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Tsay GJ, Zouali M. Cellular pathways and molecular events that shape autoantibody production in COVID-19. J Autoimmun 2024; 147:103276. [PMID: 38936147 DOI: 10.1016/j.jaut.2024.103276] [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: 12/21/2023] [Revised: 05/26/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024]
Abstract
A hallmark of COVID-19 is the variety of complications that follow SARS-CoV-2 infection in some patients, and that target multiple organs and tissues. Also remarkable are the associations with several auto-inflammatory disorders and the presence of autoantibodies directed to a vast array of antigens. The processes underlying autoantibody production in COVID-19 have not been completed deciphered. Here, we review mechanisms involved in autoantibody production in COVID-19, multisystem inflammatory syndrome in children, and post-acute sequelae of COVID19. We critically discuss how genomic integrity, loss of B cell tolerance to self, superantigen effects of the virus, and extrafollicular B cell activation could underly autoantibody proaction in COVID-19. We also offer models that may account for the pathogenic roles of autoantibodies in the promotion of inflammatory cascades, thromboembolic phenomena, and endothelial and vascular deregulations.
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Affiliation(s)
- Gregory J Tsay
- Division of Immunology and Rheumatology, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan; College of Medicine, China Medical University, Taichung, Taiwan
| | - Moncef Zouali
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.
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2
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Sarrigeorgiou I, Rouka E, Kotsiou OS, Perlepe G, Gerovasileiou ES, Gourgoulianis KI, Lymberi P, Zarogiannis SG. Natural antibodies targeting LPS in pleural effusions of various etiologies. Am J Physiol Lung Cell Mol Physiol 2024; 326:L727-L735. [PMID: 38591123 DOI: 10.1152/ajplung.00377.2023] [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: 11/28/2023] [Revised: 03/01/2024] [Accepted: 03/26/2024] [Indexed: 04/10/2024] Open
Abstract
Respiratory infection, cancer, and heart failure can cause abnormal accumulation of fluid in the pleural cavity. The immune responses within the cavity are orchestrated by leucocytes that reside in the serosal-associated lymphoid tissue. Natural antibodies (NAbs) are abundant in the serum (S) having a major role in systemic and mucosal immunity; however, their occurrence in pleural fluid (PF) remains an open question. Our aim herein was to detect and measure the levels of NAbs (IgM, IgG, IgA) targeting lipopolysaccharides (LPS) in both the pleural fluid and the serum of 78 patients with pleural effusions (PEs) of various etiologies. The values of anti-LPS NAb activity were extracted through a normalization step regarding the total IgM, IgG, and IgA levels, all determined by in-house ELISA. In addition, the ratios of PF/S values were analyzed further with other critical biochemical parameters from pleural fluids. Anti-LPS NAbs of all Ig classes were detected in most of the samples, while a significant increase of anti-LPS activity was observed in infectious and noninfectious compared with malignant PEs. Multivariate linear regression confirmed a negative correlation of IgM and IgA anti-LPS PF/S ratio with malignancy. Moreover, anti-LPS NAbs PF/S measurements led to increased positive and negative predictive power in ROC curves generated for the discrimination between benign and malignant PEs. Our results highlight the role of anti-LPS NAbs in the pleural cavity and demonstrate the potential translational impact that should be further explored.NEW & NOTEWORTHY Here we describe the detection and quantification of natural antibodies (NAbs) in the human pleural cavity. We show for the first time that IgM, IgG, and IgA anti-LPS natural antibodies are detected and measured in pleural effusions of infectious, noninfectious, and malignant etiologies and provide clinical correlates to demonstrate the translational impact of our findings.
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Affiliation(s)
- Ioannis Sarrigeorgiou
- Laboratory of Immunology, Department of Immunology, Hellenic Pasteur Institute, Athens, Greece
| | - Erasmia Rouka
- Department of Nursing, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Ourania S Kotsiou
- Department of Nursing, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Garyfallia Perlepe
- Department of Respiratory Medicine, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Efrosini S Gerovasileiou
- Department of Physiology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Konstantinos I Gourgoulianis
- Department of Respiratory Medicine, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Peggy Lymberi
- Laboratory of Immunology, Department of Immunology, Hellenic Pasteur Institute, Athens, Greece
| | - Sotirios G Zarogiannis
- Department of Physiology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Larissa, Greece
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3
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Ghorai T, Sarkar A, Roy A, Bhowmick B, Nayak D, Das S. Role of auto-antibodies in the mechanisms of dengue pathogenesis and its progression: a comprehensive review. Arch Microbiol 2024; 206:214. [PMID: 38616229 DOI: 10.1007/s00203-024-03954-0] [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: 03/01/2024] [Revised: 03/27/2024] [Accepted: 04/02/2024] [Indexed: 04/16/2024]
Abstract
A complex interaction among virulence factors, host-genes and host immune system is considered to be responsible for dengue virus (DENV) infection and disease progression. Generation of auto-antibodies during DENV infection is a major phenomenon that plays a role in the pathophysiology of dengue hemorrhagic fever and dengue shock syndrome. Hemostasis, thrombocytopenia, hepatic endothelial dysfunction, and autoimmune blistering skin disease (pemphigus) are different clinical manifestations of dengue pathogenesis; produced due to the molecular mimicry of DENV proteins with self-antigens like coagulation factors, platelets and endothelial cell proteins. This review elaborately describes the current advancements in auto-antibody-mediated immunopathogenesis which inhibits coagulation cascade and promotes hyperfibrinolysis. Auto-antibodies like anti-endothelial cell antibodies-mediated hepatic inflammation during severe DENV infection have also been discussed. Overall, this comprehensive review provides insight to target auto-antibodies that may act as potential biomarkers for disease severity, and a ground for the development of therapeutic strategy against DENV.
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Affiliation(s)
- Tanusree Ghorai
- Virology Laboratory, DAC Regional Research Institute, Kolkata, India
| | - Avipsha Sarkar
- Virology Laboratory, DAC Regional Research Institute, Kolkata, India
| | - Anirban Roy
- Virology Laboratory, DAC Regional Research Institute, Kolkata, India
| | - Bijita Bhowmick
- Virology Laboratory, DAC Regional Research Institute, Kolkata, India
| | | | - Satadal Das
- Virology Laboratory, DAC Regional Research Institute, Kolkata, India.
- Peerless Hospital and B.K. Roy Research Centre, Kolkata, India.
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4
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Thisayakorn P, Thipakorn Y, Tantavisut S, Sirivichayakul S, Vojdani A, Maes M. Increased IgA-mediated responses to the gut paracellular pathway and blood-brain barrier proteins predict delirium due to hip fracture in older adults. Front Neurol 2024; 15:1294689. [PMID: 38379706 PMCID: PMC10876854 DOI: 10.3389/fneur.2024.1294689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/25/2024] [Indexed: 02/22/2024] Open
Abstract
Introduction Delirium is accompanied by immune response system activation, which may, in theory, cause a breakdown of the gut barrier and blood-brain barrier (BBB). Some results suggest that the BBB is compromised in delirium, but there is no data regarding the gut barrier. This study investigates whether delirium is associated with impaired BBB and gut barriers in elderly adults undergoing hip fracture surgery. Methods We recruited 59 older adults and measured peak Delirium Rating Scale (DRS) scores 2-3 days after surgery, and assessed plasma IgG/IgA levels (using ELISA techniques) for zonulin, occludin, claudin-6, β-catenin, actin (indicating damage to the gut paracellular pathway), claudin-5 and S100B (reflecting BBB damage), bacterial cytolethal distending toxin (CDT), LPS-binding protein (LBP), lipopolysaccharides (LPS), Porphyromonas gingivalis, and Helicobacter pylori. Results Results from univariate analyses showed that delirium is linked to increased IgA responses to all the self-epitopes and antigens listed above, except for LPS. Part of the variance (between 45-48.3%) in the peak DRS score measured 2-3 days post-surgery was explained by independent effects of IgA directed to LPS and LBP (or bacterial CDT), baseline DRS scores, and previous mild stroke. Increased IgA reactivity to the paracellular pathway and BBB proteins and bacterial antigens is significantly associated with the activation of M1 macrophage, T helper-1, and 17 cytokine profiles. Conclusion Heightened bacterial translocation, disruption of the tight and adherens junctions of the gut and BBB barriers, elevated CDT and LPS load in the bloodstream, and aberrations in cell-cell interactions may be risk factors for delirium.
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Affiliation(s)
- Paul Thisayakorn
- Department of Psychiatry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yanin Thipakorn
- Department of Psychiatry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Saran Tantavisut
- Department of Orthopedics, Hip Fracture Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sunee Sirivichayakul
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Aristo Vojdani
- Immunosciences Lab Inc., Los Angeles, CA, United States
- Cyrex Labs LLC, Phoenix, AZ, United States
| | - Michael Maes
- Sichuan Provincial Center for Mental Health, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Key Laboratory of Psychosomatic Medicine, Chinese Academy of Medical Sciences, Chengdu, China
- Department of Psychiatry, Medical University of Plovdiv, Plovdiv, Bulgaria
- Research Institute, Medical University of Plovdiv, Plovdiv, Bulgaria
- Kyung Hee University, Seoul, Republic of Korea
- Cognitive Impairment and Dementia Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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5
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Yuuki H, Itamiya T, Nagafuchi Y, Ota M, Fujio K. B cell receptor repertoire abnormalities in autoimmune disease. Front Immunol 2024; 15:1326823. [PMID: 38361948 PMCID: PMC10867955 DOI: 10.3389/fimmu.2024.1326823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/15/2024] [Indexed: 02/17/2024] Open
Abstract
B cells play a crucial role in the immune response and contribute to various autoimmune diseases. Recent studies have revealed abnormalities in the B cell receptor (BCR) repertoire of patients with autoimmune diseases, with distinct features observed among different diseases and B cell subsets. Classically, BCR repertoire was used as an identifier of distinct antigen-specific clonotypes, but the recent advancement of analyzing large-scale repertoire has enabled us to use it as a tool for characterizing cellular biology. In this review, we provide an overview of the BCR repertoire in autoimmune diseases incorporating insights from our latest research findings. In systemic lupus erythematosus (SLE), we observed a significant skew in the usage of VDJ genes, particularly in CD27+IgD+ unswitched memory B cells and plasmablasts. Notably, autoreactive clones within unswitched memory B cells were found to be increased and strongly associated with disease activity, underscoring the clinical significance of this subset. Similarly, various abnormalities in the BCR repertoire have been reported in other autoimmune diseases such as rheumatoid arthritis. Thus, BCR repertoire analysis holds potential for enhancing our understanding of the underlying mechanisms involved in autoimmune diseases. Moreover, it has the potential to predict treatment effects and identify therapeutic targets in autoimmune diseases.
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Affiliation(s)
- Hayato Yuuki
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takahiro Itamiya
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuo Nagafuchi
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mineto Ota
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Functional Genomics and Immunological Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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6
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Lecerf M, Lacombe RV, Dimitrov JD. Polyreactivity of antibodies from different B-cell subpopulations is determined by distinct sequence patterns of variable region. Front Immunol 2023; 14:1266668. [PMID: 38077343 PMCID: PMC10710144 DOI: 10.3389/fimmu.2023.1266668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/25/2023] [Indexed: 12/18/2023] Open
Abstract
An antibody molecule that can bind to multiple distinct antigens is defined as polyreactive. In the present study, we performed statistical analyses to assess sequence correlates of polyreactivity of >600 antibodies cloned from different B-cell types of healthy humans. The data revealed several sequence patterns of variable regions of heavy and light immunoglobulin chains that determine polyreactivity. The most prominent identified patterns were increased number of basic amino acid residues, reduced frequency of acidic residues, increased number of aromatic and hydrophobic residues, and longer length of CDR L1. Importantly, our study revealed that antibodies isolated from different B-cell populations used distinct sequence patterns (or combinations of them) for polyreactive antigen binding. Furthermore, we combined the data from sequence analyses with molecular modeling of selected polyreactive antibodies and demonstrated that human antibodies can use multiple pathways for achieving antigen-binding promiscuity. These data reconcile some contradictions in the literature regarding the determinants of antibody polyreactivity. Moreover, our study demonstrates that the mechanism of polyreactivity of antibodies evolves during immune response and might be tailored to specific functional properties of different B-cell compartments. Finally, these data can be of use for efforts in the development and engineering of therapeutic antibodies.
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Affiliation(s)
| | | | - Jordan D. Dimitrov
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, Université Paris Cité, Paris, France
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Fischman S, Levin I, Rondeau JM, Štrajbl M, Lehmann S, Huber T, Nimrod G, Cebe R, Omer D, Kovarik J, Bernstein S, Sasson Y, Demishtein A, Shlamkovich T, Bluvshtein O, Grossman N, Barak-Fuchs R, Zhenin M, Fastman Y, Twito S, Vana T, Zur N, Ofran Y. "Redirecting an anti-IL-1β antibody to bind a new, unrelated and computationally predicted epitope on hIL-17A". Commun Biol 2023; 6:997. [PMID: 37773269 PMCID: PMC10542344 DOI: 10.1038/s42003-023-05369-x] [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: 01/16/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023] Open
Abstract
Antibody engineering technology is at the forefront of therapeutic antibody development. The primary goal for engineering a therapeutic antibody is the generation of an antibody with a desired specificity, affinity, function, and developability profile. Mature antibodies are considered antigen specific, which may preclude their use as a starting point for antibody engineering. Here, we explore the plasticity of mature antibodies by engineering novel specificity and function to a pre-selected antibody template. Using a small, focused library, we engineered AAL160, an anti-IL-1β antibody, to bind the unrelated antigen IL-17A, with the introduction of seven mutations. The final redesigned antibody, 11.003, retains favorable biophysical properties, binds IL-17A with sub-nanomolar affinity, inhibits IL-17A binding to its cognate receptor and is functional in a cell-based assay. The epitope of the engineered antibody can be computationally predicted based on the sequence of the template antibody, as is confirmed by the crystal structure of the 11.003/IL-17A complex. The structures of the 11.003/IL-17A and the AAL160/IL-1β complexes highlight the contribution of germline residues to the paratopes of both the template and re-designed antibody. This case study suggests that the inherent plasticity of antibodies allows for re-engineering of mature antibodies to new targets, while maintaining desirable developability profiles.
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Affiliation(s)
| | - Itay Levin
- Biolojic Design LTD, Rehovot, Israel
- Enzymit LTD, Ness Ziona, Israel
| | | | | | - Sylvie Lehmann
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Thomas Huber
- Novartis Institutes for Biomedical Research, Basel, Switzerland
- Ridgelinediscovery, Basel, Switzerland
| | | | - Régis Cebe
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - Dotan Omer
- Biolojic Design LTD, Rehovot, Israel
- EmendoBio Inc., Rehovot, Israel
| | - Jiri Kovarik
- Novartis Institutes for Biomedical Research, Basel, Switzerland
| | | | | | - Alik Demishtein
- Biolojic Design LTD, Rehovot, Israel
- Anima Biotech, Ramat-Gan, Israel
| | | | - Olga Bluvshtein
- Biolojic Design LTD, Rehovot, Israel
- Enzymit LTD, Ness Ziona, Israel
| | | | | | | | | | - Shir Twito
- Biolojic Design LTD, Rehovot, Israel
- Enzymit LTD, Ness Ziona, Israel
| | - Tal Vana
- Biolojic Design LTD, Rehovot, Israel
| | - Nevet Zur
- Biolojic Design LTD, Rehovot, Israel
| | - Yanay Ofran
- Biolojic Design LTD, Rehovot, Israel
- The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar Ilan University, Ramat Gan, Israel
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8
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Li R, Fan H, Chen Y, Huang J, Liu GL, Huang L. Application of nanoplasmonic biosensors based on nanoarrays in biological and chemical detection. OPTICS EXPRESS 2023; 31:21586-21613. [PMID: 37381254 DOI: 10.1364/oe.470786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/17/2022] [Indexed: 06/30/2023]
Abstract
Technological innovation, cost effectiveness, and miniaturization are key factors that determine the commercial adaptability and sustainability of sensing platforms. Nanoplasmonic biosensors based on nanocup or nanohole arrays are attractive for the development of various miniaturized devices for clinical diagnostics, health management, and environmental monitoring. In this review, we discuss the latest trends in the engineering and development of nanoplasmonic sensors as biodiagnostic tools for the highly sensitive detection of chemical and biological analytes. We focused on studies that have explored flexible nanosurface plasmon resonance systems using a sample and scalable detection approach in an effort to highlight multiplexed measurements and portable point-of-care applications.
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9
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Mashiko S, Shihab RR, See SB, Schahadat LGZ, Aguiar TFM, Roy P, Porcheray F, Zorn E. Broad responses to chemical adducts shape the natural antibody repertoire in early infancy. SCIENCE ADVANCES 2023; 9:eade8872. [PMID: 37172087 PMCID: PMC10181178 DOI: 10.1126/sciadv.ade8872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Natural antibodies are an integral part of innate humoral immunity yet their development and polyreactive nature are still enigmatic. Here, we show that characteristic monoclonal natural antibodies recognize common chemical moieties or adducts, supporting the view that polyreactive antibodies may often correspond to anti-adduct antibodies. We next examined the development of immunoglobulin M (IgM) and IgG to 81 ubiquitous adducts from birth to old age. Newborn IgM only reacted to a limited number of consensus determinants. This highly restricted neonatal repertoire abruptly diversified around 6 months of age through the development of antibodies to environmental antigens and age-driven epigenetic modifications. In contrast, the IgG repertoire was diverse across the entire life span. Our studies reveal an unrecognized component of humoral immunity directed to common adducts. These findings set the ground for further investigations into the role of anti-adduct B cell responses in homeostatic functions and pathological conditions.
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Affiliation(s)
- Shunya Mashiko
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ronzon R Shihab
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Sarah B See
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Luca G Z Schahadat
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Talita F M Aguiar
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Poulomi Roy
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
| | - Fabrice Porcheray
- Transplant Center, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Emmanuel Zorn
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, New York, NY, USA
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10
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Urusov AE, Aulova KS, Dmitrenok PS, Buneva VN, Nevinsky GA. EAE of Mice: Enzymatic Cross Site-Specific Hydrolysis of H2A Histone by IgGs against H2A, H1, H2B, H3, and H4 Histones and Myelin Basic Protein. Int J Mol Sci 2023; 24:ijms24108636. [PMID: 37239982 DOI: 10.3390/ijms24108636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 05/28/2023] Open
Abstract
Histones play vital roles in chromatin function and gene transcription; however, they are very harmful in the intercellular space because they stimulate systemic inflammatory and toxic responses. Myelin basic protein (MBP) is the major protein of the axon myelin-proteolipid sheath. Antibodies-abzymes with various catalytic activities are specific features of some autoimmune diseases. IgGs against individual histones (H2A, H1, H2B, H3, and H4) and MBP were isolated from the blood of experimental-autoimmune-encephalomyelitis-prone C57BL/6 mice by several affinity chromatographies. These Abs-abzymes corresponded to various stages of EAE development: spontaneous EAE, MOG, and DNA-histones accelerated the onset, acute, and remission stages. IgGs-abzymes against MBP and five individual histones showed unusual polyreactivity in the complex formation and enzymatic cross-reactivity in the specific hydrolysis of the H2A histone. All the IgGs of 3-month-old mice (zero time) against MBP and individual histones demonstrated from 4 to 35 different H2A hydrolysis sites. The spontaneous development of EAE over 60 days led to a significant change in the type and number of H2A histone hydrolysis sites by IgGs against five histones and MBP. Mice treatment with MOG and the DNA-histone complex changed the type and number of H2A hydrolysis sites compared to zero time. The minimum number (4) of different H2A hydrolysis sites was found for IgGs against H2A (zero time), while the maximum (35) for anti-H2B IgGs (60 days after mice treatment with DNA-histone complex). Overall, it was first demonstrated that at different stages of EAE evolution, IgGs-abzymes against individual histones and MBP could significantly differ in the number and type of specific sites of H2A hydrolysis. The possible reasons for the catalytic cross-reactivity and great differences in the number and type of histone H2A cleavage sites were analyzed.
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Affiliation(s)
- Andrey E Urusov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Division of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Kseniya S Aulova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Division of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Pavel S Dmitrenok
- G. B. Elyakov Pacific Institute of Bioorganic Chemistry, Far East Division, Russian Academy of Sciences, Vladivostok 690022, Russia
| | - Valentina N Buneva
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Division of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Georgy A Nevinsky
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Division of Russian Academy of Sciences, Novosibirsk 630090, Russia
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11
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Urusov AE, Aulova KS, Dmitrenok PS, Buneva VN, Nevinsky GA. EAE of Mice: Enzymatic Cross Site-Specific Hydrolysis of H2B Histone by IgGs against H1, H2A, H2B, H3, and H4 Histones and Myelin Basic Protein. Molecules 2023; 28:molecules28072973. [PMID: 37049736 PMCID: PMC10095689 DOI: 10.3390/molecules28072973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/12/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Histones have vital roles in chromatin functioning and gene transcription. At the same time, they are pernicious in intercellular space because they stimulate systemic inflammatory and toxic responses. Myelin basic protein (MBP) is the major protein of the axon myelin–proteolipid sheath. Antibody-abzymes with various catalytic activities are specific features of some autoimmune diseases. IgGs against five individual histones (H2B, H1, H2A, H3, and H4) and MBP were isolated from the blood of experimental autoimmune encephalomyelitis-prone C57BL/6 mice by affinity chromatography. Abzymes corresponding to various stages of EAE development, including spontaneous EAE, myelin oligodendrocyte glycoprotein (MOG)- and DNA-histone complex-accelerated onset, as well as acute and remission stages, were analyzed. IgG-abzymes against MBP and five individual histones showed unusual polyreactivity in complex formation and enzymatic cross-reactivity in the specific hydrolysis of H2B histone. All IgGs against MBP and individual histones in 3-month-old mice (zero time) demonstrated from 4 to 11 different H2B hydrolysis sites. Spontaneous development of EAE during 60 days led to a significant change in the type and number of H2B hydrolysis sites by IgGs against the five histones and MBP. Mouse treatment with MOG and DNA-histone complex changed the type and number of H2B hydrolysis sites compared to zero time. The minimum number (3) of different H2B hydrolysis sites was found for IgGs against H3 20 days after mouse immunization with DNA-histone complex, whereas the maximum number (33) for anti-H2B IgGs was found 60 days after mouse treatment with DNA-histone complex. Overall, this is the first study to demonstrate that at different stages of EAE evolution, IgG-abzymes against five individual histones and MBP could significantly differ in the specific sites and number of H2B hydrolysis sites. Possible reasons for the catalytic cross-reactivity and significant differences in the number and type of histone H2B cleavage sites were analyzed.
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12
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Structural mechanism of Fab domain dissociation as a measure of interface stability. J Comput Aided Mol Des 2023; 37:201-215. [PMID: 36918473 PMCID: PMC10049950 DOI: 10.1007/s10822-023-00501-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/23/2023] [Indexed: 03/16/2023]
Abstract
Therapeutic antibodies should not only recognize antigens specifically, but also need to be free from developability issues, such as poor stability. Thus, the mechanistic understanding and characterization of stability are critical determinants for rational antibody design. In this study, we use molecular dynamics simulations to investigate the melting process of 16 antigen binding fragments (Fabs). We describe the Fab dissociation mechanisms, showing a separation in the VH-VL and in the CH1-CL domains. We found that the depths of the minima in the free energy curve, corresponding to the bound states, correlate with the experimentally determined melting temperatures. Additionally, we provide a detailed structural description of the dissociation mechanism and identify key interactions in the CDR loops and in the CH1-CL interface that contribute to stabilization. The dissociation of the VH-VL or CH1-CL domains can be represented by conformational changes in the bend angles between the domains. Our findings elucidate the melting process of antigen binding fragments and highlight critical residues in both the variable and constant domains, which are also strongly germline dependent. Thus, our proposed mechanisms have broad implications in the development and design of new and more stable antigen binding fragments.
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Planchais C, Noe R, Gilbert M, Lecerf M, Kaveri SV, Lacroix-Desmazes S, Roumenina LT, Dimitrov JD. Oxidized hemoglobin triggers polyreactivity and autoreactivity of human IgG via transfer of heme. Commun Biol 2023; 6:168. [PMID: 36774392 PMCID: PMC9922299 DOI: 10.1038/s42003-023-04535-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 01/26/2023] [Indexed: 02/13/2023] Open
Abstract
Intravascular hemolysis occurs in diverse pathological conditions. Extracellular hemoglobin and heme have strong pro-oxidative and pro-inflammatory potentials that can contribute to the pathology of hemolytic diseases. However, many of the effects of extracellular hemoglobin and heme in hemolytic diseases are still not well understood. Here we demonstrate that oxidized hemoglobin (methemoglobin) can modify the antigen-binding characteristics of human immunoglobulins. Thus, incubation of polyclonal or some monoclonal human IgG in the presence of methemoglobin results in an appearance of binding reactivities towards distinct unrelated self-proteins, including the protein constituent of hemoglobin i.e., globin. We demonstrate that a transfer of heme from methemoglobin to IgG is indispensable for this acquisition of antibody polyreactivity. Our data also show that only oxidized form of hemoglobin have the capacity to induce polyreactivity of antibodies. Site-directed mutagenesis of a heme-sensitive human monoclonal IgG1 reveals details about the mechanism of methemoglobin-induced antigen-binding polyreactivity. Further here we assess the kinetics and thermodynamics of interaction of a heme-induced polyreactive human antibody with hemoglobin and myoglobin. Taken together presented data contribute to a better understanding of the functions of extracellular hemoglobin in the context of hemolytic diseases.
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Affiliation(s)
- Cyril Planchais
- Laboratory of Humoral Immunology, Institut Pasteur, Université Paris Cité, INSERM U1222, 75015 Paris, France
| | - Remi Noe
- grid.4444.00000 0001 2112 9282Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, Université Paris Cité, 75006 Paris, France
| | - Marie Gilbert
- grid.4444.00000 0001 2112 9282Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, Université Paris Cité, 75006 Paris, France
| | - Maxime Lecerf
- grid.4444.00000 0001 2112 9282Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, Université Paris Cité, 75006 Paris, France
| | - Srini V. Kaveri
- grid.4444.00000 0001 2112 9282Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, Université Paris Cité, 75006 Paris, France
| | - Sébastien Lacroix-Desmazes
- grid.4444.00000 0001 2112 9282Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, Université Paris Cité, 75006 Paris, France
| | - Lubka T. Roumenina
- grid.4444.00000 0001 2112 9282Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, Université Paris Cité, 75006 Paris, France
| | - Jordan D. Dimitrov
- grid.4444.00000 0001 2112 9282Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, Université Paris Cité, 75006 Paris, France
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14
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Maes M, Thisayakorn P, Thipakorn Y, Tantavisut S, Sirivichayakul S, Vojdani A. Reactivity to neural tissue epitopes, aquaporin 4 and heat shock protein 60 is associated with activated immune-inflammatory pathways and the onset of delirium following hip fracture surgery. Eur Geriatr Med 2023; 14:99-112. [PMID: 36520371 DOI: 10.1007/s41999-022-00729-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 12/04/2022] [Indexed: 12/23/2022]
Abstract
OBJECTIVES Activation of the immune-inflammatory response system (IRS) and a deficiency in the compensatory immunoregulatory system (CIRS), neuronal injuries, and alterations in the glutamate receptor (GlutaR), aquaporin-4 (AQP4) and heat shock protein 60 (HSP60) are involved in delirium. Increased serum levels of neurofilament protein (NFP), glial fibrillary acidic protein (GFAP) and myelin basic protein (MBP) are biomarkers of neuronal injury. This investigation delineates whether elevated IgA/IgG reactivity against those self-antigens is associated with delirium severity and IRS activation. METHODS We measured peak Delirium Rating Scale (DRS) scores on days 2 and 3 following surgery in 59 hip fractured older adults, and IgA and IgG antibody levels against MBP, NFP, GFAP and myelin oligodendrocyte glycoprotein (MOG), metabotropic glutamate receptors mGluRs 1 and 5, N-Methyl-D-Aspartate receptor (NMDAR) GLU1 (NR1) and GLU2 (NR2), APQ4 and HSP60. RESULTS The IgA antibody levels against those self-antigens, especially GFAP, MBP and HSP60, strongly predict peak DRS scores on days 2 and 3 post-surgery. IgA reactivity against NMDAR and baseline DRS scores explained 40.6% of the variance in peak DRS scores, while IgA against NMDAR, IgG against MBP and age explained 29.1% of the variance in the IRS/CIRS ratio. There was no correlation between DRS scores and IgG directed against other self-antigens. CONCLUSIONS Increased IgA levels against neuronal self-antigens, AQP4 and HSP60 are risk factors for delirium. Polyreactive antibody-associated breakdown of immune tolerance, IRS activation and injuries in the neuronal cytoskeleton, oligodendrocytes, astrocytes, glial cells, and myelin sheath are involved in the pathophysiology of delirium.
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Affiliation(s)
- Michael Maes
- Department of Psychiatry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Department of Psychiatry, Medical University of Plovdiv, Plovdiv, Bulgaria.
- IMPACT Strategic Research Center, Deakin University, Geelong, Australia.
| | - Paul Thisayakorn
- Department of Psychiatry, Hip Fracture Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
| | - Yanin Thipakorn
- Department of Psychiatry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Saran Tantavisut
- Department of Orthopedics, Hip Fracture Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sunee Sirivichayakul
- Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Aristo Vojdani
- Immunosciences Lab. Inc, Los Angeles, CA, USA
- Cyrex Labs LLC, Phoeniz, AZ, USA
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15
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Multiple Sclerosis: Enzymatic Cross Site-Specific Recognition and Hydrolysis of H3 Histone by IgGs against H3, H1, H2A, H2B, H4 Histones, Myelin Basic Protein, and DNA. Biomedicines 2022; 10:biomedicines10102663. [PMID: 36289924 PMCID: PMC9599260 DOI: 10.3390/biomedicines10102663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/21/2022] Open
Abstract
Histones have a specific key role in the remodeling of chromatin and gene transcription. In the blood, free histones are damage-connected proteins. Myelin basic protein (MBP) is the major component of the myelin-proteolipid sheath of axons. Antibodies possessing enzymatic activities (abzymes, ABZs) are the specific features of several autoimmune pathologies. IgGs against five histones, MBP, and DNA were obtained from the sera of multiple sclerosis (MS) patients using several affinity chromatographies. The sites of H3 histone splitting by Abs against five individual histones, MBP, and DNA were revealed by MALDI mass spectrometry. It was shown that the number of H3 splitting sites by IgGs against five various histones is different (number of sites): H3 (11), H1 (14), H2A (11), H4 (17), MBP (22), and DNA (29). IgGs against five different histones hydrolyze H3 at different sites, and only a few them coincide. The main reason for the enzymatic cross-reactivity of Abs against H3 and four other histones, as well as MBP, might be the high level of these proteins’ homology. The effective hydrolysis of the H3 histone at 29 sites with IgGs against DNA can be explained by the formation of chimeric abzymes against hybrid antigenic determinants formed by different histones and MBP at the junction of these protein sequences with DNA. The active centers of such abzymes contain structural elements of canonical DNases and proteases. Since free histones are pernicious proteins, antibodies–ABZs against five histones, MBP, and DNA could have a negative role in the pathogenesis of MS and probably other various autoimmune diseases.
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16
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Casadó-Llombart S, Velasco-de Andrés M, Català C, Leyton-Pereira A, Gutiérrez-Cózar R, Suárez B, Armiger N, Carreras E, Esteller M, Ricart E, Ordás I, Gisbert JP, Chaparro M, Esteve M, Márquez L, Busquets D, Iglesias E, García-Planella E, Martín-Arranz MD, Lohmann J, Ayata CK, Niess JH, Engel P, Panés J, Salas A, Domènech E, Lozano F. Experimental and genetic evidence for the impact of CD5 and CD6 expression and variation in inflammatory bowel disease. Front Immunol 2022; 13:966184. [PMID: 36211446 PMCID: PMC9532939 DOI: 10.3389/fimmu.2022.966184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/31/2022] [Indexed: 11/20/2022] Open
Abstract
Crohn’s disease (CD) and ulcerative colitis (UC) are inflammatory bowel diseases (IBD) resulting from the interaction of multiple environmental, genetic and immunological factors. CD5 and CD6 are paralogs encoding lymphocyte co-receptors involved in fine-tuning intracellular signals delivered upon antigen-specific recognition, microbial pattern recognition and cell adhesion. While CD5 and CD6 expression and variation is known to influence some immune-mediated inflammatory disorders, their role in IBD remains unclear. To this end, Cd5- and Cd6-deficient mice were subjected to dextran sulfate sodium (DSS)-induced colitis, the most widely used experimental animal model of IBD. The two mouse lines showed opposite results regarding body weight loss and disease activity index (DAI) changes following DSS-induced colitis, thus supporting Cd5 and Cd6 expression involvement in the pathophysiology of this experimental IBD model. Furthermore, DNA samples from IBD patients of the ENEIDA registry were used to test association of CD5 (rs2241002 and rs2229177) and CD6 (rs17824933, rs11230563, and rs12360861) single nucleotide polymorphisms with susceptibility and clinical parameters of CD (n=1352) and UC (n=1013). Generalized linear regression analyses showed association of CD5 variation with CD ileal location (rs2241002CC) and requirement of biological therapies (rs2241002C-rs2229177T haplotype), and with poor UC prognosis (rs2241002T-rs2229177T haplotype). Regarding CD6, association was observed with CD ileal location (rs17824933G) and poor prognosis (rs12360861G), and with left-sided or extensive UC, and absence of ankylosing spondylitis in IBD (rs17824933G). The present experimental and genetic evidence support a role for CD5 and CD6 expression and variation in IBD’s clinical manifestations and therapeutic requirements, providing insight into its pathophysiology and broadening the relevance of both immunomodulatory receptors in immune-mediated disorders.
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Affiliation(s)
- Sergi Casadó-Llombart
- Immunoreceptors del Sistema Innat i Adaptatiu, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - María Velasco-de Andrés
- Immunoreceptors del Sistema Innat i Adaptatiu, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Cristina Català
- Immunoreceptors del Sistema Innat i Adaptatiu, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Alejandra Leyton-Pereira
- Immunoreceptors del Sistema Innat i Adaptatiu, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Rebeca Gutiérrez-Cózar
- Departament de Biomedicina, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Belén Suárez
- Servei d’Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Noelia Armiger
- Immunoreceptors del Sistema Innat i Adaptatiu, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Esther Carreras
- Immunoreceptors del Sistema Innat i Adaptatiu, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Miriam Esteller
- Inflammatory Bowel Disease Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Inflammatory Bowel Disease Unit, Gastroenterology Department, Hospital Clínic de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Elena Ricart
- Inflammatory Bowel Disease Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Inflammatory Bowel Disease Unit, Gastroenterology Department, Hospital Clínic de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Ingrid Ordás
- Inflammatory Bowel Disease Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Inflammatory Bowel Disease Unit, Gastroenterology Department, Hospital Clínic de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Javier P. Gisbert
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - María Chaparro
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - María Esteve
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
- Gastroenterology Department, Hospital Universitari Mútua Terrassa, Terrassa, Spain
| | - Lucía Márquez
- Gastroenterology Department, Hospital del Mar and Institut Hospital del Mar Investigacions Mèdiques, Barcelona, Spain
| | - David Busquets
- Department of Gastroenterology, Hospital Universitari de Girona Dr Josep Trueta, Girona, Spain
| | - Eva Iglesias
- Department of Gastroenterology, Hospital Universitario Reina Sofía, Córdoba, Spain
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Córdoba, Spain
| | | | - María Dolores Martín-Arranz
- Department of Gastroenterology, and Innate Immunity Group, IdiPAZ Institute for Health Research, La Paz Hospital, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Juliane Lohmann
- Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - C. Korcan Ayata
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Jan Hendrik Niess
- Department of Biomedicine, University of Basel, Basel, Switzerland
- University Center for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital, Basel, Switzerland
| | - Pablo Engel
- Immunoreceptors del Sistema Innat i Adaptatiu, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Departament de Biomedicina, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Julián Panés
- Inflammatory Bowel Disease Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Inflammatory Bowel Disease Unit, Gastroenterology Department, Hospital Clínic de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Azucena Salas
- Departament de Biomedicina, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
- Inflammatory Bowel Disease Group, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
| | - Eugeni Domènech
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid, Spain
- Gastroenterology Department, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | - Francisco Lozano
- Immunoreceptors del Sistema Innat i Adaptatiu, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Departament de Biomedicina, Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
- Servei d’Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clínic de Barcelona, Barcelona, Spain
- *Correspondence: Francisco Lozano,
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17
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Urusov AE, Aulova KS, Dmitrenok PS, Buneva VN, Nevinsky GA. Experimental Autoimmune Encephalomyelitis of Mice: Enzymatic Cross Site-Specific Hydrolysis of H4 Histone by IgGs against Histones and Myelin Basic Protein. Int J Mol Sci 2022; 23:ijms23169182. [PMID: 36012448 PMCID: PMC9409114 DOI: 10.3390/ijms23169182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/08/2022] [Accepted: 08/11/2022] [Indexed: 11/27/2022] Open
Abstract
Histones play vital roles in chromatin functioning and gene transcription, but in intercellular space, they are harmful due to stimulating systemic inflammatory and toxic responses. Myelin basic protein (MBP) is the most important protein of the axon myelin–proteolipid sheath. Antibodies-abzymes with different catalytic activities are critical and specific features of some autoimmune diseases. Five IgG preparations against histones (H4, H1, H2A, H2B, and H3) and against MBP corresponding to different spontaneous, MOG (myelin oligodendrocyte glycoprotein of mice), and DNA–histones that accelerated onset, acute, and remission stages of experimental autoimmune encephalomyelitis (EAE; model of human multiple sclerosis) development were obtained from EAE-prone C57BL/6 mice by several affinity chromatographies. IgG-abzymes against five histones and MBP possess unusual polyreactivity in complexation and catalytic cross-reactivity in the hydrolysis of histone H4. IgGs against five histones and MBP corresponding to 3 month-old mice (zero time) in comparison with Abs corresponding to spontaneous development of EAE during 60 days differ in type and number of H4 sites for hydrolysis. Immunization of mice with MOG and DNA–histones complex results in an acceleration of EAE development associated with an increase in the activity of antibodies in H4 hydrolysis. Twenty days after mouse immunization with MOG or DNA–histones complex, the IgGs hydrolyze H4 at other additional sites compared to zero time. The maximum number of different sites of H4 hydrolysis was revealed for IgGs against five histones and MBP at 60 days after immunization of mice with MOG and DNA–histones. Overall, it first showed that at different stages of EAE development, abzymes could significantly differ in specific sites of H4 hydrolysis.
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Affiliation(s)
- Andrey E. Urusov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Division of Russian Academy of Sciences, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia
| | - Kseniya S. Aulova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Division of Russian Academy of Sciences, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia
| | - Pavel S. Dmitrenok
- G. B. Elyakov Pacific Institute of Bioorganic Chemistry, Far East Division, Russian Academy of Sciences, 690022 Vladivostok, Russia
| | - Valentina N. Buneva
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Division of Russian Academy of Sciences, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia
| | - Georgy A. Nevinsky
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Division of Russian Academy of Sciences, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia
- Correspondence:
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18
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Nevinsky GA, Buneva VN, Dmitrienok PS. Multiple Sclerosis: Enzymatic Cross Site-Specific Recognition and Hydrolysis of H2A Histone by IgGs against H2A, H1, H2B, H3 Histones, Myelin Basic Protein, and DNA. Biomedicines 2022; 10:biomedicines10081876. [PMID: 36009424 PMCID: PMC9405453 DOI: 10.3390/biomedicines10081876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/27/2022] [Accepted: 07/27/2022] [Indexed: 12/21/2022] Open
Abstract
Histones have a paramount role in chromatin remodeling and gene transcription. Free histones are damage-associated molecules in the blood; administration of histones to animals drives systemic inflammatory and toxic effects. Myelin basic protein (MBP) is the most crucial component of the axon myelin-proteolipid sheath. Antibodies-abzymes with different enzymatic activities are very toxic and an essential feature of some autoimmune diseases. Electrophoretically homogeneous IgGs against H1, H2A, H2B, H3, H4, MBP, and DNA were derived from sera of multiple sclerosis (MS) patients by several affinity chromatographies. Using MALDI-TOFF mass spectrometry, it was shown that IgGs against H2A split H2A at 12 sites; the number of H2A hydrolysis sites by antibodies against other antigens is different: H1 (19), H2B (11), H3 (15), H4 (9), MBP (10), and DNA (23), and they only partly match. Thus, the complex formation polyreactivity and the enzymatic cross-activity of pernicious humans IgGs against five histones, MBP, and DNA have been shown for the first time. The data obtained indicate that the formation of such polyspecific-polyreactive abzymes, whose single active center can recognize and hydrolyze different substrates, can occur due to the formation of antibodies against hybrid antigenic determinants consisting of several histone protein sequences. IgGs with high affinity for DNA with DNase and protease activities may be antibodies against DNA-histone complex antigenic determinants, including protein and DNA sequences. Polyreactive IgGs-abzymes against MBP, five histones, and DNA with extended cytotoxicity can play a very negative role in the pathogenesis of multiple sclerosis and probably other different diseases.
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Affiliation(s)
- Georgy A. Nevinsky
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Division of Russian Academy of Sciences, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia;
- Correspondence:
| | - Valentina N. Buneva
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Division of Russian Academy of Sciences, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia;
| | - Pavel S. Dmitrienok
- Pacific Institute of Bioorganic Chemistry, Far East Division, Russian Academy of Sciences, 690022 Vladivostok, Russia;
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19
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Nevinsky GA, Buneva VN, Dmitrienok PS. Maximally Expressed miRNAs of Milk in Cells, Plasma and Lipid Fraction of Human Milk and Antibodies-Abzymes Catalyzing Their Hydrolysis. Int J Mol Sci 2022; 23:ijms23158102. [PMID: 35897678 PMCID: PMC9368074 DOI: 10.3390/ijms23158102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
As shown in many studies, one of the earliest statistically significant indicators of the development of many autoimmune diseases (ADs) is the appearance in the blood of antibodies with catalytic activities (abzymes) hydrolyzing different autoantigens. Antibodies-abzymes having different enzymatic activities are a specific and essential feature of some ADs. Most abzymes are harmful to humans. Free histones in the blood are damage-associated proteins, and their administration to animals drives systemic inflammatory and toxic effects. Myelin basic protein (MBP) is the most critical component of the axon myelin-proteolipid sheath. Hydrolysis of MBP by abzymes leads to the disruption of nerve impulses. Here, we analyzed the possible pathways for the formation of unusual antibodies and abzymes that exhibit polyspecificity in recognition during complex formation with partially related antigens and possess the ability to catalyze several different reactions for the first time. Using IgGs of HIV-infected and multiple sclerosis patients against five individual histones (H1–H4), MBP, and DNA, it was first shown that abzymes against each of these antigens effectively recognize and hydrolyze all three antigens: histones, MBP, and DNA. The data obtained indicate that the formation of such polyspecific abzymes, whose single active center can recognize different substrates and catalyze several reactions, can occur in two main ways. They can be antibodies against DNA–protein complex hybrid antigenic determinants containing proteins and nucleic sequences. Their formation may also be associated with the previously described phenomenon of IgG extensive LH half-molecule (containing one L-light and one H-heavy chains) exchange leading to H2L2 molecules containing HL halves with variable fragments recognizing different antigens.
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Affiliation(s)
- Georgy A. Nevinsky
- Institute of Chemical Biology and Fundamental Medicine of the Siberian, Division of Russian Academy of Sciences, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia;
- Correspondence:
| | - Valentina N. Buneva
- Institute of Chemical Biology and Fundamental Medicine of the Siberian, Division of Russian Academy of Sciences, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia;
| | - Pavel S. Dmitrienok
- Pacific Institute of Bioorganic Chemistry, Far East Division, Russian Academy of Sciences, 690022 Vladivostok, Russia;
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20
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Saksena SD, Liu G, Banholzer C, Horny G, Ewert S, Gifford DK. Computational counterselection identifies nonspecific therapeutic biologic candidates. CELL REPORTS METHODS 2022; 2:100254. [PMID: 35880012 PMCID: PMC9308162 DOI: 10.1016/j.crmeth.2022.100254] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/22/2022] [Accepted: 06/17/2022] [Indexed: 01/13/2023]
Abstract
Effective biologics require high specificity and limited off-target binding, but these properties are not guaranteed by current affinity-selection-based discovery methods. Molecular counterselection against off targets is a technique for identifying nonspecific sequences but is experimentally costly and can fail to eliminate a large fraction of nonspecific sequences. Here, we introduce computational counterselection, a framework for removing nonspecific sequences from pools of candidate biologics using machine learning models. We demonstrate the method using sequencing data from single-target affinity selection of antibodies, bypassing combinatorial experiments. We show that computational counterselection outperforms molecular counterselection by performing cross-target selection and individual binding assays to determine the performance of each method at retaining on-target, specific antibodies and identifying and eliminating off-target, nonspecific antibodies. Further, we show that one can identify generally polyspecific antibody sequences using a general model trained on affinity data from unrelated targets with potential affinity for a broad range of sequences.
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Affiliation(s)
- Sachit Dinesh Saksena
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ge Liu
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Geraldine Horny
- Novartis Institute of BioMedical Research (NIBR), Basel, Switzerland
| | - Stefan Ewert
- Novartis Institute of BioMedical Research (NIBR), Basel, Switzerland
| | - David K Gifford
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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21
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Genetic background affects the mucosal SIgA levels, parasite burden, lung inflammation and susceptibility of male mice to Ascaris suum infection. Infect Immun 2021; 90:e0059521. [PMID: 34807734 DOI: 10.1128/iai.00595-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ascariasis is a neglected tropical disease, widespread in the world and causing important socioeconomic impacts. The presence of various stages of worm development in the pulmonary and intestinal mucosa induces a humoral and cellular immune response. However, although there is much evidence of the protective role of mucosal immunity against various pathogens, including helminthes, there is still a gap in the knowledge about the immune response and the mechanisms of action that are involved in protection against diseases, especially in the initial phase of ascariasis. Then, the aim of this study was to evaluate the kinetic aspects of the immune parasitological parameters in intestinal and pulmonary mucosa in male mice with early ascariasis. Therefore, two mice strains showed a different susceptibility to ascariasis (BALB/c and C57BL6/j), when experimentally infected with 2,500 infective eggs of Ascaris suum from time-point 0 and the immune parasitological parameters evaluated each two days after infection, during the period of 12 days. The results were suggestive of a synergetic action of intestinal and pulmonary SIgA contributing for the protection against early ascariasis by reducing the amount of migrating larval as well as the influx of leukocytes in the lung and the consequent impair of the pulmonary capacity.
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22
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Kompaneets IY, Sedykh SE, Buneva VN, Dmitrenok PS, Nevinsky GA. Secretory immunoglobulin A from human milk hydrolyzes 5 histones and myelin basic protein. J Dairy Sci 2021; 105:950-964. [PMID: 34802738 DOI: 10.3168/jds.2021-20917] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/10/2021] [Indexed: 11/19/2022]
Abstract
Mother's milk provides newborns with various nutrients (e.g., enzymes, proteins, peptides, hormones, antibodies) that help babies grow and protect them from bacterial and viral infections. The functions of many components of breast milk can be very different from their corresponding functions in body fluids of healthy adults. Catalytic antibodies (abzymes) that hydrolyze peptides, proteins, DNA, RNA, and oligosaccharides were detected not only in human milk, but also in the blood sera of autoimmune patients. However, abzymes with unexpected synthetic activities (lipids, oligosaccharides, and protein kinase activities) were revealed in milk that were not found in the blood of autoimmune patients. The nutrition of infants with fresh milk has a very specific role; newborns are well protected by antibodies of mother's milk (passive immunity). Protease abzymes were found in the blood sera of autoimmune patients, whereas healthy humans usually do not contain such autoantibodies. Here, we present the first evidence that the milk of healthy mothers contains secretory (s)IgA that effectively hydrolyze 5 histones (e.g., H1, H2A, H2B, H3, and H4) and myelin basic protein (MBP). Several rigid criteria were applied to show that protease activity is an intrinsic property of sIgA. Milk abzymes against 5 histones cannot hydrolyze different control proteins except histones and MBP, whereas autoantibodies against MBP split this protein and 5 histones. Antibodies against histones and MBP exhibit complexation polyreactivity as well as specific and unusual catalytic cross-reactivity. With some exceptions, the specific sites of hydrolysis of H1, H2A, and H2B by sIgA against histones do not coincide with the sites of hydrolysis by abzymes against MBP. On the whole, fresh human milk is a very specific source of many of the most unusual antibodies and abzymes.
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Affiliation(s)
- Ivan Yu Kompaneets
- Institute of Chemical Biology and Fundamental Medicine of Siberian Branch of Russian Academy of Sciences, 8 Lavrentiev Ave., Novosibirsk 630,090, Russia
| | - Sergey E Sedykh
- Institute of Chemical Biology and Fundamental Medicine of Siberian Branch of Russian Academy of Sciences, 8 Lavrentiev Ave., Novosibirsk 630,090, Russia
| | - Valentina N Buneva
- Institute of Chemical Biology and Fundamental Medicine of Siberian Branch of Russian Academy of Sciences, 8 Lavrentiev Ave., Novosibirsk 630,090, Russia
| | - Pavel S Dmitrenok
- G. B. Elyakov Pacific Institute of Bioorganic Chemistry, Far East Division, Russian Academy of Sciences, Vladivostok 690,022, Russia
| | - Georgy A Nevinsky
- Institute of Chemical Biology and Fundamental Medicine of Siberian Branch of Russian Academy of Sciences, 8 Lavrentiev Ave., Novosibirsk 630,090, Russia.
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23
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Intrathymic differentiation of natural antibody-producing plasma cells in human neonates. Nat Commun 2021; 12:5761. [PMID: 34599177 PMCID: PMC8486820 DOI: 10.1038/s41467-021-26069-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/14/2021] [Indexed: 02/08/2023] Open
Abstract
The thymus is a central lymphoid organ primarily responsible for the development of T cells. A small proportion of B cells, however, also reside in the thymus to assist negative selection of self-reactive T cells. Here we show that the thymus of human neonates contains a consistent contingent of CD138+ plasma cells, producing all classes and subclasses of immunoglobulins with the exception of IgD. These antibody-secreting cells are part of a larger subset of B cells that share the expression of signature genes defining mouse B1 cells, yet lack the expression of complement receptors CD21 and CD35. Data from single-cell transcriptomic, clonal correspondence and in vitro differentiation assays support the notion of intrathymic CD138+ plasma cell differentiation, alongside other B cell subsets with distinctive molecular phenotypes. Lastly, neonatal thymic plasma cells also include clones reactive to commensal and pathogenic bacteria that commonly infect children born with antibody deficiency. Thus, our findings point to the thymus as a source of innate humoral immunity in human neonates.
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24
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Hanna SJ, Tatovic D, Thayer TC, Dayan CM. Insights From Single Cell RNA Sequencing Into the Immunology of Type 1 Diabetes- Cell Phenotypes and Antigen Specificity. Front Immunol 2021; 12:751701. [PMID: 34659258 PMCID: PMC8519581 DOI: 10.3389/fimmu.2021.751701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/14/2021] [Indexed: 01/10/2023] Open
Abstract
In the past few years, huge advances have been made in techniques to analyse cells at an individual level using RNA sequencing, and many of these have precipitated exciting discoveries in the immunology of type 1 diabetes (T1D). This review will cover the first papers to use scRNAseq to characterise human lymphocyte phenotypes in T1D in the peripheral blood, pancreatic lymph nodes and islets. These have revealed specific genes such as IL-32 that are differentially expressed in islet -specific T cells in T1D. scRNAseq has also revealed wider gene expression patterns that are involved in T1D and can predict its development even predating autoantibody production. Single cell sequencing of TCRs has revealed V genes and CDR3 motifs that are commonly used to target islet autoantigens, although truly public TCRs remain elusive. Little is known about BCR repertoires in T1D, but scRNAseq approaches have revealed that insulin binding BCRs commonly use specific J genes, share motifs between donors and frequently demonstrate poly-reactivity. This review will also summarise new developments in scRNAseq technology, the insights they have given into other diseases and how they could be leveraged to advance research in the type 1 diabetes field to identify novel biomarkers and targets for immunotherapy.
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Affiliation(s)
- Stephanie J. Hanna
- Diabetes Research Group, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Danijela Tatovic
- Diabetes Research Group, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Terri C. Thayer
- Diabetes Research Group, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Department of Biological and Chemical Sciences, School of Natural and Social Sciences, Roberts Wesleyan College, Rochester, NY, United States
| | - Colin M. Dayan
- Diabetes Research Group, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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25
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Nevinsky GA, Baranova SV, Buneva VN, Dmitrenok PS. Multiple Sclerosis: Enzymatic Cross Site-Specific Hydrolysis of H1 Histone by IgGs against H1, H2A, H2B, H3, H4 Histones, and Myelin Basic Protein. Biomolecules 2021; 11:biom11081140. [PMID: 34439806 PMCID: PMC8392522 DOI: 10.3390/biom11081140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/22/2021] [Accepted: 07/29/2021] [Indexed: 12/16/2022] Open
Abstract
Histones play a key role in chromatin remodeling and gene transcription. Further, free histones in the blood act as damage-associated molecules. Administration of histones to animals results in systemic inflammatory and toxic effects. Myelin basic protein is the principal constituent element of the myelin-proteolipid sheath of axons. Abzymes (antibodies with catalytic activities) are the original features of some autoimmune diseases. In this study, electrophoretically homogeneous IgGs against H1, H2A, H2B, H3, and H4 histones and myelin basic protein (MBP) were isolated from the blood sera of multiple sclerosis (MS) patients by several affinity chromatographies. Using MALDI mass spectrometry, the sites of H1 histone cleavage by IgGs against H1, H2A, H2B, H3, H4, and MBP were determined. It was shown that IgGs against H1 split H1 at 12 sites, while the number of cleavage sites by abzymes against other histones was lower: H2A (9), H2B (7), H3 (3), and H4 (3). The minimum rate of H1 hydrolysis was observed for antibodies against H3 and H4. A high rate of hydrolysis and the maximum number of H1 hydrolysis sites (17) were found for antibodies against MBP. Only a few sites of H1 hydrolysis by anti-H1 antibodies coincided with those for IgGs against H2A, H2B, H3, H4, and MBP. Thus, the polyreactivity of complexation and the enzymatic cross-activity of antibodies against H1, four other histones, and MBP have first been shown. Since histones act as damage molecules, abzymes against histones and MBP can play a negative role in the pathogenesis of MS and probably other different diseases as well.
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Affiliation(s)
- Georgy A. Nevinsky
- Siberian Division, Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (S.V.B.); (V.N.B.)
- Correspondence:
| | - Svetlana V. Baranova
- Siberian Division, Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (S.V.B.); (V.N.B.)
| | - Valentina N. Buneva
- Siberian Division, Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (S.V.B.); (V.N.B.)
| | - Pavel S. Dmitrenok
- Far East Division, Pacific Institute of Bioorganic Chemistry, Russian Academy of Sciences, 690022 Vladivostok, Russia;
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26
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Feldman J, Bals J, Altomare CG, St Denis K, Lam EC, Hauser BM, Ronsard L, Sangesland M, Moreno TB, Okonkwo V, Hartojo N, Balazs AB, Bajic G, Lingwood D, Schmidt AG. Naive human B cells engage the receptor binding domain of SARS-CoV-2, variants of concern, and related sarbecoviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33594359 PMCID: PMC7885909 DOI: 10.1101/2021.02.02.429458] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Exposure to a pathogen elicits an adaptive immune response aimed to control and eradicate. Interrogating the abundance and specificity of the naive B cell repertoire contributes to understanding how to potentially elicit protective responses. Here, we isolated naive B cells from 8 seronegative human donors targeting the SARS-CoV-2 receptor-binding domain (RBD). Single B cell analysis showed diverse gene usage with no restricted complementarity determining region lengths. We show that recombinant antibodies engage SARS-CoV-2 RBD, circulating variants, and pre-emergent coronaviruses. Representative antibodies signal in a B cell activation assay and can be affinity matured through directed evolution. Structural analysis of a naive antibody in complex with spike shows a conserved mode of recognition shared with infection-induced antibodies. Lastly, both naive and affinity-matured antibodies can neutralize SARS-CoV-2. Understanding the naive repertoire may inform potential responses recognizing variants or emerging coronaviruses enabling the development of pan-coronavirus vaccines aimed at engaging germline responses. Isolation of antibody germline precursors targeting the receptor binding domain of coronaviruses.
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Affiliation(s)
- Jared Feldman
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Julia Bals
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Clara G Altomare
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kerri St Denis
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Evan C Lam
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Blake M Hauser
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Larance Ronsard
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Maya Sangesland
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | | | - Vintus Okonkwo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Nathania Hartojo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | | | - Goran Bajic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Daniel Lingwood
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Aaron G Schmidt
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA.,Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
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27
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Sasaki Y, Yoshino N, Okuwa T, Odagiri T, Satoh T, Muraki Y. A mouse monoclonal antibody against influenza C virus attenuates acetaminophen-induced liver injury in mice. Sci Rep 2021; 11:11816. [PMID: 34083649 PMCID: PMC8175586 DOI: 10.1038/s41598-021-91251-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/24/2021] [Indexed: 11/09/2022] Open
Abstract
Molecular mimicry is one of the main processes for producing autoantibodies during infections. Although some autoantibodies are associated with autoimmune diseases, the functions of many autoantibodies remain unknown. Previously, we reported that S16, a mouse (BALB/c) monoclonal antibody against the hemagglutinin-esterase fusion glycoprotein of influenza C virus, recognizes host proteins in some species of animals, but we could not succeed in identifying the proteins. In the present study, we found that S16 cross-reacted with acetyl-CoA acyltransferase 2 (ACAA2), which is expressed in the livers of BALB/c mice. ACAA2 was released into the serum after acetaminophen (APAP) administration, and its serum level correlated with serum alanine aminotransferase (ALT) activity. Furthermore, we observed that S16 injected into mice with APAP-induced hepatic injury prompted the formation of an immune complex between S16 and ACAA2 in the serum. The levels of serum ALT (p < 0.01) and necrotic areas in the liver (p < 0.01) were reduced in the S16-injected mice. These results suggest that S16 may have a mitigation function in response to APAP-induced hepatotoxicity. This study shows the therapeutic function of an autoantibody and suggests that an antibody against extracellular ACAA2 might be a candidate for treating APAP-induced hepatic injury.
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Affiliation(s)
- Yutaka Sasaki
- Division of Infectious Diseases and Immunology, Department of Microbiology, School of Medicine, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Naoto Yoshino
- Division of Infectious Diseases and Immunology, Department of Microbiology, School of Medicine, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Takako Okuwa
- Department of Microbiology, Kanazawa Medical University School of Medicine, Ishikawa, Japan
| | - Takashi Odagiri
- Division of Infectious Diseases and Immunology, Department of Microbiology, School of Medicine, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Takashi Satoh
- Department of Pathology, School of Medicine, Iwate Medical University, Iwate, Japan
| | - Yasushi Muraki
- Division of Infectious Diseases and Immunology, Department of Microbiology, School of Medicine, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan.
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28
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Baranova SV, Dmitrenok PS, Buneva VN, Sedykh SE, Nevinsky GA. HIV-Infected Patients: Cross Site-Specific Hydrolysis of H3 and H4 Histones and Myelin Basic Protein with Antibodies against These Three Proteins. Molecules 2021; 26:E316. [PMID: 33435385 PMCID: PMC7826842 DOI: 10.3390/molecules26020316] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/03/2021] [Accepted: 01/05/2021] [Indexed: 11/16/2022] Open
Abstract
Histones play important roles in chromatin functioning and gene transcription, but in the intercellular space, they are harmful since they stimulate systemic inflammatory and toxic responses. Electrophoretically homogeneous IgGs against myelin basic protein (MBP), as well as H3 and H4 histones, were isolated from sera of HIV-infected patients. In contrast to known classical proteases, these IgGs split exclusively only histones and MBP but no other control proteins. Among 13 sites of hydrolysis of H3 by IgGs against H3 and 14 sites for anti-MBP IgGs, only two sites of the hydrolysis were the same. Between seven cleavage sites of H4 with IgGs against H4 and 9 sites of this histone hydrolysis by antibodies against MBP, only three sites were the same. The sites of hydrolysis of H3 (and H4) with abzymes against these histones and against MBP were different, but several expended protein clusters containing hydrolysis sites are partially overlapped. The existence of enzymatic cross-reactivity of abzymes against H3 and H4 and MBP represents a great menace to humans since due to cell apoptosis, histones constantly occur in human blood. They can hydrolyze MBP of the myelin sheath of axons and play a negative role in the pathogenesis of HIV-infected patients.
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Affiliation(s)
- Svetlana V. Baranova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (S.V.B.); (V.N.B.); (S.E.S.)
| | - Pavel S. Dmitrenok
- G. B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Brunch of the Russian Academy of Sciences, 159 Pr. 100 let Vladivostoku, 690022 Vladivostok, Russia;
| | - Valentina N. Buneva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (S.V.B.); (V.N.B.); (S.E.S.)
| | - Sergey E. Sedykh
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (S.V.B.); (V.N.B.); (S.E.S.)
| | - Georgy A. Nevinsky
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (S.V.B.); (V.N.B.); (S.E.S.)
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29
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Kreye J, Reincke SM, Kornau HC, Sánchez-Sendin E, Corman VM, Liu H, Yuan M, Wu NC, Zhu X, Lee CCD, Trimpert J, Höltje M, Dietert K, Stöffler L, von Wardenburg N, van Hoof S, Homeyer MA, Hoffmann J, Abdelgawad A, Gruber AD, Bertzbach LD, Vladimirova D, Li LY, Barthel PC, Skriner K, Hocke AC, Hippenstiel S, Witzenrath M, Suttorp N, Kurth F, Franke C, Endres M, Schmitz D, Jeworowski LM, Richter A, Schmidt ML, Schwarz T, Müller MA, Drosten C, Wendisch D, Sander LE, Osterrieder N, Wilson IA, Prüss H. A Therapeutic Non-self-reactive SARS-CoV-2 Antibody Protects from Lung Pathology in a COVID-19 Hamster Model. Cell 2020; 183:1058-1069.e19. [PMID: 33058755 PMCID: PMC7510528 DOI: 10.1016/j.cell.2020.09.049] [Citation(s) in RCA: 243] [Impact Index Per Article: 60.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/14/2020] [Accepted: 09/18/2020] [Indexed: 12/15/2022]
Abstract
The emergence of SARS-CoV-2 led to pandemic spread of coronavirus disease 2019 (COVID-19), manifesting with respiratory symptoms and multi-organ dysfunction. Detailed characterization of virus-neutralizing antibodies and target epitopes is needed to understand COVID-19 pathophysiology and guide immunization strategies. Among 598 human monoclonal antibodies (mAbs) from 10 COVID-19 patients, we identified 40 strongly neutralizing mAbs. The most potent mAb, CV07-209, neutralized authentic SARS-CoV-2 with an IC50 value of 3.1 ng/mL. Crystal structures of two mAbs in complex with the SARS-CoV-2 receptor-binding domain at 2.55 and 2.70 Å revealed a direct block of ACE2 attachment. Interestingly, some of the near-germline SARS-CoV-2-neutralizing mAbs reacted with mammalian self-antigens. Prophylactic and therapeutic application of CV07-209 protected hamsters from SARS-CoV-2 infection, weight loss, and lung pathology. Our results show that non-self-reactive virus-neutralizing mAbs elicited during SARS-CoV-2 infection are a promising therapeutic strategy.
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MESH Headings
- Angiotensin-Converting Enzyme 2
- Animals
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/immunology
- Antibodies, Viral/therapeutic use
- Antigen-Antibody Reactions
- Betacoronavirus/immunology
- Betacoronavirus/metabolism
- Betacoronavirus/pathogenicity
- Binding Sites
- COVID-19
- Coronavirus Infections/drug therapy
- Coronavirus Infections/pathology
- Coronavirus Infections/virology
- Cricetinae
- Crystallography, X-Ray
- Disease Models, Animal
- Humans
- Kinetics
- Lung/immunology
- Lung/metabolism
- Lung/pathology
- Mice
- Mice, Inbred C57BL
- Molecular Dynamics Simulation
- Pandemics
- Peptidyl-Dipeptidase A/chemistry
- Peptidyl-Dipeptidase A/metabolism
- Pneumonia, Viral/drug therapy
- Pneumonia, Viral/pathology
- Pneumonia, Viral/virology
- Protein Binding
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- Jakob Kreye
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Department of Pediatric Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany.
| | - S Momsen Reincke
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Hans-Christian Kornau
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Neuroscience Research Center (NWFZ), Cluster NeuroCure, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Elisa Sánchez-Sendin
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Victor Max Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany, and German Centre for Infection Research (DZIF), 10117 Berlin, Germany
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicholas C Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chang-Chun D Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jakob Trimpert
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany
| | - Markus Höltje
- Institute of Integrative Neuroanatomy Berlin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Kristina Dietert
- Institute of Veterinary Pathology, Freie Universität Berlin, 14163 Berlin, Germany; Veterinary Centre for Resistance Research, Freie Universität Berlin, 14163 Berlin, Germany
| | - Laura Stöffler
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Niels von Wardenburg
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Scott van Hoof
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Marie A Homeyer
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Julius Hoffmann
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Azza Abdelgawad
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany
| | - Achim D Gruber
- Institute of Veterinary Pathology, Freie Universität Berlin, 14163 Berlin, Germany
| | - Luca D Bertzbach
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany
| | - Daria Vladimirova
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany
| | - Lucie Y Li
- Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Institute of Integrative Neuroanatomy Berlin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Paula Charlotte Barthel
- Institute of Integrative Neuroanatomy Berlin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Karl Skriner
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Andreas C Hocke
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Stefan Hippenstiel
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Martin Witzenrath
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Norbert Suttorp
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine and I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20359 Hamburg, Germany
| | - Christiana Franke
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Matthias Endres
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Center for Stroke Research Berlin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; Excellence Cluster NeuroCure Berlin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany; German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10785 Berlin, Germany
| | - Dietmar Schmitz
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Neuroscience Research Center (NWFZ), Cluster NeuroCure, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Lara Maria Jeworowski
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany, and German Centre for Infection Research (DZIF), 10117 Berlin, Germany
| | - Anja Richter
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany, and German Centre for Infection Research (DZIF), 10117 Berlin, Germany
| | - Marie Luisa Schmidt
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany, and German Centre for Infection Research (DZIF), 10117 Berlin, Germany
| | - Tatjana Schwarz
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany, and German Centre for Infection Research (DZIF), 10117 Berlin, Germany
| | - Marcel Alexander Müller
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany, and German Centre for Infection Research (DZIF), 10117 Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany, and German Centre for Infection Research (DZIF), 10117 Berlin, Germany
| | - Daniel Wendisch
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Leif E Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Nikolaus Osterrieder
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany; Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Harald Prüss
- German Center for Neurodegenerative Diseases (DZNE) Berlin, 10117 Berlin, Germany; Helmholtz Innovation Lab BaoBab (Brain Antibody-omics and B-cell Lab), 10117 Berlin, Germany; Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, 10117 Berlin, Germany.
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Baranova SV, Dmitrienok PS, Buneva VN, Nevinsky GA. HIV-Infected Patients: Cross Site-Specific Hydrolysis of H2a and H2b Histones and Myelin Basic Protein with Antibodies against These Three Proteins. Biomolecules 2020; 10:E1501. [PMID: 33143355 PMCID: PMC7693679 DOI: 10.3390/biom10111501] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/05/2020] [Accepted: 10/27/2020] [Indexed: 01/28/2023] Open
Abstract
Anti-DNA antibodies are usually produced against histone-DNA complexes appearing during cell apoptosis, while histones are known as damage-associated molecules. A myelin sheath of axons contains myelin basic protein (MBP) playing an important role in the pathogenesis of autoimmune diseases. Antibodies with enzymatic activities (abzymes) are distinctive features of some autoimmune and viral diseases. Abzymes against different proteins can usually only hydrolyze these specific proteins. Using sequential chromatographies of homogeneous IgG preparations from sera of HIV-infected patients on columns with immobilized MBP, H2a, and H2b histones, the anti-MBP, anti-H2a, and anti-H2b antibodies were obtained. It was first shown that IgGs against H2a and H2b effectively hydrolyze these histones and MBP, while anti-MBP split MBP, H2a, and H2b, but no other control proteins. Using the MALDI mass spectrometry, the cleavage sites of H2a, H2b, and MBP by abzymes against these three proteins were found. Among 14 sites of hydrolysis of H2a by IgGs against H2a and 10 sites by anti-MBP IgGs, only one site of hydrolysis was the same for these abzymes. Eleven cleavage sites of H2b with IgGs against H2b and 10 sites of its hydrolysis with antibodies against MBP were different. Anti-H2a, anti-H2b, and anti-MBP abzymes are unpredictable examples of IgGs possessing not only cross-complexation but also catalytic cross-reactivity, which may be a common phenomenon for such abzymes in patients with different autoimmune diseases. The existence of cross-reactivity of abzymes against H2a and H2b histones and MBP represent a great danger to humans since, in contrast with MBP, histones due to cell apoptosis constantly occur in human blood. Anti-H2a, anti-H2b, and anti-MBP can attack and hydrolyze myelin basic protein of the myelin sheath of axons and plays a negative role in the pathogenesis of several pathologies.
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Affiliation(s)
- Svetlana V. Baranova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, 630090 Lavrentiev, Russia; (S.V.B.); (V.N.B.)
| | - Pavel S. Dmitrienok
- Pacific Institute of Bioorganic Chemistry, Far East Division, Russian Academy of Sciences, 690022 Vladivostok, Russia;
| | - Valentina N. Buneva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, 630090 Lavrentiev, Russia; (S.V.B.); (V.N.B.)
| | - Georgy A. Nevinsky
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, 630090 Lavrentiev, Russia; (S.V.B.); (V.N.B.)
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31
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Fernández-Quintero ML, Pomarici ND, Math BA, Kroell KB, Waibl F, Bujotzek A, Georges G, Liedl KR. Antibodies exhibit multiple paratope states influencing V H-V L domain orientations. Commun Biol 2020; 3:589. [PMID: 33082531 PMCID: PMC7576833 DOI: 10.1038/s42003-020-01319-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 09/23/2020] [Indexed: 11/17/2022] Open
Abstract
In the last decades, antibodies have emerged as one of the most important and successful classes of biopharmaceuticals. The highest variability and diversity of an antibody is concentrated on six hypervariable loops, also known as complementarity determining regions (CDRs) shaping the antigen-binding site, the paratope. Whereas it was assumed that certain sequences can only adopt a limited set of backbone conformations, in this study we present a kinetic classification of several paratope states in solution. Using molecular dynamics simulations in combination with experimental structural information we capture the involved conformational transitions between different canonical clusters and additional dominant solution structures occurring in the micro-to-millisecond timescale. Furthermore, we observe a strong correlation of CDR loop movements. Another important aspect when characterizing different paratope states is the relative VH/VL orientation and the influence of the distinct CDR loop states on the VH/VL interface. Conformational rearrangements of the CDR loops do not only have an effect on the relative VH/VL orientations, but also influence in some cases the elbow-angle dynamics and shift the respective distributions. Thus, our results show that antibodies exist as several interconverting paratope states, each contributing to the antibody's properties.
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Affiliation(s)
- Monica L Fernández-Quintero
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Nancy D Pomarici
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Barbara A Math
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Katharina B Kroell
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Franz Waibl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria
| | - Alexander Bujotzek
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Guy Georges
- Roche Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Klaus R Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020, Innsbruck, Austria.
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32
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Conformational diversity facilitates antibody mutation trajectories and discrimination between foreign and self-antigens. Proc Natl Acad Sci U S A 2020; 117:22341-22350. [PMID: 32855302 PMCID: PMC7486785 DOI: 10.1073/pnas.2005102117] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Conformational diversity and self-cross-reactivity of antigens have been correlated with evasion from neutralizing antibody responses. We utilized single cell B cell sequencing, biolayer interferometry and X-ray crystallography to trace mutation selection pathways where the antibody response must resolve cross-reactivity between foreign and self-proteins bearing near-identical contact surfaces, but differing in conformational flexibility. Recurring antibody mutation trajectories mediate long-range rearrangements of framework (FW) and complementarity determining regions (CDRs) that increase binding site conformational diversity. These antibody mutations decrease affinity for self-antigen 19-fold and increase foreign affinity 67-fold, to yield a more than 1,250-fold increase in binding discrimination. These results demonstrate how conformational diversity in antigen and antibody does not act as a barrier, as previously suggested, but rather facilitates high affinity and high discrimination between foreign and self.
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33
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Kreye J, Reincke SM, Kornau HC, Sánchez-Sendin E, Max Corman V, Liu H, Yuan M, Wu NC, Zhu X, Lee CCD, Trimpert J, Höltje M, Dietert K, Stöffler L, von Wardenburg N, van Hoof S, Homeyer MA, Hoffmann J, Abdelgawad A, Gruber AD, Bertzbach LD, Vladimirova D, Li LY, Barthel PC, Skriner K, Hocke AC, Hippenstiel S, Witzenrath M, Suttorp N, Kurth F, Franke C, Endres M, Schmitz D, Jeworowski LM, Richter A, Schmidt ML, Schwarz T, Müller MA, Drosten C, Wendisch D, Sander LE, Osterrieder N, Wilson IA, Prüss H. A SARS-CoV-2 neutralizing antibody protects from lung pathology in a COVID-19 hamster model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.08.15.252320. [PMID: 32817952 PMCID: PMC7430590 DOI: 10.1101/2020.08.15.252320] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The emergence of SARS-CoV-2 led to pandemic spread of coronavirus disease 2019 (COVID-19), manifesting with respiratory symptoms and multi-organ dysfunction. Detailed characterization of virus-neutralizing antibodies and target epitopes is needed to understand COVID-19 pathophysiology and guide immunization strategies. Among 598 human monoclonal antibodies (mAbs) from ten COVID-19 patients, we identified 40 strongly neutralizing mAbs. The most potent mAb CV07-209 neutralized authentic SARS-CoV-2 with IC50 of 3.1 ng/ml. Crystal structures of two mAbs in complex with the SARS-CoV-2 receptor-binding domain at 2.55 and 2.70 A revealed a direct block of ACE2 attachment. Interestingly, some of the near-germline SARS-CoV-2 neutralizing mAbs reacted with mammalian self-antigens. Prophylactic and therapeutic application of CV07-209 protected hamsters from SARS-CoV-2 infection, weight loss and lung pathology. Our results show that non-self-reactive virus-neutralizing mAbs elicited during SARS-CoV-2 infection are a promising therapeutic strategy.
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Affiliation(s)
- Jakob Kreye
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
- Department of Pediatric Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - S Momsen Reincke
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Hans-Christian Kornau
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Neuroscience Research Center (NWFZ), Cluster NeuroCure, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Elisa Sánchez-Sendin
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Victor Max Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nicholas C. Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xueyong Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chang-Chun D. Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jakob Trimpert
- Institute of Virology, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany
| | - Markus Höltje
- Institute of Integrative Neuroanatomy Berlin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Kristina Dietert
- Institute of Veterinary Pathology, Freie Universität Berlin, Robert-von-Ostertag-Str. 15, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research, Freie Universität Berlin, Robert-von-Ostertag-Str. 8, 14163 Berlin, Germany
| | - Laura Stöffler
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Niels von Wardenburg
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Scott van Hoof
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Marie A Homeyer
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
- Berlin Institute of Health (BIH), 10178 Berlin, Germany
| | - Julius Hoffmann
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Azza Abdelgawad
- Institute of Virology, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany
| | - Achim D Gruber
- Institute of Veterinary Pathology, Freie Universität Berlin, Robert-von-Ostertag-Str. 15, 14163 Berlin, Germany
| | - Luca D Bertzbach
- Institute of Virology, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany
| | - Daria Vladimirova
- Institute of Virology, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany
| | - Lucie Y Li
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
- Institute of Integrative Neuroanatomy Berlin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Paula Charlotte Barthel
- Institute of Integrative Neuroanatomy Berlin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Karl Skriner
- Department of Rheumatology and Clinical Immunology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Andreas C Hocke
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Stefan Hippenstiel
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Martin Witzenrath
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Norbert Suttorp
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine and I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christiana Franke
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Matthias Endres
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
- Center for Stroke Research Berlin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
- Excellence Cluster NeuroCure Berlin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), partner site Berlin, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Dietmar Schmitz
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Neuroscience Research Center (NWFZ), Cluster NeuroCure, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Lara Maria Jeworowski
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Anja Richter
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Marie Luisa Schmidt
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Tatjana Schwarz
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Marcel Alexander Müller
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany, and German Centre for Infection Research (DZIF), Berlin, Germany
| | - Daniel Wendisch
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Leif E Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Nikolaus Osterrieder
- Institute of Virology, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Harald Prüss
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
- Helmholtz Innovation Lab BaoBab (Brain antibody-omics and B-cell Lab), Berlin, Germany
- Department of Neurology and Experimental Neurology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
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34
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Fernández-Quintero ML, Loeffler JR, Bacher LM, Waibl F, Seidler CA, Liedl KR. Local and Global Rigidification Upon Antibody Affinity Maturation. Front Mol Biosci 2020; 7:182. [PMID: 32850970 PMCID: PMC7426445 DOI: 10.3389/fmolb.2020.00182] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/13/2020] [Indexed: 01/03/2023] Open
Abstract
During the affinity maturation process the immune system produces antibodies with higher specificity and activity through various rounds of somatic hypermutations in response to an antigen. Elucidating the affinity maturation process is fundamental in understanding immunity and in the development of biotherapeutics. Therefore, we analyzed 10 pairs of antibody fragments differing in their specificity and in distinct stages of affinity maturation using metadynamics in combination with molecular dynamics (MD) simulations. We investigated differences in flexibility of the CDR-H3 loop and global changes in plasticity upon affinity maturation. Among all antibody pairs we observed a substantial rigidification in flexibility and plasticity reflected in a substantial decrease of conformational diversity. To visualize and characterize these findings we used Markov-states models to reconstruct the kinetics of CDR-H3 loop dynamics and for the first time provide a method to define and localize surface plasticity upon affinity maturation.
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Affiliation(s)
- Monica L Fernández-Quintero
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Johannes R Loeffler
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Lisa M Bacher
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Franz Waibl
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Clarissa A Seidler
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
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35
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Guzman NA, Guzman DE. A Two-Dimensional Affinity Capture and Separation Mini-Platform for the Isolation, Enrichment, and Quantification of Biomarkers and Its Potential Use for Liquid Biopsy. Biomedicines 2020; 8:biomedicines8080255. [PMID: 32751506 PMCID: PMC7459796 DOI: 10.3390/biomedicines8080255] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/22/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023] Open
Abstract
Biomarker detection for disease diagnosis, prognosis, and therapeutic response is becoming increasingly reliable and accessible. Particularly, the identification of circulating cell-free chemical and biochemical substances, cellular and subcellular entities, and extracellular vesicles has demonstrated promising applications in understanding the physiologic and pathologic conditions of an individual. Traditionally, tissue biopsy has been the gold standard for the diagnosis of many diseases, especially cancer. More recently, liquid biopsy for biomarker detection has emerged as a non-invasive or minimally invasive and less costly method for diagnosis of both cancerous and non-cancerous diseases, while also offering information on the progression or improvement of disease. Unfortunately, the standardization of analytical methods to isolate and quantify circulating cells and extracellular vesicles, as well as their extracted biochemical constituents, is still cumbersome, time-consuming, and expensive. To address these limitations, we have developed a prototype of a portable, miniaturized instrument that uses immunoaffinity capillary electrophoresis (IACE) to isolate, concentrate, and analyze cell-free biomarkers and/or tissue or cell extracts present in biological fluids. Isolation and concentration of analytes is accomplished through binding to one or more biorecognition affinity ligands immobilized to a solid support, while separation and analysis are achieved by high-resolution capillary electrophoresis (CE) coupled to one or more detectors. When compared to other existing methods, the process of this affinity capture, enrichment, release, and separation of one or a panel of biomarkers can be carried out on-line with the advantages of being rapid, automated, and cost-effective. Additionally, it has the potential to demonstrate high analytical sensitivity, specificity, and selectivity. As the potential of liquid biopsy grows, so too does the demand for technical advances. In this review, we therefore discuss applications and limitations of liquid biopsy and hope to introduce the idea that our affinity capture-separation device could be used as a form of point-of-care (POC) diagnostic technology to isolate, concentrate, and analyze circulating cells, extracellular vesicles, and viruses.
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Affiliation(s)
- Norberto A. Guzman
- Princeton Biochemicals, Inc., Princeton, NJ 08816, USA
- Correspondence: ; Tel.: +1-908-510-5258
| | - Daniel E. Guzman
- Princeton Biochemicals, Inc., Princeton, NJ 08816, USA
- Department of Internal Medicine, University of California at San Francisco, San Francisco, CA 94143, USA; or
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36
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Sobel RA, Eaton MJ, Jaju PD, Lowry E, Hinojoza JR. Anti-Myelin Proteolipid Protein Peptide Monoclonal Antibodies Recognize Cell Surface Proteins on Developing Neurons and Inhibit Their Differentiation. J Neuropathol Exp Neurol 2020; 78:819-843. [PMID: 31400116 PMCID: PMC6703999 DOI: 10.1093/jnen/nlz058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/30/2019] [Accepted: 06/18/2019] [Indexed: 12/15/2022] Open
Abstract
Using a panel of monoclonal antibodies (mAbs) to myelin proteolipid protein (PLP) peptides, we found that in addition to CNS myelin, mAbs to external face but not cytoplasmic face epitopes immunostained neurons in immature human CNS tissues and in adult hippocampal dentate gyrus and olfactory bulbs, that is neural stem cell niches (NSCN). To explore the pathobiological significance of these observations, we assessed the mAb effects on neurodifferentiation in vitro. The mAbs to PLP 50-69 (IgG1κ and IgG2aκ), and 178-191 and 200-219 (both IgG1κ) immunostained live cell surfaces and inhibited neurite outgrowth of E18 rat hippocampal precursor cells and of PC12 cells, which do not express PLP. Proteins immunoprecipitated from PC12 cell extracts and captured by mAb-coated magnetic beads were identified by GeLC-MS/MS. Each neurite outgrowth-inhibiting mAb captured a distinct set of neurodifferentiation molecules including sequence-similar M6 proteins and other unrelated membrane and extracellular matrix proteins, for example integrins, Eph receptors, NCAM-1, and protocadherins. These molecules are expressed in adult human NSCN and are implicated in the pathogenesis of many chronic CNS disease processes. Thus, diverse anti-PLP epitope autoantibodies may inhibit neuronal precursor cell differentiation via multispecific recognition of cell surface molecules thereby potentially impeding endogenous neuroregeneration in NSCN and in vivo differentiation of exogenous neural stem cells.
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Affiliation(s)
- Raymond A Sobel
- Laboratory Service, Veterans Affairs Health Care System, Palo Alto, California.,Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Mary Jane Eaton
- Laboratory Service, Veterans Affairs Health Care System, Palo Alto, California.,Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Prajakta Dilip Jaju
- Laboratory Service, Veterans Affairs Health Care System, Palo Alto, California.,Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Eugene Lowry
- Laboratory Service, Veterans Affairs Health Care System, Palo Alto, California.,Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Julian R Hinojoza
- Laboratory Service, Veterans Affairs Health Care System, Palo Alto, California.,Department of Pathology, Stanford University School of Medicine, Stanford, California
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37
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Kumar D, Romero Y, Schuck KN, Smalley H, Subedi B, Fleming SD. Drivers and regulators of humoral innate immune responses to infection and cancer. Mol Immunol 2020; 121:99-110. [PMID: 32199212 PMCID: PMC7207242 DOI: 10.1016/j.molimm.2020.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/21/2022]
Abstract
The complement cascade consists of cell bound and serum proteins acting together to protect the host from pathogens, remove cancerous cells and effectively links innate and adaptive immune responses. Despite its usefulness in microbial neutralization and clearance of cancerous cells, excessive complement activation causes an immune imbalance and tissue damage in the host. Hence, a series of complement regulatory proteins present at a higher concentration in blood plasma and on cell surfaces tightly regulate the cascade. The complement cascade can be initiated by B-1 B cell production of natural antibodies. Natural antibodies arise spontaneously without any known exogenous antigenic or microbial stimulus and protect against invading pathogens, clear apoptotic cells, provide tissue homeostasis, and modulate adaptive immune functions. Natural IgM antibodies recognize microbial and cancer antigens and serve as an activator of complement mediated lysis. This review will discuss advances in complement activation and regulation in bacterial and viral infections, and cancer. We will also explore the crosstalk of natural antibodies with bacterial populations and cancer.
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MESH Headings
- Antigens, Bacterial/immunology
- Antigens, Bacterial/metabolism
- Antigens, Neoplasm/immunology
- Antigens, Neoplasm/metabolism
- Antigens, Viral/immunology
- Antigens, Viral/metabolism
- Apoptosis/immunology
- B-Lymphocytes/immunology
- B-Lymphocytes/metabolism
- Bacterial Infections/immunology
- Complement Activation
- Complement System Proteins/immunology
- Complement System Proteins/metabolism
- Humans
- Immunity, Humoral
- Immunity, Innate
- Immunoglobulin M/immunology
- Immunoglobulin M/metabolism
- Neoplasms/immunology
- Receptors, Complement/immunology
- Receptors, Complement/metabolism
- Tumor Escape
- Virus Diseases/immunology
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Affiliation(s)
- Deepak Kumar
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Yeni Romero
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, USA
| | - Kaitlynn N Schuck
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Haley Smalley
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Bibek Subedi
- Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Sherry D Fleming
- Division of Biology, Kansas State University, Manhattan, KS, USA.
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38
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Valeff N, Juriol L, Quadrana F, Muzzio DO, Zygmunt M, Quiroga MF, Ventimiglia MS, Jensen F. Expression of IL-33 Receptor Is Significantly Up-Regulated in B Cells During Pregnancy and in the Acute Phase of Preterm Birth in Mice. Front Immunol 2020; 11:446. [PMID: 32292403 PMCID: PMC7118206 DOI: 10.3389/fimmu.2020.00446] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 02/26/2020] [Indexed: 12/22/2022] Open
Abstract
Interleukin-33 (IL-33) is a mucosal alarmin belonging to the IL-1 cytokine family and is now recognized to have a key role in innate and adaptive immunity, contributing to tissue homeostasis and response to environmental stresses. In addition, IL-33 has also been shown to work as a positive regulator that initiates and maintains a Th2 immune response. In the context of pregnancy, it has been recently demonstrated that upon certain stress conditions, such as an infection induced inflammation, IL-33 is released from the uterine mucosa and triggers decidual B cells to produce anti-inflammatory molecules, which in turn restore immune homeostasis and prevents the development of preterm birth. In this study we therefore performed a detailed characterization of IL-33 receptor (Il1rl1 or ST2) expression in B cells during normal pregnancy, as well as in a mouse model of preterm birth. We observed that splenic B cells significantly up-regulate the expression of Il1rl1 during pregnancy and identified the B1 B cell population as the main ST2-expressing B cell subset. A further kinetic analysis showed that percentages of ST2-expressing B1 B cells are significantly augmented on days 12 and 14 of pregnancy, both in the spleen and peritoneal cavity of pregnant mice, and then drop toward the end of pregnancy to the levels observed in non-pregnant animals. Furthermore, using a mouse model of LPS-induced preterm birth, we demonstrated that not only are the percentages of ST2-expressing B1 B cells significantly enlarged in the spleen during the acute phase of preterm birth, but decidual B cells also significantly up-regulate ST2 expression as compared to term-pregnant mice. Overall, our results suggest a functional role of ST2 expression in B cells during pregnancy and reinforce the importance of the IL-33/ST2 axis in B cells as a critical mechanism to control inflammation-induced preterm birth.
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Affiliation(s)
- Natalin Valeff
- Laboratory for Immunology of Pregnancy, Center for Pharmacological and Botanical Studies (CEFYBO-CONICET-UBA), Buenos Aires, Argentina
| | - Lorena Juriol
- Laboratory for Immunology of Pregnancy, Center for Pharmacological and Botanical Studies (CEFYBO-CONICET-UBA), Buenos Aires, Argentina
| | - Florencia Quadrana
- Laboratory for Immunology of Pregnancy, Center for Pharmacological and Botanical Studies (CEFYBO-CONICET-UBA), Buenos Aires, Argentina
| | - Damián Oscar Muzzio
- Research Laboratory, Department of Obstetrics and Gynecology, University of Greifswald, Greifswald, Germany
| | - Marek Zygmunt
- Research Laboratory, Department of Obstetrics and Gynecology, University of Greifswald, Greifswald, Germany
| | - Maria Florencia Quiroga
- Instituto de Investigaciones Biomédicas en Retrovirus y Sida (INBIRS), Facultad de Medicina, Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - María Silvia Ventimiglia
- Laboratory for Immunology of Pregnancy, Center for Pharmacological and Botanical Studies (CEFYBO-CONICET-UBA), Buenos Aires, Argentina
| | - Federico Jensen
- Laboratory for Immunology of Pregnancy, Center for Pharmacological and Botanical Studies (CEFYBO-CONICET-UBA), Buenos Aires, Argentina.,Institute of Health Sciences, National University Arturo Jauretche, Buenos Aires, Argentina
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Trueeb BS, Braun RO, Auray G, Kuhnert P, Summerfield A. Differential innate immune responses induced by Mycoplasma hyopneumoniae and Mycoplasma hyorhinis in various types of antigen presenting cells. Vet Microbiol 2019; 240:108541. [PMID: 31902489 DOI: 10.1016/j.vetmic.2019.108541] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 01/08/2023]
Abstract
Mycoplasma (M.) hyopneumoniae is the etiological agent of enzootic pneumonia in pigs and is closely related to M. hyorhinis, which can be isolated from the healthy mucosal surfaces of the upper respiratory tract. In rare cases it can also cause arthritis and polyserositis. Since the innate immune system is an important first line of defense and promotes adaptive immune responses, we characterized the innate immune response of various antigen presenting cells (APCs) to M. hyopneumoniae and M. hyorhinis, which differ in their pathogenicity in vivo. Porcine peripheral blood mononuclear cells were infected with different multiplicities of infection (MOI) of live and inactivated porcine mycoplasmas. Both Mycoplasma species induced strong tumour necrosis factor (TNF) responses in monocytes, with a stronger activation by M. hyorhinis. This higher stimulatory activity was also confirmed for CD40 upregulation. Conventional and plasmacytoid dendritic cells (cDC and pDC, respectively) did not or poorly respond to mycoplasmas in terms of TNF expression but more efficiently in terms of CD40 upregulation. Again, these responses were generally stronger with M. hyorhinis than with M. hyopneumoniae. Both Mycoplasma species also activated B cells in terms of CD25 upregulation, proliferation, and IgM secretion. Interestingly, while the induction of CD25 and in particular proliferation was higher with M. hyorhinis, the IgM secretion did not differ between the two species with the exception of the highest dose of M. hyopneumoniae,which appeared to suppress IgM responses. Taken together, our results provide a comparative analysis of innate immune response with different porcine APCs and demonstrate Mycoplasma species-dependent differences, which could relate to their different pathogenicity in vivo.
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Affiliation(s)
- Bettina S Trueeb
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland.
| | - Roman Othmar Braun
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of Bern, Switzerland.
| | - Gaël Auray
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland.
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Switzerland.
| | - Artur Summerfield
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland; Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Switzerland.
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40
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Blandino R, Baumgarth N. Secreted IgM: New tricks for an old molecule. J Leukoc Biol 2019; 106:1021-1034. [PMID: 31302940 PMCID: PMC6803036 DOI: 10.1002/jlb.3ri0519-161r] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/25/2019] [Accepted: 06/26/2019] [Indexed: 12/27/2022] Open
Abstract
Secreted IgM (sIgM) is a multifunctional evolutionary conserved antibody that is critical for the maintenance of tissue homeostasis as well as the development of fully protective humoral responses to pathogens. Constitutive secretion of self- and polyreactive natural IgM, produced mainly by B-1 cells, provides a circulating antibody that engages with autoantigens as well as invading pathogens, removing apoptotic and other cell debris and initiating strong immune responses. Pathogen-induced IgM production by B-1 and conventional B-2 cells strengthens this early, passive layer of IgM-mediated immune defense and regulates subsequent IgG production. The varied effects of secreted IgM on immune homeostasis and immune defense are facilitated through its binding to numerous different cell types via different receptors. Recent studies identified a novel function for pentameric IgM, namely as a transporter for the effector protein ″apoptosis-inhibitor of macrophages″ (AIM/CD5L). This review aims to provide a summary of the known functions and effects of sIgM on immune homeostasis and immune defense, and its interaction with its various receptors, and to highlight the many critical immune regulatory functions of this ancient and fascinating immunoglobulin.
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Affiliation(s)
- Rebecca Blandino
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis
- Center for Comparative Medicine and University of California, Davis
| | - Nicole Baumgarth
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis
- Center for Comparative Medicine and University of California, Davis
- Dept. Pathology, Microbiology & Immunology, University of California, Davis
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41
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Abstract
Natural antibodies are an innate-like subset of serum antibodies involved in host defense, tumor surveillance, homeostasis, and autoimmunity. Defining the natural antibody repertoire is critical for identifying biomarkers, developing vaccines, controlling and preventing autoimmunity, and understanding the development and organization of the immune system. While natural antibodies to protein antigens have been studied in depth, little is known about natural antibodies to carbohydrate antigens. To address this, we profiled IgM from umbilical cord blood and matched maternal sera on a glycan microarray. Since standard methods to detect maternal contamination in cord serum did not have sufficient sensitivity for our study, we developed a highly sensitive microarray-based assay. Using this method, we found that over 50% of the cord samples had unacceptable levels of maternal contamination. For the cord samples with high purity, anti-glycan IgM antibodies were prevalent and recognized a broad range of non-human and human glycans. Using principal component analysis and hierarchical clustering, cord IgM repertoires showed a high degree of similarity with each other but were distinct from maternal IgM repertoires. Our results demonstrate that many anti-glycan antibodies in human serum are natural antibodies and provide new insights into the development of anti-glycan antibody repertoires.
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42
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Bobrovnik SA, Demchenko MO, Komisarenko SV. Kinetics of interaction between polyreactive immunoglobulins and antigen. The theory. UKRAINIAN BIOCHEMICAL JOURNAL 2019. [DOI: 10.15407/ubj91.04.088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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43
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Abstract
PURPOSE OF REVIEW B cells have recently emerged as important immune players in solid organ rejection, especially in cardiac allograft vasculopathy (CAV), a chronic form of rejection following heart transplantation. B cells can exert either regulatory or effector functions. This review will provide an update on effector B cells in CAV. RECENT FINDINGS Independent studies reported the abundance of B cells in graft infiltrates during CAV, especially around coronary arteries. Infiltrates comprise CD20+ CD27+ memory B cells together with differentiated CD20-CD138+ plasma cells, which are almost always associated with T cells and macrophages. The structure of some of these infiltrates evokes that of germinal centers, suggesting the generation of tertiary lymphoid organs in the graft. Remarkably, B-cell infiltrates are most often detected in the absence of circulating donor human leukocyte antigen-specific antibodies, strongly suggesting that the two components are unrelated. Characterization of B-cell clones isolated from explanted human cardiac graft infiltrates revealed the prevalence of polyreactive innate, B1-like B cells. Accumulating evidence suggests that these cells act primarily as antigen-presenting cells in situ. Additional effector functions, such as local antibody secretion and pro-inflammatory cytokine production, promoting T-cell polarization, macrophage activation and fibrosis are also considered. SUMMARY Converging observations made through animal and human studies add substantial support for an effector B-cell role in the pathophysiology of CAV. On the basis of these collective findings, a therapeutic strategy targeting B cells could reasonably be envisaged to prevent or treat this complication.
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Affiliation(s)
- Emmanuel Zorn
- Columbia Center for Translational Immunology, New York Presbyterian Hospital, Columbia University Medical Center, New York, New York, USA
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44
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Fernández-Quintero ML, Loeffler JR, Kraml J, Kahler U, Kamenik AS, Liedl KR. Characterizing the Diversity of the CDR-H3 Loop Conformational Ensembles in Relationship to Antibody Binding Properties. Front Immunol 2019; 9:3065. [PMID: 30666252 PMCID: PMC6330313 DOI: 10.3389/fimmu.2018.03065] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 12/11/2018] [Indexed: 11/23/2022] Open
Abstract
We present an approach to assess antibody CDR-H3 loops according to their dynamic properties using molecular dynamics simulations. We selected six antibodies in three pairs differing substantially in their individual promiscuity respectively specificity. For two pairs of antibodies crystal structures are available in different states of maturation and used as starting structures for the analyses. For a third pair we chose two antibody CDR sequences obtained from a synthetic library and predicted the respective structures. For all three pairs of antibodies we performed metadynamics simulations to overcome the limitations in conformational sampling imposed by high energy barriers. Additionally, we used classic molecular dynamics simulations to describe nano- to microsecond flexibility and to estimate up to millisecond kinetics of captured conformational transitions. The methodology represents the antibodies as conformational ensembles and allows comprehensive analysis of structural diversity, thermodynamics of conformations and kinetics of structural transitions. Referring to the concept of conformational selection we investigated the link between promiscuity and flexibility of the antibodies' binding interfaces. The obtained detailed characterization of the binding interface clearly indicates a link between structural flexibility and binding promiscuity for this set of antibodies.
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Affiliation(s)
- Monica L Fernández-Quintero
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Johannes R Loeffler
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Johannes Kraml
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Ursula Kahler
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Anna S Kamenik
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Klaus R Liedl
- Center for Molecular Biosciences Innsbruck (CMBI), Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, Innsbruck, Austria
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45
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Vala M, Jordan LR, Warrington AE, Maher LJ, Rodriguez M, Wittenberg NJ, Oh SH. Surface Plasmon Resonance Sensing on Naturally Derived Membranes: A Remyelination-Promoting Human Antibody Binds Myelin with Extraordinary Affinity. Anal Chem 2018; 90:12567-12573. [DOI: 10.1021/acs.analchem.8b02664] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Milan Vala
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Luke R. Jordan
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Arthur E. Warrington
- Departments of Neurology and Immunology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - L. James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Moses Rodriguez
- Departments of Neurology and Immunology, Mayo Clinic, Rochester, Minnesota 55905, United States
| | - Nathan J. Wittenberg
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Sang-Hyun Oh
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota 55455, United States
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46
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Avrameas S, Alexopoulos H, Moutsopoulos HM. Natural Autoantibodies: An Undersugn Hero of the Immune System and Autoimmune Disorders-A Point of View. Front Immunol 2018; 9:1320. [PMID: 29946320 PMCID: PMC6005843 DOI: 10.3389/fimmu.2018.01320] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/28/2018] [Indexed: 12/25/2022] Open
Affiliation(s)
- Stratis Avrameas
- Laboratory of Immunology, Hellenic Pasteur Institute, Athens, Greece
| | - Haris Alexopoulos
- Department of Pathophysiology, Faculty of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Harry M Moutsopoulos
- Department of Pathophysiology, Faculty of Medicine, National and Kapodistrian University of Athens, Athens, Greece.,Academy of Athens, Athens, Greece
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47
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Hu F, Zhang W, Shi L, Liu X, Jia Y, Xu L, Zhu H, Li Y, Xu D, Lu L, Qiu X, Liu W, Qiao J, Wang Y, Li Z. Impaired CD27 +IgD + B Cells With Altered Gene Signature in Rheumatoid Arthritis. Front Immunol 2018; 9:626. [PMID: 29628928 PMCID: PMC5877504 DOI: 10.3389/fimmu.2018.00626] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/13/2018] [Indexed: 12/29/2022] Open
Abstract
Natural antibodies, particularly natural IgM, are proved to play indispensable roles in the immune defenses against common infections. More recently, the protective roles of these natural IgM were also recognized in autoimmune diseases. They are mainly produced by B-1 and innate-like B cells (ILBs). Human CD19+CD27+IgD+ B cells, also termed as un-switched memory B cells, were proposed to be a kind of ILBs. However, functional features and characteristics of these cells in rheumatoid arthritis (RA) remained poorly understood. In this study, we found that human CD27+IgD+ B cells could produce natural antibody-like IgM. Under RA circumstance, the frequencies of these cells were significantly decreased. Moreover, the IgM-producing capacities of these cells were also dampened. Interestingly, the BCR repertoire of these cells was altered in RA, demonstrating decreased diversity with preferential usage alteration from VH3-23D to VH1-8. Single cell sequencing further revealed the proinflammatory biased features of these cells in RA. These CD27+IgD+ B cells were negatively correlated with RA patient disease activities and clinical manifestations. After effective therapy with disease remission in RA, these cells could be recovered. Taken together, these results have revealed that CD27+IgD+ B cells were impaired in RA with dysfunctional features, which might contribute to the disease perpetuation.
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Affiliation(s)
- Fanlei Hu
- Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Wei Zhang
- Department of Rheumatology and Immunology, First Hospital Affiliated to Baotou Medical College, Inner Mongolia Key Laboratory of Autoimmunity, Baotou, China
| | - Lianjie Shi
- Department of Rheumatology and Immunology, Peking University International Hospital, Beijing, China
| | - Xu Liu
- Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Yuan Jia
- Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Liling Xu
- Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Huaqun Zhu
- Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Yingni Li
- Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China
| | - Dakang Xu
- Department of Molecular and Translational Science, Faculty of Medicine, Hudson Institute of Medical Research, Monash University, Melbourne, VIC, Australia
| | - Liwei Lu
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong
| | - Xiaoyan Qiu
- Department of Immunology, School of Basic Medical Science, Peking University, Beijing, China
| | - Wanli Liu
- MOE Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing, China
| | - Junjie Qiao
- Department of Orthopedics, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Yongfu Wang
- Department of Rheumatology and Immunology, First Hospital Affiliated to Baotou Medical College, Inner Mongolia Key Laboratory of Autoimmunity, Baotou, China
| | - Zhanguo Li
- Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, China.,Peking-Tsinghua Center for Life Sciences, Beijing, China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, China
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Harmon AW, Moitra R, Xu Z, Byrnes AP. Hexons from adenovirus serotypes 5 and 48 differentially protect adenovirus vectors from neutralization by mouse and human serum. PLoS One 2018; 13:e0192353. [PMID: 29401488 PMCID: PMC5798830 DOI: 10.1371/journal.pone.0192353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/22/2018] [Indexed: 11/28/2022] Open
Abstract
Adenovirus vectors are widely used in gene therapy clinical trials, and preclinical studies with these vectors are often conducted in mice. It is therefore critical to understand whether mouse studies adequately predict the behavior of adenovirus vectors in humans. The most commonly-used adenovirus vectors are derived from adenovirus serotype 5 (Ad5). The Ad5 hexon protein can bind coagulation factor X (FX), and binding of FX has a major impact on vector interactions with other blood proteins. In mouse serum, FX protects Ad5 vectors from neutralization by natural antibodies and complement. In the current study, we similarly find that human FX inhibits neutralization of Ad5 vectors by human serum, and this finding is consistent among individual human sera. We show that human IgM and human IgG can each induce complement-mediated neutralization when Ad5 vectors are not protected by FX. Although mouse and human serum had similar effects on Ad5 vectors, we found that this was not true for a chimeric Ad5 vector that incorporated hexon regions from adenovirus serotype 48. Interestingly, this hexon-chimeric vector was neutralized by human serum, but not by mouse serum. These findings indicate that studies in mouse serum accurately predict the behavior of Ad5 vectors in human serum, but mouse serum is not an accurate model system for all adenovirus vectors.
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Affiliation(s)
- Andrew W. Harmon
- Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Rituparna Moitra
- Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Zhili Xu
- Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Andrew P. Byrnes
- Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
- * E-mail:
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49
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50
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Castro R, Navelsaker S, Krasnov A, Du Pasquier L, Boudinot P. Describing the diversity of Ag specific receptors in vertebrates: Contribution of repertoire deep sequencing. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 75:28-37. [PMID: 28259700 DOI: 10.1016/j.dci.2017.02.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/16/2017] [Accepted: 02/22/2017] [Indexed: 06/06/2023]
Abstract
During the last decades, gene and cDNA cloning identified TCR and Ig genes across vertebrates; genome sequencing of TCR and Ig loci in many species revealed the different organizations selected during evolution under the pressure of generating diverse repertoires of Ag receptors. By detecting clonotypes over a wide range of frequency, deep sequencing of Ig and TCR transcripts provides a new way to compare the structure of expressed repertoires in species of various sizes, at different stages of development, with different physiologies, and displaying multiple adaptations to the environment. In this review, we provide a short overview of the technologies currently used to produce global description of immune repertoires, describe how they have already been used in comparative immunology, and we discuss the future potential of such approaches. The development of these methodologies in new species holds promise for new discoveries concerning particular adaptations. As an example, understanding the development of adaptive immunity across metamorphosis in frogs has been made possible by such approaches. Repertoire sequencing is now widely used, not only in basic research but also in the context of immunotherapy and vaccination. Analysis of fish responses to pathogens and vaccines has already benefited from these methods. Finally, we also discuss potential advances based on repertoire sequencing of multigene families of immune sensors and effectors in invertebrates.
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Affiliation(s)
- Rosario Castro
- Department of Animal Health, Faculty of Veterinary Sciences, Complutense University, Madrid, Spain
| | - Sofie Navelsaker
- Norwegian University of Life Sciences, Faculty of Veterinary Medicine, Department of Basic Sciences and Aquatic Medicine, Adamstuen Campus, Oslo 0454, Norway; Virologie et Immunologie Moléculaires, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | | | | | - Pierre Boudinot
- Virologie et Immunologie Moléculaires, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
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