDEs), were used to selectively cleave therapeutic mAbs above the hinge region to separate antibody subunits for further Fc glycan analysis by means of the UHMU/LC-HRMS workflow. The complexity of the mass spectra of IGDEs-digested mAbs was significantly reduced compared to the intact MS level, enabling reliable assignment and relative quantitation of paired Fc glycoforms. The results of the UHMU/LC-HRMS analysis of nine approved therapeutics highlight the significance of this approach for in-depth glycoform profiling.
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Affiliation(s)
- Natalia Mesonzhnik
- Resource Centre of Analytical Methods, Laboratory Complex, Sirius University of Science and Technology, Olympic Ave. 1, 354340 Sochi, Russia; (P.N.); (M.A.)
| | - Anton Belushenko
- Federal Hygienic and Epidemiological Center of Rospotrebnadzor, Varshavskoe Highway 19a, 117105 Moscow, Russia;
| | - Polina Novikova
- Resource Centre of Analytical Methods, Laboratory Complex, Sirius University of Science and Technology, Olympic Ave. 1, 354340 Sochi, Russia; (P.N.); (M.A.)
| | - Alexey Kukharenko
- Laboratory of Pharmacokinetics and Metabolomic Analysis, Institute of Translational Medicine and Biotechnology, I.M. Sechenov First Moscow Medical University, 8/2 Trubetskaya, 119991 Moscow, Russia
| | - Mikhail Afonin
- Resource Centre of Analytical Methods, Laboratory Complex, Sirius University of Science and Technology, Olympic Ave. 1, 354340 Sochi, Russia; (P.N.); (M.A.)
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2
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Oganesyan I, Jenkins TP, Laustsen AH, Zenobi R, Harrison JA. Streamlining the Analysis of Proteins from Snake Venom. J Proteome Res 2024; 23:2367-2375. [PMID: 38814071 DOI: 10.1021/acs.jproteome.4c00013] [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] [Indexed: 05/31/2024]
Abstract
Investigating snake venom is necessary for developing new treatments for envenoming and harnessing the therapeutic potential that lies within venom toxins. Despite considerable efforts in previous research, several technical challenges remain for characterizing the individual components within such complex mixtures. Here, we present native and top-down mass spectrometry (MS) workflows that enable the analysis of individual venom proteins within complex mixtures and showcase the utility of these methodologies on King cobra (Ophiophagus hannah) venom. First, we coupled ion mobility spectrometry for separation and electron capture dissociation for charge reduction to resolve highly convoluted mass spectra containing multiple proteins with masses ranging from 55 to 127 kDa. Next, we performed a top-down glycomic analysis of a 25.5 kDa toxin, showing that this protein contains a fucosylated complex glycan. Finally, temperature-controlled nanoelectrospray mass spectrometry facilitated the top-down sequence analysis of a β-cardiotoxin, which cannot be fragmented by collisional energy due to its disulfide bond pattern. The work presented here demonstrates the applicability of new and promising MS methods for snake venom analysis.
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Affiliation(s)
- Irina Oganesyan
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Timothy P Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Andreas H Laustsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- VenomAid Diagnostics ApS, DK-2800 Kongens Lyngby, Denmark
| | - Renato Zenobi
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Julian A Harrison
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093 Zurich, Switzerland
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Ivanov DG, Cheung K, Kaltashov IA. Probing the Architecture of Multisubunit Protein Complexes with In-line Disulfide Reduction and Native MS Analysis. Anal Chem 2024; 96:8243-8248. [PMID: 38733603 DOI: 10.1021/acs.analchem.4c00879] [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: 05/13/2024]
Abstract
Native mass spectrometry (MS) continues to enjoy growing popularity as a means of providing a wealth of information on noncovalent biopolymer assemblies ranging from composition and binding stoichiometry to characterization of the topology of these assemblies. The latter frequently relies on supplementing MS measurements with limited fragmentation of the noncovalent complexes in the gas phase to identify the pairs of neighboring subunits. While this approach has met with much success in the past two decades, its implementation remains difficult (and the success record relatively modest) within one class of noncovalent assemblies: protein complexes in which at least one binding partner has multiple subunits cross-linked by disulfide bonds. We approach this problem by inducing chemical reduction of disulfide bonds under nondenaturing conditions in solution followed by native MS analysis with online buffer exchange to remove unconsumed reagents that are incompatible with the electrospray ionization process. While this approach works well with systems comprised of thiol-linked subunits that remain stable upon reduction of the disulfide bridges (such as immunoglobulins), chemical reduction frequently gives rise to species that are unstable (prone to aggregation). This problem is circumvented by taking advantage of the recently introduced cross-path reactive chromatography platform (XPRC), which allows the disulfide reduction to be carried out in-line, thereby minimizing the loss of metastable protein subunits and their noncovalent complexes with the binding partners prior to MS analysis. The feasibility of this approach is demonstrated using hemoglobin complexes with haptoglobin 1-1, a glycoprotein consisting of four polypeptide chains cross-linked by disulfide bonds.
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Affiliation(s)
- Daniil G Ivanov
- Department of Chemistry, University of Massachusetts─Amherst, Amherst, Massachusetts 01002, United States
| | - Kevin Cheung
- Department of Chemistry, University of Massachusetts─Amherst, Amherst, Massachusetts 01002, United States
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts─Amherst, Amherst, Massachusetts 01002, United States
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Nguyen SN, Le SH, Ivanov DG, Ivetic N, Nazy I, Kaltashov IA. Structural Characterization of a Pathogenic Antibody Underlying Vaccine-Induced Immune Thrombotic Thrombocytopenia (VITT). Anal Chem 2024; 96:6209-6217. [PMID: 38607319 DOI: 10.1021/acs.analchem.3c05253] [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: 04/13/2024]
Abstract
Vaccine-induced immune thrombotic thrombocytopenia (VITT) is a rare but dangerous side effect of adenoviral-vectored COVID-19 vaccines. VITT had been linked to production of autoantibodies recognizing platelet factor 4 (PF4). Here, we characterize anti-PF4 antibodies obtained from a VITT patient's blood. Intact mass measurements indicate that a significant fraction of these antibodies represent a limited number of clones. MS analysis of large antibody fragments (the light chain and the Fc/2 and Fd fragments of the heavy chain) confirms the monoclonal nature of this component of the anti-PF4 antibodies repertoire and reveals the presence of a mature complex biantennary N-glycan within the Fd segment. Peptide mapping using two complementary proteases and LC-MS/MS was used to determine the amino acid sequence of the entire light chain and over 98% of the heavy chain (excluding a short N-terminal segment). The sequence analysis allows the monoclonal antibody to be assigned to the IgG2 subclass and verifies that the light chain belongs to the λ-type. Incorporation of enzymatic de-N-glycosylation into the peptide mapping routine allows the N-glycan in the Fab region of the antibody to be localized to the framework 3 region of the VH domain. This novel N-glycosylation site is the result of a single mutation within the germline sequence. Peptide mapping also provides information on lower-abundance (polyclonal) components of the anti-PF4 antibody ensemble, revealing the presence of all four subclasses (IgG1-IgG4) and both types of the light chain (λ and κ). This case study demonstrates the power of combining the intact, middle-down, and bottom-up MS approaches for meaningful characterization of ultralow quantities of pathogenic antibodies extracted directly from patients' blood.
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Affiliation(s)
- Son N Nguyen
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Si-Hung Le
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Daniil G Ivanov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Nikola Ivetic
- Department of Medicine, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Ishac Nazy
- Department of Medicine, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
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Yang Y, Du Y, Ivanov D, Niu C, Clare R, Smith JW, Nazy I, Kaltashov IA. Molecular architecture and platelet-activating properties of small immune complexes assembled on heparin and platelet factor 4. Commun Biol 2024; 7:308. [PMID: 38467823 PMCID: PMC10928113 DOI: 10.1038/s42003-024-05982-4] [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: 02/21/2023] [Accepted: 02/27/2024] [Indexed: 03/13/2024] Open
Abstract
Heparin-induced thrombocytopenia (HIT) is an adverse reaction to heparin leading to a reduction in circulating platelets with an increased risk of thrombosis. It is precipitated by polymerized immune complexes consisting of pathogenic antibodies that recognize a small chemokine platelet factor 4 (PF4) bound to heparin. Characterization of these immune complexes is extremely challenging due to the enormous structural heterogeneity of such macromolecular assemblies and their constituents. Native mass spectrometry demonstrates that up to three PF4 tetramers can be assembled on a heparin chain, consistent with the molecular modeling studies showing facile polyanion wrapping along the polycationic belt on the PF4 surface. Although these assemblies can accommodate a maximum of only two antibodies, the resulting immune complexes are capable of platelet activation despite their modest size. Taken together, these studies provide further insight into molecular mechanisms of HIT and other immune disorders where anti-PF4 antibodies play a central role.
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Affiliation(s)
- Yang Yang
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Yi Du
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Daniil Ivanov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Chendi Niu
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Rumi Clare
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - James W Smith
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Ishac Nazy
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA.
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Yang Y, Ivanov DG, Levin MD, Olenyuk B, Cordova-Robles O, Cederstrom B, Schnitzer JE, Kaltashov IA. Characterization of Large Immune Complexes with Size Exclusion Chromatography and Native Mass Spectrometry Supplemented with Gas Phase Ion Chemistry. Anal Chem 2024. [PMID: 38319243 DOI: 10.1021/acs.analchem.3c03278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Large immune complexes formed by the cross-linking of antibodies with polyvalent antigens play critical roles in modulating cell-mediated immunity. While both the size and the shape of immune complexes are important determinants in Fc receptor-mediated signaling responsible for phagocytosis, degranulation, and, in some instances, autoimmune pathologies, their characterization remains extremely challenging due to their large size and structural heterogeneity. We use native mass spectrometry (MS) supplemented with limited charge reduction in the gas phase to determine the stoichiometry of immune complexes formed by a bivalent (homodimeric) antigen, a 163 kDa aminopeptidase P2 (APP2), and a monoclonal antibody (mAb) to APP2. The observed (APP2·mAb)n complexes populate a wide range of stoichiometries (n = 1-4) with the largest detected species exceeding 1 MDa, although the gas-phase dissociation products are also evident in the mass spectra. While frequently considering a nuisance that complicates interpretation of native MS data, limited dissociation provides an additional dimension for characterization of the immune complex quaternary structure. APP2/mAb associations with identical composition but slightly different elution times in size exclusion chromatography exhibit notable differences in their spontaneous fragmentation profiles. The latter indicates the presence of both extended linear and cyclized (APP2·mAb)n configurations. The unique ability of MS to distinguish between such isomeric structures will be invaluable for a variety of applications where the biological effects of immune complexes are determined by their ability to assemble Fc receptor clusters of certain density on cell surfaces, such as platelet activation by clustering the low-affinity receptors FcγRIIa on their surface.
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Affiliation(s)
- Yang Yang
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, USA
| | - Daniil G Ivanov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, USA
| | - Michael D Levin
- Proteogenomics Research Institute for Systems Medicine, La Jolla, California 92037, USA
| | - Bogdan Olenyuk
- Proteogenomics Research Institute for Systems Medicine, La Jolla, California 92037, USA
| | - Oscar Cordova-Robles
- Proteogenomics Research Institute for Systems Medicine, La Jolla, California 92037, USA
| | - Brittany Cederstrom
- Proteogenomics Research Institute for Systems Medicine, La Jolla, California 92037, USA
| | - Jan E Schnitzer
- Proteogenomics Research Institute for Systems Medicine, La Jolla, California 92037, USA
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, USA
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Nguyen SN, Le SH, Ivanov DG, Ivetic N, Nazy I, Kaltashov IA. Structural characterization of a pathogenic antibody underlying vaccine-induced immune thrombotic thrombocytopenia (VITT). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.28.542636. [PMID: 37398203 PMCID: PMC10312456 DOI: 10.1101/2023.05.28.542636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Vaccine-induced immune thrombotic thrombocytopenia (VITT) is a rare but extremely dangerous side effect that has been reported for several adenoviral (Ad)-vectored COVID-19 vaccines. VITT pathology had been linked to production of antibodies that recognize platelet factor 4 (PF4), an endogenous chemokine. In this work we characterize anti-PF4 antibodies obtained from a VITT patient's blood. Intact-mass MS measurements indicate that a significant fraction of this ensemble is comprised of antibodies representing a limited number of clones. MS analysis of large antibody fragments (the light chain, as well as the Fc/2 and Fd fragments of the heavy chain) confirms the monoclonal nature of this component of the anti-PF4 antibodies repertoire, and reveals the presence of a fully mature complex biantennary N-glycan within its Fd segment. Peptide mapping using two complementary proteases and LC-MS/MS analysis were used to determine the amino acid sequence of the entire light chain and over 98% of the heavy chain (excluding a short N-terminal segment). The sequence analysis allows the monoclonal antibody to be assigned to IgG2 subclass and verify that the light chain belongs to the λ-type. Incorporation of enzymatic de- N -glycosylation into the peptide mapping routine allows the N -glycan in the Fab region of the antibody to be localized to the framework 3 region of the V H domain. This novel N -glycosylation site (absent in the germline sequence) is a result of a single mutation giving rise to an NDT motif in the antibody sequence. Peptide mapping also provides a wealth of information on lower-abundance proteolytic fragments derived from the polyclonal component of the anti-PF4 antibody ensemble, revealing the presence of all four subclasses (IgG1 through IgG4) and both types of the light chain (λ and κ). The structural information reported in this work will be indispensable for understanding the molecular mechanism of VITT pathogenesis.
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