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Vu MH, Robert PA, Akbar R, Swiatczak B, Sandve GK, Haug DTT, Greiff V. Linguistics-based formalization of the antibody language as a basis for antibody language models. NATURE COMPUTATIONAL SCIENCE 2024; 4:412-422. [PMID: 38877120 DOI: 10.1038/s43588-024-00642-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 05/13/2024] [Indexed: 06/16/2024]
Abstract
Apparent parallels between natural language and antibody sequences have led to a surge in deep language models applied to antibody sequences for predicting cognate antigen recognition. However, a linguistic formal definition of antibody language does not exist, and insight into how antibody language models capture antibody-specific binding features remains largely uninterpretable. Here we describe how a linguistic formalization of the antibody language, by characterizing its tokens and grammar, could address current challenges in antibody language model rule mining.
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Affiliation(s)
- Mai Ha Vu
- Department of Linguistics and Scandinavian Studies, University of Oslo, Oslo, Norway.
| | - Philippe A Robert
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Rahmad Akbar
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Bartlomiej Swiatczak
- Department of History of Science and Scientific Archeology, University of Science and Technology of China, Hefei, China
| | | | | | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
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2
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Robert PA, Arulraj T, Meyer-Hermann M. Germinal centers are permissive to subdominant antibody responses. Front Immunol 2024; 14:1238046. [PMID: 38274834 PMCID: PMC10808553 DOI: 10.3389/fimmu.2023.1238046] [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: 06/10/2023] [Accepted: 12/13/2023] [Indexed: 01/27/2024] Open
Abstract
Introduction A protective humoral response to pathogens requires the development of high affinity antibodies in germinal centers (GC). The combination of antigens available during immunization has a strong impact on the strength and breadth of the antibody response. Antigens can display various levels of immunogenicity, and a hierarchy of immunodominance arises when the GC response to an antigen dampens the response to other antigens. Immunodominance is a challenge for the development of vaccines to mutating viruses, and for the development of broadly neutralizing antibodies. The extent by which antigens with different levels of immunogenicity compete for the induction of high affinity antibodies and therefore contribute to immunodominance is not known. Methods Here, we perform in silico simulations of the GC response, using a structural representation of antigens with complex surface amino acid composition and topology. We generate antigens with complex domains of different levels of immunogenicity and perform simulations with combinations of these domains. Results We found that GC dynamics were driven by the most immunogenic domain and immunodominance arose as affinity maturation to less immunogenic domain was inhibited. However, this inhibition was moderate since the less immunogenic domain exhibited a weak GC response in the absence of the most immunogenic domain. Less immunogenic domains reduced the dominance of GC responses to more immunogenic domains, albeit at a later time point. Discussion The simulations suggest that increased vaccine valency may decrease immunodominance of the GC response to strongly immunogenic domains and therefore, act as a potential strategy for the natural induction of broadly neutralizing antibodies in GC reactions.
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Affiliation(s)
- Philippe A. Robert
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Theinmozhi Arulraj
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Michael Meyer-Hermann
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
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3
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García-Valiente R, Merino Tejero E, Stratigopoulou M, Balashova D, Jongejan A, Lashgari D, Pélissier A, Caniels TG, Claireaux MAF, Musters A, van Gils MJ, Rodríguez Martínez M, de Vries N, Meyer-Hermann M, Guikema JEJ, Hoefsloot H, van Kampen AHC. Understanding repertoire sequencing data through a multiscale computational model of the germinal center. NPJ Syst Biol Appl 2023; 9:8. [PMID: 36927990 PMCID: PMC10019394 DOI: 10.1038/s41540-023-00271-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Abstract
Sequencing of B-cell and T-cell immune receptor repertoires helps us to understand the adaptive immune response, although it only provides information about the clonotypes (lineages) and their frequencies and not about, for example, their affinity or antigen (Ag) specificity. To further characterize the identified clones, usually with special attention to the particularly abundant ones (dominant), additional time-consuming or expensive experiments are generally required. Here, we present an extension of a multiscale model of the germinal center (GC) that we previously developed to gain more insight in B-cell repertoires. We compare the extent that these simulated repertoires deviate from experimental repertoires established from single GCs, blood, or tissue. Our simulations show that there is a limited correlation between clonal abundance and affinity and that there is large affinity variability among same-ancestor (same-clone) subclones. Our simulations suggest that low-abundance clones and subclones, might also be of interest since they may have high affinity for the Ag. We show that the fraction of plasma cells (PCs) with high B-cell receptor (BcR) mRNA content in the GC does not significantly affect the number of dominant clones derived from single GCs by sequencing BcR mRNAs. Results from these simulations guide data interpretation and the design of follow-up experiments.
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Affiliation(s)
- Rodrigo García-Valiente
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Elena Merino Tejero
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Maria Stratigopoulou
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
| | - Daria Balashova
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Aldo Jongejan
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Danial Lashgari
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Aurélien Pélissier
- IBM Research Zurich, 8803, Rüschlikon, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Tom G Caniels
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Mathieu A F Claireaux
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Anne Musters
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands
| | - Marit J van Gils
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | | | - Niek de Vries
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands
| | - Michael Meyer-Hermann
- Department for Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jeroen E J Guikema
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Pathology, Lymphoma and Myeloma Center Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Huub Hoefsloot
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Antoine H C van Kampen
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands.
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands.
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands.
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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4
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Pennell M, Rodriguez OL, Watson CT, Greiff V. The evolutionary and functional significance of germline immunoglobulin gene variation. Trends Immunol 2023; 44:7-21. [PMID: 36470826 DOI: 10.1016/j.it.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/07/2022] [Indexed: 12/04/2022]
Abstract
The recombination between immunoglobulin (IG) gene segments determines an individual's naïve antibody repertoire and, consequently, (auto)antigen recognition. Emerging evidence suggests that mammalian IG germline variation impacts humoral immune responses associated with vaccination, infection, and autoimmunity - from the molecular level of epitope specificity, up to profound changes in the architecture of antibody repertoires. These links between IG germline variants and immunophenotype raise the question on the evolutionary causes and consequences of diversity within IG loci. We discuss why the extreme diversity in IG loci remains a mystery, why resolving this is important for the design of more effective vaccines and therapeutics, and how recent evidence from multiple lines of inquiry may help us do so.
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Affiliation(s)
- Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA; Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
| | - Oscar L Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
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5
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Robert PA, Akbar R, Frank R, Pavlović M, Widrich M, Snapkov I, Slabodkin A, Chernigovskaya M, Scheffer L, Smorodina E, Rawat P, Mehta BB, Vu MH, Mathisen IF, Prósz A, Abram K, Olar A, Miho E, Haug DTT, Lund-Johansen F, Hochreiter S, Haff IH, Klambauer G, Sandve GK, Greiff V. Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for antibody specificity prediction. NATURE COMPUTATIONAL SCIENCE 2022; 2:845-865. [PMID: 38177393 DOI: 10.1038/s43588-022-00372-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/09/2022] [Indexed: 01/06/2024]
Abstract
Machine learning (ML) is a key technology for accurate prediction of antibody-antigen binding. Two orthogonal problems hinder the application of ML to antibody-specificity prediction and the benchmarking thereof: the lack of a unified ML formalization of immunological antibody-specificity prediction problems and the unavailability of large-scale synthetic datasets to benchmark real-world relevant ML methods and dataset design. Here we developed the Absolut! software suite that enables parameter-based unconstrained generation of synthetic lattice-based three-dimensional antibody-antigen-binding structures with ground-truth access to conformational paratope, epitope and affinity. We formalized common immunological antibody-specificity prediction problems as ML tasks and confirmed that for both sequence- and structure-based tasks, accuracy-based rankings of ML methods trained on experimental data hold for ML methods trained on Absolut!-generated data. The Absolut! framework has the potential to enable real-world relevant development and benchmarking of ML strategies for biotherapeutics design.
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Affiliation(s)
- Philippe A Robert
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
| | - Rahmad Akbar
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Robert Frank
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | | | - Michael Widrich
- ELLIS Unit Linz and LIT AI Lab, Institute for Machine Learning, Johannes Kepler University Linz, Linz, Austria
| | - Igor Snapkov
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Andrei Slabodkin
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Maria Chernigovskaya
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | | | - Eva Smorodina
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Puneet Rawat
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Brij Bhushan Mehta
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Mai Ha Vu
- Department of Linguistics and Scandinavian Studies, University of Oslo, Oslo, Norway
| | | | - Aurél Prósz
- Danish Cancer Society Research Center, Translational Cancer Genomics, Copenhagen, Denmark
| | - Krzysztof Abram
- The Novo Nordisk Foundation Center for Biosustainability, Autoflow, DTU Biosustain and IT University of Copenhagen, Copenhagen, Denmark
| | - Alex Olar
- Department of Complex Systems in Physics, Eötvös Loránd University, Budapest, Hungary
| | - Enkelejda Miho
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
- aiNET GmbH, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | | | - Sepp Hochreiter
- ELLIS Unit Linz and LIT AI Lab, Institute for Machine Learning, Johannes Kepler University Linz, Linz, Austria
- Institute of Advanced Research in Artificial Intelligence (IARAI), Vienna, Austria
| | | | - Günter Klambauer
- ELLIS Unit Linz and LIT AI Lab, Institute for Machine Learning, Johannes Kepler University Linz, Linz, Austria
| | | | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
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6
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Yan Z, Qi H, Lan Y. The role of geometric features in a germinal center. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:8304-8333. [PMID: 35801467 DOI: 10.3934/mbe.2022387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The germinal center (GC) is a self-organizing structure produced in the lymphoid follicle during the T-dependent immune response and is an important component of the humoral immune system. However, the impact of the special structure of GC on antibody production is not clear. According to the latest biological experiments, we establish a spatiotemporal stochastic model to simulate the whole self-organization process of the GC including the appearance of two specific zones: the dark zone (DZ) and the light zone (LZ), the development of which serves to maintain an effective competition among different cells and promote affinity maturation. A phase transition is discovered in this process, which determines the critical GC volume for a successful growth in both the stochastic and the deterministic model. Further increase of the volume does not make much improvement on the performance. It is found that the critical volume is determined by the distance between the activated B cell receptor (BCR) and the target epitope of the antigen in the shape space. The observation is confirmed in both 2D and 3D simulations and explains partly the variability of the observed GC size.
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Affiliation(s)
- Zishuo Yan
- School of Science, Beijing University of Posts and Telecommunications, Beijing 100876, China
| | - Hai Qi
- Beijing Key Lab for Immunological Research on Chronic Diseases, Tsinghua University, Beijing 100084, China
| | - Yueheng Lan
- School of Science, Beijing University of Posts and Telecommunications, Beijing 100876, China
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7
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Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIV. PLoS Comput Biol 2022; 18:e1009391. [PMID: 35442968 PMCID: PMC9020693 DOI: 10.1371/journal.pcbi.1009391] [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: 08/11/2021] [Accepted: 03/24/2022] [Indexed: 11/29/2022] Open
Abstract
The design of vaccines against highly mutable pathogens, such as HIV and influenza, requires a detailed understanding of how the adaptive immune system responds to encountering multiple variant antigens (Ags). Here, we describe a multiscale model of B cell receptor (BCR) affinity maturation that employs actual BCR nucleotide sequences and treats BCR/Ag interactions in atomistic detail. We apply the model to simulate the maturation of a broadly neutralizing Ab (bnAb) against HIV. Starting from a germline precursor sequence of the VRC01 anti-HIV Ab, we simulate BCR evolution in response to different vaccination protocols and different Ags, which were previously designed by us. The simulation results provide qualitative guidelines for future vaccine design and reveal unique insights into bnAb evolution against the CD4 binding site of HIV. Our model makes possible direct comparisons of simulated BCR populations with results of deep sequencing data, which will be explored in future applications. Vaccination has saved more lives than any other medical procedure. But, we do not have robust ways to develop vaccines against highly mutable pathogens. For example, there is no effective vaccine against HIV, and a universal vaccine against diverse strains of influenza is also not available. The development of immunization strategies to elicit antibodies that can neutralize diverse strains of highly mutable pathogens (so-called ‘broadly neutralizing antibodies’, or bnAbs) would enable the design of universal vaccines against such pathogens, as well as other viruses that may emerge in the future. In this paper, we present an agent-based model of affinity maturation–the Darwinian process by which antibodies evolve against a pathogen–that, for the first time, enables the in silico investigation of real germline nucleotide sequences of antibodies known to evolve into potent bnAbs, evolving against real amino acid sequences of HIV-based vaccine-candidate proteins. Our results provide new insights into bnAb evolution against HIV, and can be used to qualitatively guide the future design of vaccines against highly mutable pathogens.
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8
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Ovchinnikov V, Karplus M. A Coarse-Grained Model of Affinity Maturation Indicates the Importance of B-Cell Receptor Avidity in Epitope Subdominance. Front Immunol 2022; 13:816634. [PMID: 35371013 PMCID: PMC8971376 DOI: 10.3389/fimmu.2022.816634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/24/2022] [Indexed: 12/02/2022] Open
Abstract
The elicitation of broadly neutralizing antibodies (bnAbs) is a major goal in the design of vaccines against rapidly-mutating viruses. In the case of influenza, many bnAbs that target conserved epitopes on the stem of the hemagglutinin protein (HA) have been discovered. However, these antibodies are rare, are not boosted well upon reinfection, and often have low neutralization potency, compared to strain-specific antibodies directed to the HA head. Different hypotheses have been proposed to explain this phenomenon. We use a coarse-grained computational model of the germinal center reaction to investigate how B-cell receptor binding valency affects the growth and affinity maturation of competing B-cells. We find that receptors that are unable to bind antigen bivalently, and also those that do not bind antigen cooperatively, have significantly slower rates of growth, memory B-cell production, and, under certain conditions, rates of affinity maturation. The corresponding B-cells are predicted to be outcompeted by B-cells that bind bivalently and cooperatively. We use the model to explore strategies for a universal influenza vaccine, e.g., how to boost the concentrations of the slower growing cross-reactive antibodies directed to the stem. The results suggest that, upon natural reinfections subsequent to vaccination, the protectiveness of such vaccines would erode, possibly requiring regular boosts. Collectively, our results strongly support the importance of bivalent antibody binding in immunodominance, and suggest guidelines for developing a universal influenza vaccine.
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Affiliation(s)
- Victor Ovchinnikov
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, United States
- *Correspondence: Victor Ovchinnikov, ; ; Martin Karplus,
| | - Martin Karplus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, United States
- Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, Strasbourg, France
- *Correspondence: Victor Ovchinnikov, ; ; Martin Karplus,
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9
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Dong C, Wang BZ. Engineered Nanoparticulate Vaccines to Combat Recurring and Pandemic Influenza Threats. ADVANCED NANOBIOMED RESEARCH 2022; 2:2100122. [PMID: 35754779 PMCID: PMC9231845 DOI: 10.1002/anbr.202100122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Reoccurring seasonal flu epidemics and occasional pandemics are among the most severe threats to public health. Current seasonal influenza vaccines provide limited protection against drifted circulating strains and no protection against influenza pandemics. Next-generation influenza vaccines, designated as universal influenza vaccines, should be safe, affordable, and elicit long-lasting cross-protective influenza immunity. Nanotechnology plays a critical role in the development of such novel vaccines. Engineered nanoparticles can incorporate multiple advantageous properties into the same nanoparticulate platforms to improve vaccine potency and breadth. These immunological properties include virus-like biomimicry, high antigen-load, controlled antigen release, targeted delivery, and induction of innate signaling pathways. Many nanoparticle influenza vaccines have shown promising results in generating potent and broadly protective immune responses. This review will summarize the necessity and characteristics of next-generation influenza vaccines and the immunological correlates of broad influenza immunity and focus on how cutting-edge nanoparticle technology contributes to such vaccine development. The review will give new insights into the rational design of nanoparticle universal vaccines to combat influenza epidemics and pandemics.
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Affiliation(s)
- Chunhong Dong
- Center for Inflammation, Immunity and Infection Georgia State University Institute for Biomedical Sciences Atlanta GA USA
| | - Bao-Zhong Wang
- Center for Inflammation, Immunity and Infection Georgia State University Institute for Biomedical Sciences Atlanta GA USA
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10
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Akbar R, Robert PA, Weber CR, Widrich M, Frank R, Pavlović M, Scheffer L, Chernigovskaya M, Snapkov I, Slabodkin A, Mehta BB, Miho E, Lund-Johansen F, Andersen JT, Hochreiter S, Hobæk Haff I, Klambauer G, Sandve GK, Greiff V. In silico proof of principle of machine learning-based antibody design at unconstrained scale. MAbs 2022; 14:2031482. [PMID: 35377271 PMCID: PMC8986205 DOI: 10.1080/19420862.2022.2031482] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Generative machine learning (ML) has been postulated to become a major driver in the computational design of antigen-specific monoclonal antibodies (mAb). However, efforts to confirm this hypothesis have been hindered by the infeasibility of testing arbitrarily large numbers of antibody sequences for their most critical design parameters: paratope, epitope, affinity, and developability. To address this challenge, we leveraged a lattice-based antibody-antigen binding simulation framework, which incorporates a wide range of physiological antibody-binding parameters. The simulation framework enables the computation of synthetic antibody-antigen 3D-structures, and it functions as an oracle for unrestricted prospective evaluation and benchmarking of antibody design parameters of ML-generated antibody sequences. We found that a deep generative model, trained exclusively on antibody sequence (one dimensional: 1D) data can be used to design conformational (three dimensional: 3D) epitope-specific antibodies, matching, or exceeding the training dataset in affinity and developability parameter value variety. Furthermore, we established a lower threshold of sequence diversity necessary for high-accuracy generative antibody ML and demonstrated that this lower threshold also holds on experimental real-world data. Finally, we show that transfer learning enables the generation of high-affinity antibody sequences from low-N training data. Our work establishes a priori feasibility and the theoretical foundation of high-throughput ML-based mAb design.
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Affiliation(s)
- Rahmad Akbar
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Norway
| | - Philippe A Robert
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Norway
| | - Cédric R Weber
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Michael Widrich
- Ellis Unit Linz and Lit Ai Lab, Institute for Machine Learning, Johannes Kepler University Linz, Linz, Austria
| | - Robert Frank
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Norway
| | | | | | - Maria Chernigovskaya
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Norway
| | - Igor Snapkov
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Norway
| | - Andrei Slabodkin
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Norway
| | - Brij Bhushan Mehta
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Norway
| | - Enkelejda Miho
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
| | - Fridtjof Lund-Johansen
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Norway
| | - Jan Terje Andersen
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Norway.,Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
| | - Sepp Hochreiter
- Ellis Unit Linz and Lit Ai Lab, Institute for Machine Learning, Johannes Kepler University Linz, Linz, Austria.,Institute of Advanced Research in Artificial Intelligence (IARAI), Austria
| | | | - Günter Klambauer
- Ellis Unit Linz and Lit Ai Lab, Institute for Machine Learning, Johannes Kepler University Linz, Linz, Austria
| | | | - Victor Greiff
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Norway
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11
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Zhang YN, Paynter J, Sou C, Fourfouris T, Wang Y, Abraham C, Ngo T, Zhang Y, He L, Zhu J. Mechanism of a COVID-19 nanoparticle vaccine candidate that elicits a broadly neutralizing antibody response to SARS-CoV-2 variants. SCIENCE ADVANCES 2021; 7:eabj3107. [PMID: 34669468 PMCID: PMC8528426 DOI: 10.1126/sciadv.abj3107] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/27/2021] [Indexed: 05/12/2023]
Abstract
Vaccines that induce potent neutralizing antibody (NAb) responses against emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are essential for combating the coronavirus disease 2019 (COVID-19) pandemic. We demonstrated that mouse plasma induced by self-assembling protein nanoparticles (SApNPs) that present 20 rationally designed S2GΔHR2 spikes of the ancestral Wuhan-Hu-1 strain can neutralize the B.1.1.7, B.1.351, P.1, and B.1.617 variants with comparable potency. The adjuvant effect on vaccine-induced immunity was investigated by testing 16 formulations for the multilayered I3-01v9 SApNP. Using single-cell sorting, monoclonal antibodies (mAbs) with diverse neutralization breadth and potency were isolated from mice immunized with the receptor binding domain (RBD), S2GΔHR2 spike, and SApNP vaccines. The mechanism of vaccine-induced immunity was examined in the mouse model. Compared with the soluble spike, the I3-01v9 SApNP showed sixfold longer retention, fourfold greater presentation on follicular dendritic cell dendrites, and fivefold stronger germinal center reactions in lymph node follicles.
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Affiliation(s)
- Yi-Nan Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jennifer Paynter
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Cindy Sou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tatiana Fourfouris
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ying Wang
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA 19140, USA
- Department of Microbiology and Immunology, Temple University, Philadelphia, PA 19140, USA
| | - Ciril Abraham
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA 19140, USA
| | - Timothy Ngo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yi Zhang
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA 19140, USA
- Department of Microbiology and Immunology, Temple University, Philadelphia, PA 19140, USA
| | - Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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12
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Robert PA, Arulraj T, Meyer-Hermann M. Ymir: A 3D structural affinity model for multi-epitope vaccine simulations. iScience 2021; 24:102979. [PMID: 34485861 PMCID: PMC8405928 DOI: 10.1016/j.isci.2021.102979] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 07/10/2021] [Accepted: 08/11/2021] [Indexed: 11/05/2022] Open
Abstract
Vaccine development is challenged by the hierarchy of immunodominance between target antigen epitopes and the emergence of antigenic variants by pathogen mutation. The strength and breadth of antibody responses relies on selection and mutation in the germinal center and on the structural similarity between antigens. Computational methods for assessing the breadth of germinal center responses to multivalent antigens are critical to speed up vaccine development. Yet, such methods have poorly reflected the 3D antigen structure and antibody breadth. Here, we present Ymir, a new 3D-lattice-based framework that calculates in silico antibody-antigen affinities. Key physiological properties naturally emerge from Ymir such as affinity jumps, cross-reactivity, and differential epitope accessibility. We validated Ymir by replicating known features of germinal center dynamics. We show that combining antigens with mutated but structurally related epitopes enhances vaccine breadth. Ymir opens a new avenue for understanding vaccine potency based on the structural relationship between vaccine antigens.
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Affiliation(s)
- Philippe A. Robert
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38106 Braunschweig, Germany
| | - Theinmozhi Arulraj
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38106 Braunschweig, Germany
| | - Michael Meyer-Hermann
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, 38106 Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
- Centre for Individualised Infection Medicine (CIIM), Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
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13
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Progress and challenges in mass spectrometry-based analysis of antibody repertoires. Trends Biotechnol 2021; 40:463-481. [PMID: 34535228 DOI: 10.1016/j.tibtech.2021.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 12/22/2022]
Abstract
Humoral immunity is divided into the cellular B cell and protein-level antibody responses. High-throughput sequencing has advanced our understanding of both these fundamental aspects of B cell immunology as well as aspects pertaining to vaccine and therapeutics biotechnology. Although the protein-level serum and mucosal antibody repertoire make major contributions to humoral protection, the sequence composition and dynamics of antibody repertoires remain underexplored. This limits insight into important immunological and biotechnological parameters such as the number of antigen-specific antibodies, which are for example, relevant for pathogen neutralization, microbiota regulation, severity of autoimmunity, and therapeutic efficacy. High-resolution mass spectrometry (MS) has allowed initial insights into the antibody repertoire. We outline current challenges in MS-based sequence analysis of antibody repertoires and propose strategies for their resolution.
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14
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Zhang YN, Paynter J, Sou C, Fourfouris T, Wang Y, Abraham C, Ngo T, Zhang Y, He L, Zhu J. Mechanism of a COVID-19 nanoparticle vaccine candidate that elicits a broadly neutralizing antibody response to SARS-CoV-2 variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.26.437274. [PMID: 33791704 PMCID: PMC8010731 DOI: 10.1101/2021.03.26.437274] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Vaccines that induce potent neutralizing antibody (NAb) responses against emerging variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are essential for combating the coronavirus disease 2019 (COVID-19) pandemic. We demonstrated that mouse plasma induced by self-assembling protein nanoparticles (SApNPs) that present 20 rationally designed S2GΔHR2 spikes of the ancestral Wuhan-Hu-1 strain can neutralize the B.1.1.7, B.1.351, P.1, and B.1.617 variants with the same potency. The adjuvant effect on vaccine-induced immunity was investigated by testing 16 formulations for the multilayered I3-01v9 SApNP. Using single-cell sorting, monoclonal antibodies (mAbs) with diverse neutralization breadth and potency were isolated from mice immunized with the receptor binding domain (RBD), S2GΔHR2 spike, and SApNP vaccines. The mechanism of vaccine-induced immunity was examined in mice. Compared with the soluble spike, the I3-01v9 SApNP showed 6-fold longer retention, 4-fold greater presentation on follicular dendritic cell dendrites, and 5-fold stronger germinal center reactions in lymph node follicles.
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Affiliation(s)
- Yi-Nan Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Jennifer Paynter
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Cindy Sou
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Tatiana Fourfouris
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Ying Wang
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania 19140, USA
- Department of Microbiology and Immunology, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Ciril Abraham
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Timothy Ngo
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Yi Zhang
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, Pennsylvania 19140, USA
- Department of Microbiology and Immunology, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Linling He
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - Jiang Zhu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California 92037, USA
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15
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Meyer-Hermann M. A molecular theory of germinal center B cell selection and division. Cell Rep 2021; 36:109552. [PMID: 34433043 DOI: 10.1016/j.celrep.2021.109552] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 04/06/2021] [Accepted: 07/27/2021] [Indexed: 01/30/2023] Open
Abstract
The selection of B cells (BCs) in germinal centers (GCs) is pivotal to the generation of high-affinity antibodies and memory BCs, but it lacks global understanding. Based on the idea of a single Tfh-cell signal that controls BC selection and division, experiments appear contradictory. Here, we use the current knowledge on the molecular pathways of GC BCs to develop a theory of GC BC selection and division based on the dynamics of molecular factors. This theory explains the seemingly contradictory experiments by the separation of signals for BC fate decision from signals controlling the number of BC divisions. Three model variants are proposed and experiments are predicted that allow one to distinguish those. Understanding information processing in molecular BC states is critical for targeted immune interventions, and the proposed theory implies that selection and division can be controlled independently in GC reactions.
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Affiliation(s)
- Michael Meyer-Hermann
- Department of Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Rebenring 56, Braunschweig 38106, Germany; Centre for Individualised Infection Medicine (CIIM), Hannover, Germany; Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Carl-Neuberg-Str. 1, Hannover 30625, Germany.
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16
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Molari M, Monasson R, Cocco S. Survival probability and size of lineages in antibody affinity maturation. Phys Rev E 2021; 103:052413. [PMID: 34134280 DOI: 10.1103/physreve.103.052413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/06/2021] [Indexed: 11/07/2022]
Abstract
Affinity maturation (AM) is the process through which the immune system is able to develop potent antibodies against new pathogens it encounters, and is at the base of the efficacy of vaccines. At its core AM is analogous to a Darwinian evolutionary process, where B cells mutate and are selected on the base of their affinity for an antigen (Ag), and Ag availability tunes the selective pressure. In cases when this selective pressure is high, the number of B cells might quickly decrease and the population might risk extinction in what is known as a population bottleneck. Here we study the probability for a B-cell lineage to survive this bottleneck scenario as a function of the progenitor affinity for the Ag. Using recursive relations and probability generating functions we derive expressions for the average extinction time and progeny size for lineages that go extinct. We then extend our results to the full population, both in the absence and presence of competition for T-cell help, and quantify the population survival probability as a function of Ag concentration and initial population size. Our study suggests the population bottleneck phenomenology might represent a limit case in the space of biologically plausible maturation scenarios, whose characterization could help guide the process of vaccine development.
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Affiliation(s)
- Marco Molari
- Laboratoire de Physique de l'École Normale Supérieure, ENS, PSL University, CNRS UMR8023, Sorbonne Université, Université de Paris, 24 rue Lhomond, 75005 Paris, France
| | - Rémi Monasson
- Laboratoire de Physique de l'École Normale Supérieure, ENS, PSL University, CNRS UMR8023, Sorbonne Université, Université de Paris, 24 rue Lhomond, 75005 Paris, France
| | - Simona Cocco
- Laboratoire de Physique de l'École Normale Supérieure, ENS, PSL University, CNRS UMR8023, Sorbonne Université, Université de Paris, 24 rue Lhomond, 75005 Paris, France
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17
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Hernandez-Mejia G, Hernandez-Vargas EA. Uncovering antibody cross-reaction dynamics in influenza A infections. BIOINFORMATICS (OXFORD, ENGLAND) 2021; 37:229-235. [PMID: 32730562 DOI: 10.1101/2020.01.06.896274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/03/2020] [Accepted: 07/23/2020] [Indexed: 05/27/2023]
Abstract
MOTIVATION Influenza viruses are a cause of large outbreaks and pandemics with high death tolls. A key obstacle is that flu vaccines have inconsistent performance, in the best cases up to 60% effectiveness, but it can be as low as 10%. Uncovering the hidden pathways of how antibodies (Abs) induced by one influenza strain are effective against another, cross-reaction, is a central vexation for the design of universal flu vaccines. RESULTS We conceive a stochastic model that successfully represents the antibody cross-reactive data from mice infected with H3N2 influenza strains and further validation with cross-reaction data of H1N1 strains. Using a High-Performance Computing cluster, several aspects and parameters in the model were tested. Computational simulations highlight that changes in time of infection and the B-cells population are relevant, however, the affinity threshold of B-cells between consecutive infections is a necessary condition for the successful Abs cross-reaction. Our results suggest a 3-D reformulation of the current influenza antibody landscape for the representation and modeling of cross-reactive data. AVAILABILITY AND IMPLEMENTATION The full code as a testing/simulation platform is freely available here: https://github.com/systemsmedicine/Antibody_cross-reaction_dynamics. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Gustavo Hernandez-Mejia
- Frankfurt Institute for Advanced Studies, 60438 Frankfurt am Main, Germany
- Faculty of Biological Sciences, Goethe University, 60438 Frankfurt am Main, Germany
| | - Esteban A Hernandez-Vargas
- Frankfurt Institute for Advanced Studies, 60438 Frankfurt am Main, Germany
- Instituto de Matemáticas, Universidad Nacional Autonoma de Mexico, Blv. Juriquilla 3001, 76230 Juriquilla, Querétaro, México
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18
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Garg AK, Desikan R, Dixit NM. Preferential Presentation of High-Affinity Immune Complexes in Germinal Centers Can Explain How Passive Immunization Improves the Humoral Response. Cell Rep 2020; 29:3946-3957.e5. [PMID: 31851925 PMCID: PMC7116025 DOI: 10.1016/j.celrep.2019.11.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 09/12/2019] [Accepted: 11/06/2019] [Indexed: 12/13/2022] Open
Abstract
Passive immunization (PI) with external antibodies has been used classically for rapid but temporary alleviation of disease. Transcending this role, recent studies have shown PI to induce lasting improvements in natural antibody production, suggesting that PI could become a powerful tool to engineer humoral responses. We propose a mechanism with which PI can alter the humoral response. Antigen-specific B cells evolve and get selected in germinal centers (GCs) on the basis of their ability to acquire antigen from antibody-antigen complexes presented in GCs. When external antibodies of high affinity for antigen are used, they form the majority of the complexes in GCs, letting only B cells with even higher affinities be selected. Using an in silico GC reaction model, we show that this mechanism explains the improved humoral responses following PI. The model also synthesizes several independent experimental observations, indicating the robustness of the mechanism, and proposes tunable handles to optimize PI.
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Affiliation(s)
- Amar K Garg
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru 560012, India
| | - Rajat Desikan
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru 560012, India
| | - Narendra M Dixit
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru 560012, India; Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru 560012, India.
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19
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Optimizing immunization protocols to elicit broadly neutralizing antibodies. Proc Natl Acad Sci U S A 2020; 117:20077-20087. [PMID: 32747563 DOI: 10.1073/pnas.1919329117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Natural infections and vaccination with a pathogen typically stimulate the production of potent antibodies specific for the pathogen through a Darwinian evolutionary process known as affinity maturation. Such antibodies provide protection against reinfection by the same strain of a pathogen. A highly mutable virus, like HIV or influenza, evades recognition by these strain-specific antibodies via the emergence of new mutant strains. A vaccine that elicits antibodies that can bind to many diverse strains of the virus-known as broadly neutralizing antibodies (bnAbs)-could protect against highly mutable pathogens. Despite much work, the mechanisms by which bnAbs emerge remain uncertain. Using a computational model of affinity maturation, we studied a wide variety of vaccination strategies. Our results suggest that an effective strategy to maximize bnAb evolution is through a sequential immunization protocol, wherein each new immunization optimally increases the pressure on the immune system to target conserved antigenic sites, thus conferring breadth. We describe the mechanisms underlying why sequentially driving the immune system increasingly further from steady state, in an optimal fashion, is effective. The optimal protocol allows many evolving B cells to become bnAbs via diverse evolutionary paths.
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21
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Abstract
A large array of broadly neutralizing antibodies (bnAbs) against HIV have been isolated and described, particularly in the last decade. This continually expanding array of bnAbs has crucially led to the identification of novel epitopes on the HIV envelope protein via which antibodies can block a broad range of HIV strains. Moreover, these studies have produced high-resolution understanding of these sites of vulnerability on the envelope protein. They have also clarified the mechanisms of action of bnAbs and provided detailed descriptions of B cell ontogenies from which they arise. However, it is still not possible to predict which HIV-infected individuals will go onto develop breath nor is it possible to induce neutralization breadth by immunization in humans. This review aims to discuss the major insights gained so far and also to evaluate the requirement to continue isolating and characterizing new bnAbs. While new epitopes may remain to be uncovered, a clearer probable benefit of further bnAb characterization is a greater understanding of key decision points in bnAb development within the anti-HIV immune response. This in turn may lead to new insights into how to trigger bnAbs by immunization and more clearly define the challenges to using bnAbs as therapeutic agents.
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Affiliation(s)
- Laura E McCoy
- Division of Infection and Immunity, University College London, London, UK.
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