1
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Deguine J, Xavier RJ. B cell tolerance and autoimmunity: Lessons from repertoires. J Exp Med 2024; 221:e20231314. [PMID: 39093312 DOI: 10.1084/jem.20231314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
Adaptive immune cell function is regulated by a highly diverse receptor recombined from variable germline-encoded segments that can recognize an almost unlimited array of epitopes. While this diversity enables the recognition of any pathogen, it also poses a risk of self-recognition, leading to autoimmunity. Many layers of regulation are present during both the generation and activation of B cells to prevent this phenomenon, although they are evidently imperfect. In recent years, our ability to analyze immune repertoires at scale has drastically increased, both through advances in sequencing and single-cell analyses. Here, we review the current knowledge on B cell repertoire analyses, focusing on their implication for autoimmunity. These studies demonstrate that a failure of tolerance occurs at multiple independent checkpoints in different autoimmune contexts, particularly during B cell maturation, plasmablast differentiation, and within germinal centers. These failures are marked by distinct repertoire features that may be used to identify disease- or patient-specific therapeutic approaches.
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Affiliation(s)
- Jacques Deguine
- Immunology Program, Broad Institute of Massachusetts Institute of Technology and Harvard , Cambridge, MA, USA
| | - Ramnik J Xavier
- Immunology Program, Broad Institute of Massachusetts Institute of Technology and Harvard , Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School , Boston, MA, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
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2
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Siniscalco ER, Williams A, Eisenbarth SC. All roads lead to IgA: Mapping the many pathways of IgA induction in the gut. Immunol Rev 2024. [PMID: 39046160 DOI: 10.1111/imr.13369] [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] [Indexed: 07/25/2024]
Abstract
The increasing prevalence of food allergy and related pathologies in recent years has underscored the need to understand the factors affecting adverse reactions to food. Food allergy is caused when food-specific IgE triggers the release of histamine from mast cells. However, other food-specific antibody isotypes exist as well, including IgG and IgA. IgA is the main antibody isotype in the gut and mediates noninflammatory reactions to toxins, commensal bacteria, and food antigens. It has also been thought to induce tolerance to food, thus antagonizing the role of food-specific IgE. However, this has remained unclear as food-specific IgA generation is poorly understood. Particularly, the location of IgA induction, the role of T cell help, and the fates of food-specific B cells remain elusive. In this review, we outline what is known about food-specific IgA induction and highlight areas requiring further study. We also explore how knowledge of food-specific IgA induction can be informed by and subsequently contribute to our overall knowledge of gut immunity.
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Affiliation(s)
- Emily R Siniscalco
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
- Center for Human Immunobiology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Adam Williams
- Center for Human Immunobiology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Allergy and Immunology, The Department Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Stephanie C Eisenbarth
- Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
- Center for Human Immunobiology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Allergy and Immunology, The Department Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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3
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Raposo B, Klareskog L, Robinson WH, Malmström V, Grönwall C. The peculiar features, diversity and impact of citrulline-reactive autoantibodies. Nat Rev Rheumatol 2024; 20:399-416. [PMID: 38858604 DOI: 10.1038/s41584-024-01124-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2024] [Indexed: 06/12/2024]
Abstract
Since entering the stage 25 years ago as a highly specific serological biomarker for rheumatoid arthritis, anti-citrullinated protein antibodies (ACPAs) have been a topic of extensive research. This hallmark B cell response arises years before disease onset, displays interpatient autoantigen variability, and is associated with poor clinical outcomes. Technological and scientific advances have revealed broad clonal diversity and intriguing features including high levels of somatic hypermutation, variable-domain N-linked glycosylation, hapten-like peptide interactions, and clone-specific multireactivity to citrullinated, carbamylated and acetylated epitopes. ACPAs have been found in different isotypes and subclasses, in both circulation and tissue, and are secreted by both plasmablasts and long-lived plasma cells. Notably, although some disease-promoting features have been reported, results now demonstrate that certain monoclonal ACPAs therapeutically block arthritis and inflammation in mouse models. A wealth of functional studies using patient-derived polyclonal and monoclonal antibodies have provided evidence for pathogenic and protective effects of ACPAs in the context of arthritis. To understand the roles of ACPAs, one needs to consider their immunological properties by incorporating different facets such as rheumatoid arthritis B cell biology, environmental triggers and chronic antigen exposure. The emerging picture points to a complex role of citrulline-reactive autoantibodies, in which the diversity and dynamics of antibody clones could determine clinical progression and manifestations.
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Affiliation(s)
- Bruno Raposo
- Department of Medicine, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lars Klareskog
- Department of Medicine, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - William H Robinson
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Vivianne Malmström
- Department of Medicine, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
| | - Caroline Grönwall
- Department of Medicine, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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4
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Celentano M, DeWitt WS, Prillo S, Song YS. Exact and efficient phylodynamic simulation from arbitrarily large populations. ARXIV 2024:arXiv:2402.17153v1. [PMID: 38463501 PMCID: PMC10925381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Many biological studies involve inferring the genealogical history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a comprehensive population tree and is distorted by survivorship and sampling biases. Inferring evolutionary parameters from ascertained trees requires modeling both the underlying population dynamics and the ascertainment process. A crucial component of this phylodynamic modeling involves tree simulation, which is used to benchmark probabilistic inference methods. To simulate an ascertained tree, one must first simulate the full population tree and then prune unobserved lineages. Consequently, the computational cost is determined not by the size of the final simulated tree, but by the size of the population tree in which it is embedded. In most biological scenarios, simulations of the entire population are prohibitively expensive due to computational demands placed on lineages without sampled descendants. Here, we address this challenge by proving that, for any partially ascertained process from a general multi-type birth-death-mutation-sampling (BDMS) model, there exists an equivalent pure birth process (i.e., no death) with mutation and complete sampling. The final trees generated under these processes have exactly the same distribution. Leveraging this property, we propose a highly efficient algorithm for simulating trees under a general BDMS model. Our algorithm scales linearly with the size of the final simulated tree and is independent of the population size, enabling simulations from extremely large populations beyond the reach of current methods but essential for various biological applications. We anticipate that this unprecedented speedup will significantly advance the development of novel inference methods that require extensive training data.
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Affiliation(s)
| | | | | | - Yun S Song
- Computer Science Division, University of California, Berkeley
- Department of Statistics, University of California, Berkeley
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5
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Lasrado N, Collier ARY, Miller J, Hachmann NP, Liu J, Anand T, A. Bondzie E, Fisher JL, Mazurek CR, Patio RC, Rodrigues SL, Rowe M, Surve N, Ty DM, Wu C, Chicz TM, Tong X, Korber B, McNamara RP, Barouch DH. Waning immunity and IgG4 responses following bivalent mRNA boosting. SCIENCE ADVANCES 2024; 10:eadj9945. [PMID: 38394195 PMCID: PMC10889350 DOI: 10.1126/sciadv.adj9945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 01/22/2024] [Indexed: 02/25/2024]
Abstract
Messenger RNA (mRNA) vaccines were highly effective against the ancestral SARS-CoV-2 strain, but the efficacy of bivalent mRNA boosters against XBB variants was substantially lower. Here, we show limited durability of neutralizing antibody (NAb) responses against XBB variants and isotype switching to immunoglobulin G4 (IgG4) responses following bivalent mRNA boosting. Bivalent mRNA boosting elicited modest XBB.1-, XBB.1.5-, and XBB.1.16-specific NAbs that waned rapidly within 3 months. In contrast, bivalent mRNA boosting induced more robust and sustained NAbs against the ancestral WA1/2020 strain, suggesting immune imprinting. Following bivalent mRNA boosting, serum antibody responses were primarily IgG2 and IgG4 responses with poor Fc functional activity. In contrast, a third monovalent mRNA immunization boosted all isotypes including IgG1 and IgG3 with robust Fc functional activity. These data show substantial immune imprinting for the ancestral spike and isotype switching to IgG4 responses following bivalent mRNA boosting, with important implications for future booster designs and boosting strategies.
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Affiliation(s)
- Ninaad Lasrado
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Ai-ris Y. Collier
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jessica Miller
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Nicole P. Hachmann
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jinyan Liu
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Trisha Anand
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Esther A. Bondzie
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jana L. Fisher
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Camille R. Mazurek
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Robert C. Patio
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | - Marjorie Rowe
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Nehalee Surve
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Darren M. Ty
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Cindy Wu
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Taras M. Chicz
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Xin Tong
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Bette Korber
- Los Alamos National Laboratory and New Mexico Consortium, Los Alamos, NM, USA
| | | | - Dan H. Barouch
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
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6
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Tang T, Zhao H, Shen S, Yang L, Lim CT. Enhancing single-cell encapsulation in droplet microfluidics with fine-tunable on-chip sample enrichment. MICROSYSTEMS & NANOENGINEERING 2024; 10:3. [PMID: 38169721 PMCID: PMC10758392 DOI: 10.1038/s41378-023-00631-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/17/2023] [Accepted: 10/30/2023] [Indexed: 01/05/2024]
Abstract
Single-cell encapsulation in droplet microfluidics is commonly hindered by the tradeoff between cell suspension density and on-chip focusing performance. In this study, we introduce a novel droplet microfluidic chip to overcome this challenge. The chip comprises a double spiral focusing unit, a flow resistance-based sample enrichment module with fine-tunable outlets, and a crossflow droplet generation unit. Utilizing a low-density cell/bead suspension (2 × 106 objects/mL), cells/beads are focused into a near-equidistant linear arrangement within the double spiral microchannel. The excess water phase is diverted while cells/beads remain focused and sequentially encapsulated in individual droplets. Focusing performance was assessed through numerical simulations and experiments at three flow rates (40, 60, 80 μL/min), demonstrating successful focusing at 40 and 80 μL/min for beads and cells, respectively. In addition, both simulation and experimental results revealed that the flow resistance at the sample enrichment module is adjustable by punching different outlets, allowing over 50% of the aqueous phase to be removed. YOLOv8n-based droplet detection algorithms realized the counting of cells/beads in droplets, statistically demonstrating single-cell and bead encapsulation rates of 72.2% and 79.2%, respectively. All the results indicate that this on-chip sample enrichment approach can be further developed and employed as a critical component in single-cell encapsulation in water-in-oil droplets.
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Affiliation(s)
- Tao Tang
- Department of Biomedical Engineering, National University of Singapore, 117583 Singapore, Singapore
| | - Hao Zhao
- Department of Biomedical Engineering, National University of Singapore, 117583 Singapore, Singapore
- Integrative Sciences and Engineering Programme, NUS Graduate School, National University of Singapore, 119077 Singapore, Singapore
| | - Shaofei Shen
- Shanxi Key Lab for Modernization of TCVM, College of Life Science, Shanxi Agricultural University, Taigu, Shanxi 030801 China
| | - Like Yang
- Department of Biomedical Engineering, National University of Singapore, 117583 Singapore, Singapore
| | - Chwee Teck Lim
- Department of Biomedical Engineering, National University of Singapore, 117583 Singapore, Singapore
- Institute for Health Innovation & Technology, National University of Singapore, 117599 Singapore, Singapore
- Mechanobiology Institute, National University of Singapore, 117411 Singapore, Singapore
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 636921 Singapore, Singapore
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7
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Budeus B, Kibler A, Küppers R. Human IgM-expressing memory B cells. Front Immunol 2023; 14:1308378. [PMID: 38143767 PMCID: PMC10748387 DOI: 10.3389/fimmu.2023.1308378] [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: 10/06/2023] [Accepted: 11/27/2023] [Indexed: 12/26/2023] Open
Abstract
A hallmark of T cell dependent (TD) humoral immune responses is the generation of long-lived memory B cells. The generation of these cells occurs primarily in the germinal center (GC) reaction, where antigen-activated B cells undergo affinity maturation as a major consequence of the combined processes of proliferation, somatic hypermutation of their immunoglobulin V (IgV) region genes, and selection for improved affinity of their B-cell antigen receptors. As many B cells also undergo class-switching to IgG or IgA in these TD responses, there was traditionally a focus on class-switched memory B cells in both murine and human studies on memory B cells. However, it has become clear that there is also a large subset of IgM-expressing memory B cells, which have important phenotypic and functional similarities but also differences to class-switched memory B cells. There is an ongoing discussion about the origin of distinct subsets of human IgM+ B cells with somatically mutated IgV genes. We argue here that the vast majority of human IgM-expressing B cells with somatically mutated IgV genes in adults is indeed derived from GC reactions, even though a generation of some mostly lowly mutated IgM+ B cells from other differentiation pathways, mainly in early life, may exist.
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Affiliation(s)
| | | | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg–Essen, Essen, Germany
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8
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Weber LL, Reiman D, Roddur MS, Qi Y, El-Kebir M, Khan AA. TRIBAL: Tree Inference of B cell Clonal Lineages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.27.568874. [PMID: 38076836 PMCID: PMC10705245 DOI: 10.1101/2023.11.27.568874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
B cells are a critical component of the adaptive immune system, responsible for producing antibodies that help protect the body from infections and foreign substances. Single cell RNA-sequencing (scRNA-seq) has allowed for both profiling of B cell receptor (BCR) sequences and gene expression. However, understanding the adaptive and evolutionary mechanisms of B cells in response to specific stimuli remains a significant challenge in the field of immunology. We introduce a new method, TRIBAL, which aims to infer the evolutionary history of clonally related B cells from scRNA-seq data. The key insight of TRIBAL is that inclusion of isotype data into the B cell lineage inference problem is valuable for reducing phylogenetic uncertainty that arises when only considering the receptor sequences. Consequently, the TRIBAL inferred B cell lineage trees jointly capture the somatic mutations introduced to the B cell receptor during affinity maturation and isotype transitions during class switch recombination. In addition, TRIBAL infers isotype transition probabilities that are valuable for gaining insight into the dynamics of class switching. Via in silico experiments, we demonstrate that TRIBAL infers isotype transition probabilities with the ability to distinguish between direct versus sequential switching in a B cell population. This results in more accurate B cell lineage trees and corresponding ancestral sequence and class switch reconstruction compared to competing methods. Using real-world scRNA-seq datasets, we show that TRIBAL recapitulates expected biological trends in a model affinity maturation system. Furthermore, the B cell lineage trees inferred by TRIBAL were equally plausible for the BCR sequences as those inferred by competing methods but yielded lower entropic partitions for the isotypes of the sequenced B cell. Thus, our method holds the potential to further advance our understanding of vaccine responses, disease progression, and the identification of therapeutic antibodies.
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Affiliation(s)
- Leah L. Weber
- Department of Computer Science, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Derek Reiman
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Mrinmoy S. Roddur
- Department of Computer Science, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Yuanyuan Qi
- Department of Computer Science, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Mohammed El-Kebir
- Department of Computer Science, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Aly A. Khan
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
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Herman JD, Atyeo C, Zur Y, Cook CE, Patel NJ, Vanni KM, Kowalski EN, Qian G, Srivatsan S, Shadick NA, Rao DA, Kellman B, Mann CJ, Lauffenburger D, Wallace ZS, Sparks JA, Alter G. Humoral immunity to an endemic coronavirus is associated with postacute sequelae of COVID-19 in individuals with rheumatic diseases. Sci Transl Med 2023; 15:eadf6598. [PMID: 37672567 PMCID: PMC10764151 DOI: 10.1126/scitranslmed.adf6598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 08/05/2023] [Indexed: 09/08/2023]
Abstract
Beyond the acute illness caused by severe acute respiratory coronavirus 2 (SARS-CoV-2) infection, about one-fifth of infections result in long-term persistence of symptoms despite the apparent clearance of infection. Insights into the mechanisms that underlie postacute sequelae of COVID-19 (PASC) will be critical for the prevention and clinical management of long-term complications of COVID-19. Several hypotheses have been proposed that may account for the development of PASC, including persistence of virus and dysregulation of immune responses. Among the immunological changes noted in PASC, alterations in humoral immunity have been observed in some patient subsets. To begin to determine whether SARS-CoV-2- or other pathogen-specific humoral immune responses evolve uniquely in PASC, we performed comprehensive antibody profiling against SARS-CoV-2, a panel of endemic pathogens, and a panel of routine vaccine antigens using systems serology in two cohorts of patients with preexisting systemic autoimmune rheumatic disease (SARD) who either developed or did not develop PASC. A distinct qualitative shift observed in Fcγ receptor (FcγR) binding was observed in individuals with PASC. Specifically, individuals with PASC harbored weaker FcγR-binding anti-SARS-CoV-2 antibodies and stronger FcγR-binding antibody responses against the endemic coronavirus OC43. Individuals with PASC developed an OC43 S2-specific antibody response with stronger FcγR binding, linked to cross-reactivity across SARS-CoV-2 and common coronaviruses. These findings identify previous coronavirus imprinting as a potential marker for the development of PASC in individuals with SARDs.
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Affiliation(s)
- Jonathan D Herman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Division of Infectious Disease, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Yonatan Zur
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Claire E Cook
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Naomi J Patel
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kathleen M Vanni
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Emily N Kowalski
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Grace Qian
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Shruthi Srivatsan
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nancy A Shadick
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Benjamin Kellman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Colin J Mann
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Douglas Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zachary S Wallace
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jeffrey A Sparks
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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10
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Deng DZQ, Verhage J, Neudorf C, Corbett-Detig R, Mekonen H, Castaldi PJ, Vollmers C. R2C2+UMI: Combining concatemeric consensus sequencing with unique molecular identifiers enables ultra-accurate sequencing of amplicons on Oxford Nanopore Technologies sequencers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.19.553937. [PMID: 37662385 PMCID: PMC10473586 DOI: 10.1101/2023.08.19.553937] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
The sequencing of PCR amplicons is a core application of high-throughput sequencing technology. Using unique molecular identifiers (UMIs), individual amplified molecules can be sequenced to very high accuracy on an Illumina sequencer. However, Illumina sequencers have limited read length and are therefore restricted to sequencing amplicons shorter than 600bp unless using inefficient synthetic long-read approaches. Native long-read sequencers from Pacific Biosciences and Oxford Nanopore Technologies can, using consensus read approaches, match or exceed Illumina quality while achieving much longer read lengths. Using a circularization-based concatemeric consensus sequencing approach (R2C2) paired with UMIs (R2C2+UMI) we show that we can sequence ~550nt antibody heavy-chain (IGH) and ~1500nt 16S amplicons at accuracies up to and exceeding Q50 (<1 error in 100,0000 sequenced bases), which exceeds accuracies of UMI-supported Illumina paired sequencing as well as synthetic long-read approaches.
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Affiliation(s)
- Dori Z Q Deng
- Department of Molecular, Cellular, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California, USA
| | - Jack Verhage
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Celine Neudorf
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Honey Mekonen
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
- Current address: Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA,USA
- Division of General Internal Medicine and Primary Care, Brigham and Women's Hospital, Boston, MA, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
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11
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Xie S, Yan R, Zheng A, Shi M, Tang L, Li X, Liu J, Gan Y, Wang Y, Jiang D, Liu L, Wu H, Wang Z. T cell receptor and B cell receptor exhibit unique signatures in tumor and adjacent non-tumor tissues of hepatocellular carcinoma. Front Immunol 2023; 14:1161417. [PMID: 37313417 PMCID: PMC10258310 DOI: 10.3389/fimmu.2023.1161417] [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: 02/08/2023] [Accepted: 05/16/2023] [Indexed: 06/15/2023] Open
Abstract
Background The tumor microenvironment in hepatocellular carcinoma (HCC) is complicated. Tumor-infiltrating T and B cells play a pivotal role in anti-tumor immunity. T cell receptor (TCR) and B cell receptor (BCR) features may reflect the disease-associated antigen response. Methods By combining bulk TCR/BCR-sequencing, RNA-sequencing, whole exome-sequencing, and human leukocyte antigen-sequencing, we examined the immune repertoire (IR) features of tumor and adjacent non-tumor tissues obtained from 64 HCC patients. Results High IR heterogeneity with weak similarity was discovered between tumor and non-tumor tissues. Higher BCR diversity, richness, and somatic hypermutation (SHM) were found in non-tumor tissues, while TCRα and TCRβ diversity and richness were comparable or higher in tumor. Additionally, lower immune infiltration was found in tumor than non-tumor tissues; the microenvironment in tumor appeared to keep stably inhibited and changed slightly with tumor progression. Moreover, BCR SHM was stronger, whereas TCR/BCR diversity declined with HCC progression. Importantly, we found that higher IR evenness in tumor and lower TCR richness in non-tumor tissues indicated better survival in HCC patients. Collectively, the results revealed that TCR and BCR exhibited distinct features in tumor and non-tumor tissues. Conclusions We demonstrated that IR features vary between different tissues of HCC. IR features may represent a biomarker for the diagnosis and treatment of HCC patients, providing references for subsequent immunotherapy research and strategy selection.
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Affiliation(s)
- Shi Xie
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Rong Yan
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Anqi Zheng
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mengfen Shi
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | | | - Xueying Li
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jiabang Liu
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yifan Gan
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yu Wang
- Department of Hepatobiliary Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Deke Jiang
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Li Liu
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hongkai Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Zhanhui Wang
- Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
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12
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Ford EE, Tieri D, Rodriguez OL, Francoeur NJ, Soto J, Kos JT, Peres A, Gibson WS, Silver CA, Deikus G, Hudson E, Woolley CR, Beckmann N, Charney A, Mitchell TC, Yaari G, Sebra RP, Watson CT, Smith ML. FLAIRR-Seq: A Method for Single-Molecule Resolution of Near Full-Length Antibody H Chain Repertoires. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:1607-1619. [PMID: 37027017 PMCID: PMC10152037 DOI: 10.4049/jimmunol.2200825] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/14/2023] [Indexed: 04/08/2023]
Abstract
Current Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) using short-read sequencing strategies resolve expressed Ab transcripts with limited resolution of the C region. In this article, we present the near-full-length AIRR-seq (FLAIRR-seq) method that uses targeted amplification by 5' RACE, combined with single-molecule, real-time sequencing to generate highly accurate (99.99%) human Ab H chain transcripts. FLAIRR-seq was benchmarked by comparing H chain V (IGHV), D (IGHD), and J (IGHJ) gene usage, complementarity-determining region 3 length, and somatic hypermutation to matched datasets generated with standard 5' RACE AIRR-seq using short-read sequencing and full-length isoform sequencing. Together, these data demonstrate robust FLAIRR-seq performance using RNA samples derived from PBMCs, purified B cells, and whole blood, which recapitulated results generated by commonly used methods, while additionally resolving H chain gene features not documented in IMGT at the time of submission. FLAIRR-seq data provide, for the first time, to our knowledge, simultaneous single-molecule characterization of IGHV, IGHD, IGHJ, and IGHC region genes and alleles, allele-resolved subisotype definition, and high-resolution identification of class switch recombination within a clonal lineage. In conjunction with genomic sequencing and genotyping of IGHC genes, FLAIRR-seq of the IgM and IgG repertoires from 10 individuals resulted in the identification of 32 unique IGHC alleles, 28 (87%) of which were previously uncharacterized. Together, these data demonstrate the capabilities of FLAIRR-seq to characterize IGHV, IGHD, IGHJ, and IGHC gene diversity for the most comprehensive view of bulk-expressed Ab repertoires to date.
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Affiliation(s)
- Easton E. Ford
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, KY
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY
| | - David Tieri
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY
| | - Oscar L. Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY
| | - Nancy J. Francoeur
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY
| | - Juan Soto
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY
| | - Justin T. Kos
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY
| | - Ayelet Peres
- Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - William S. Gibson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY
| | - Catherine A. Silver
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY
| | - Elizabeth Hudson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY
| | - Cassandra R. Woolley
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, KY
| | - Noam Beckmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY
| | - Alexander Charney
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY
| | - Thomas C. Mitchell
- Department of Microbiology and Immunology, University of Louisville School of Medicine, Louisville, KY
| | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
- Bar Ilan Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Robert P. Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY
| | - Corey T. Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY
| | - Melissa L. Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY
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13
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Abstract
Repeated doses of mRNA vaccines for COVID-19 result in increased proportions of anti-spike antibodies of the IgG4 subclass, which are known to neutralize well and to form mixed immune complexes with IgG1 but, in a pure form, might be less effective than IgG1 or IgG3 antibodies in facilitating opsonization by phagocytes, complement fixation, and NK cell-dependent elimination of infected cells (see related Research Article by Irrgang et al.).
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Affiliation(s)
- Shiv Pillai
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
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14
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Laumont CM, Nelson BH. B cells in the tumor microenvironment: Multi-faceted organizers, regulators, and effectors of anti-tumor immunity. Cancer Cell 2023; 41:466-489. [PMID: 36917951 DOI: 10.1016/j.ccell.2023.02.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/11/2023] [Accepted: 02/12/2023] [Indexed: 03/14/2023]
Abstract
Our understanding of tumor-infiltrating lymphocytes (TILs) is rapidly expanding beyond T cell-centric perspectives to include B cells and plasma cells, collectively referred to as TIL-Bs. In many cancers, TIL-Bs carry strong prognostic significance and are emerging as key predictors of response to immune checkpoint inhibitors. TIL-Bs can perform multiple functions, including antigen presentation and antibody production, which allow them to focus immune responses on cognate antigen to support both T cell responses and innate mechanisms involving complement, macrophages, and natural killer cells. In the stroma of the most immunologically "hot" tumors, TIL-Bs are prominent components of tertiary lymphoid structures, which resemble lymph nodes structurally and functionally. Additionally, TIL-Bs participate in a variety of other lympho-myeloid aggregates and engage in dynamic interactions with the tumor stroma. Here, we summarize our current understanding of TIL-Bs in human cancer, highlighting the compelling therapeutic opportunities offered by their unique tumor recognition and effector mechanisms.
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Affiliation(s)
- Céline M Laumont
- Deeley Research Centre, BC Cancer, Victoria, BC V8R 6V5, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Brad H Nelson
- Deeley Research Centre, BC Cancer, Victoria, BC V8R 6V5, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 3E6, Canada.
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15
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Swift M, Horns F, Quake SR. Lineage tracing reveals fate bias and transcriptional memory in human B cells. Life Sci Alliance 2023; 6:e202201792. [PMID: 36639222 PMCID: PMC9840405 DOI: 10.26508/lsa.202201792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 01/15/2023] Open
Abstract
We combined single-cell transcriptomics and lineage tracing to understand fate choice in human B cells. Using the antibody sequences of B cells, we tracked clones during in vitro differentiation. Clonal analysis revealed a subset of IgM+ B cells which were more proliferative than other B-cell types. Whereas the population of B cells adopted diverse states during differentiation, clones had a restricted set of fates available to them; there were two times more single-fate clones than expected given population-level cell-type diversity. This implicated a molecular memory of initial cell states that was propagated through differentiation. We then identified the genes which had strongest coherence within clones. These genes significantly overlapped known B-cell fate determination programs, suggesting the genes which determine cell identity are most robustly controlled on a clonal level. Persistent clonal identities were also observed in human plasma cells from bone marrow, indicating that these transcriptional programs maintain long-term cell identities in vivo. Thus, we show how cell-intrinsic fate bias influences differentiation outcomes in vitro and in vivo.
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Affiliation(s)
- Michael Swift
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Felix Horns
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, USA
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Applied Physics, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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16
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Irrgang P, Gerling J, Kocher K, Lapuente D, Steininger P, Habenicht K, Wytopil M, Beileke S, Schäfer S, Zhong J, Ssebyatika G, Krey T, Falcone V, Schülein C, Peter AS, Nganou-Makamdop K, Hengel H, Held J, Bogdan C, Überla K, Schober K, Winkler TH, Tenbusch M. Class switch toward noninflammatory, spike-specific IgG4 antibodies after repeated SARS-CoV-2 mRNA vaccination. Sci Immunol 2023; 8:eade2798. [PMID: 36548397 PMCID: PMC9847566 DOI: 10.1126/sciimmunol.ade2798] [Citation(s) in RCA: 88] [Impact Index Per Article: 88.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
RNA vaccines are efficient preventive measures to combat the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. High levels of neutralizing SARS-CoV-2 antibodies are an important component of vaccine-induced immunity. Shortly after the initial two mRNA vaccine doses, the immunoglobulin G (IgG) response mainly consists of the proinflammatory subclasses IgG1 and IgG3. Here, we report that several months after the second vaccination, SARS-CoV-2-specific antibodies were increasingly composed of noninflammatory IgG4, which were further boosted by a third mRNA vaccination and/or SARS-CoV-2 variant breakthrough infections. IgG4 antibodies among all spike-specific IgG antibodies rose, on average, from 0.04% shortly after the second vaccination to 19.27% late after the third vaccination. This induction of IgG4 antibodies was not observed after homologous or heterologous SARS-CoV-2 vaccination with adenoviral vectors. Single-cell sequencing and flow cytometry revealed substantial frequencies of IgG4-switched B cells within the spike-binding memory B cell population [median of 14.4%; interquartile range (IQR) of 6.7 to 18.1%] compared with the overall memory B cell repertoire (median of 1.3%; IQR of 0.9 to 2.2%) after three immunizations. This class switch was associated with a reduced capacity of the spike-specific antibodies to mediate antibody-dependent cellular phagocytosis and complement deposition. Because Fc-mediated effector functions are critical for antiviral immunity, these findings may have consequences for the choice and timing of vaccination regimens using mRNA vaccines, including future booster immunizations against SARS-CoV-2.
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Affiliation(s)
- Pascal Irrgang
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg; Schlossgarten 4, 91054 Erlangen, Germany
| | - Juliane Gerling
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU); Erlangen, Germany
| | - Katharina Kocher
- Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg; Wasserturmstr. 3/5, 91054 Erlangen, Germany
| | - Dennis Lapuente
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg; Schlossgarten 4, 91054 Erlangen, Germany
| | - Philipp Steininger
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg; Schlossgarten 4, 91054 Erlangen, Germany
| | - Katharina Habenicht
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU); Erlangen, Germany
| | - Monika Wytopil
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg; Schlossgarten 4, 91054 Erlangen, Germany
| | - Stephanie Beileke
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg; Schlossgarten 4, 91054 Erlangen, Germany
| | - Simon Schäfer
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU); Erlangen, Germany
| | - Jahn Zhong
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU); Erlangen, Germany
| | - George Ssebyatika
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck; Luebeck, Germany
| | - Thomas Krey
- Center of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Luebeck; Luebeck, Germany
| | - Valeria Falcone
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg; Freiburg, Germany
| | - Christine Schülein
- Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg; Wasserturmstr. 3/5, 91054 Erlangen, Germany
| | - Antonia Sophia Peter
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg; Schlossgarten 4, 91054 Erlangen, Germany
| | - Krystelle Nganou-Makamdop
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg; Schlossgarten 4, 91054 Erlangen, Germany.,Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054 Erlangen, Germany
| | - Hartmut Hengel
- Institute of Virology, Freiburg University Medical Center, Faculty of Medicine, University of Freiburg; Freiburg, Germany
| | - Jürgen Held
- Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg; Wasserturmstr. 3/5, 91054 Erlangen, Germany
| | - Christian Bogdan
- Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg; Wasserturmstr. 3/5, 91054 Erlangen, Germany.,Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054 Erlangen, Germany
| | - Klaus Überla
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg; Schlossgarten 4, 91054 Erlangen, Germany.,Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054 Erlangen, Germany
| | - Kilian Schober
- Mikrobiologisches Institut – Klinische Mikrobiologie, Immunologie und Hygiene, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg; Wasserturmstr. 3/5, 91054 Erlangen, Germany.,Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054 Erlangen, Germany.,Corresponding author. (K.S.); (T.H.W.); (M.T.)
| | - Thomas H. Winkler
- Department of Biology, Division of Genetics, Nikolaus-Fiebiger-Center for Molecular Medicine, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU); Erlangen, Germany.,Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054 Erlangen, Germany.,Corresponding author. (K.S.); (T.H.W.); (M.T.)
| | - Matthias Tenbusch
- Institut für klinische und molekulare Virologie, Universitätsklinikum Erlangen und Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg; Schlossgarten 4, 91054 Erlangen, Germany.,Medical Immunology Campus Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Schlossplatz 1, 91054 Erlangen, Germany.,Corresponding author. (K.S.); (T.H.W.); (M.T.)
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17
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Blazso P, Csomos K, Tipton CM, Ujhazi B, Walter JE. Lineage Reconstruction of In Vitro Identified Antigen-Specific Autoreactive B Cells from Adaptive Immune Receptor Repertoires. Int J Mol Sci 2022; 24:ijms24010225. [PMID: 36613668 PMCID: PMC9820449 DOI: 10.3390/ijms24010225] [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: 11/16/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
The emergence, survival, growth and maintenance of autoreactive (AR) B-cell clones, the hallmark of humoral autoimmunity, leave their footprints in B-cell receptor repertoires. Collecting IgH sequences related to polyreactive (PR) ones from adaptive immune receptor repertoire (AIRR) datasets make the reconstruction and analysis of PR/AR B-cell lineages possible. We developed a computational approach, named ImmChainTracer, to extract members and to visualize clonal relationships of such B-cell lineages. Our approach was successfully applied on the IgH repertoires of patients suffering from monogenic hypomorphic RAG1 and 2 deficiency (pRD) or polygenic systemic lupus erythematosus (SLE) autoimmune diseases to identify relatives of AR IgH sequences and to track their fate in AIRRs. Signs of clonal expansion, affinity maturation and class-switching events in PR/AR and non-PR/AR B-cell lineages were revealed. An extension of our method towards B-cell expansion caused by any trigger (e.g., infection, vaccination or antibody development) may provide deeper insight into antigen specific B-lymphogenesis.
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Affiliation(s)
- Peter Blazso
- Department of Pediatrics, University of Szeged, 6720 Szeged, Hungary
- Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
- Correspondence: (P.B.); (J.E.W.)
| | - Krisztian Csomos
- Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
| | - Christopher M. Tipton
- Department of Medicine, Division of Rheumatology, Emory University, Atlanta, GA 30322, USA
| | - Boglarka Ujhazi
- Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
| | - Jolan E. Walter
- Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
- Division of Allergy and Immunology, Massachusetts General Hospital for Children, Boston, MA 02114, USA
- Correspondence: (P.B.); (J.E.W.)
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18
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Zhang C, Bzikadze AV, Safonova Y, Mirarab S. A scalable model for simulating multi-round antibody evolution and benchmarking of clonal tree reconstruction methods. Front Immunol 2022; 13:1014439. [PMID: 36618367 PMCID: PMC9815712 DOI: 10.3389/fimmu.2022.1014439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/26/2022] [Indexed: 12/12/2022] Open
Abstract
Affinity maturation (AM) of B cells through somatic hypermutations (SHMs) enables the immune system to evolve to recognize diverse pathogens. The accumulation of SHMs leads to the formation of clonal lineages of antibody-secreting b cells that have evolved from a common naïve B cell. Advances in high-throughput sequencing have enabled deep scans of B cell receptor repertoires, paving the way for reconstructing clonal trees. However, it is not clear if clonal trees, which capture microevolutionary time scales, can be reconstructed using traditional phylogenetic reconstruction methods with adequate accuracy. In fact, several clonal tree reconstruction methods have been developed to fix supposed shortcomings of phylogenetic methods. Nevertheless, no consensus has been reached regarding the relative accuracy of these methods, partially because evaluation is challenging. Benchmarking the performance of existing methods and developing better methods would both benefit from realistic models of clonal lineage evolution specifically designed for emulating B cell evolution. In this paper, we propose a model for modeling B cell clonal lineage evolution and use this model to benchmark several existing clonal tree reconstruction methods. Our model, designed to be extensible, has several features: by evolving the clonal tree and sequences simultaneously, it allows modeling selective pressure due to changes in affinity binding; it enables scalable simulations of large numbers of cells; it enables several rounds of infection by an evolving pathogen; and, it models building of memory. In addition, we also suggest a set of metrics for comparing clonal trees and measuring their properties. Our results show that while maximum likelihood phylogenetic reconstruction methods can fail to capture key features of clonal tree expansion if applied naively, a simple post-processing of their results, where short branches are contracted, leads to inferences that are better than alternative methods.
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Affiliation(s)
- Chao Zhang
- Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, United States
| | - Andrey V. Bzikadze
- Bioinformatics and Systems Biology, University of California, San Diego, San Diego, CA, United States
| | - Yana Safonova
- Computer Science and Engineering Department, University of California, San Diego, San Diego, CA, United States
| | - Siavash Mirarab
- Electrical and Computer Engineering Department, University of California, San Diego, San Diego, CA, United States,*Correspondence: Siavash Mirarab,
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19
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Herman JD, Atyeo C, Zur Y, Cook CE, Patel NJ, Vanni KM, Kowalski EN, Qian G, Shadick NA, Laffenburger D, Wallace ZS, Sparks JA, Alter G. Impact of cross-coronavirus immunity in post-acute sequelae of COVID-19. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.09.25.22280335. [PMID: 36203557 PMCID: PMC9536039 DOI: 10.1101/2022.09.25.22280335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Beyond the unpredictable acute illness caused by SARS-CoV-2, one-fifth of infections unpredictably result in long-term persistence of symptoms despite the apparent clearance of infection. Insights into the mechanisms that underlie post-acute sequelae of COVID-19 (PASC) will be critical for the prevention and clinical management of long-term complications of COVID-19. Several hypotheses have been proposed that may account for the development of PASC, including persistence of virus or the dysregulation of immunity. Among the immunological changes noted in PASC, alterations in humoral immunity have been observed in some patient subsets. To begin to determine whether SARS-CoV-2 or other pathogen specific humoral immune responses evolve uniquely in PASC, we performed comprehensive antibody profiling against SARS-CoV-2 and a panel of endemic pathogens or routine vaccine antigens using Systems Serology in a cohort of patients with pre-existing rheumatic disease who either developed or did not develop PASC. A distinct humoral immune response was observed in individuals with PASC. Specifically, individuals with PASC harbored less inflamed and weaker Fcγ receptor binding anti-SARS-CoV-2 antibodies and a significantly expanded and more inflamed antibody response against endemic Coronavirus OC43. Individuals with PASC, further, generated more avid IgM responses and developed an expanded inflammatory OC43 S2-specific Fc-receptor binding response, linked to cross reactivity across SARS-CoV-2 and common coronaviruses. These findings implicate previous common Coronavirus imprinting as a marker for the development of PASC.
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Affiliation(s)
- Jonathan D Herman
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Division of Infectious Disease, Brigham and Women's Hospital, Boston, MA, USA
| | - Caroline Atyeo
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Yonatan Zur
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Claire E Cook
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, USA
| | - Naomi J Patel
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, USA
| | - Kathleen M Vanni
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Emily N Kowalski
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Grace Qian
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Nancy A Shadick
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Douglas Laffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zachary S Wallace
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA, USA
| | - Jeffrey A Sparks
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
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20
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Davies LRL, Cizmeci D, Guo W, Luedemann C, Alexander-Parrish R, Grant L, Isturiz R, Theilacker C, Jodar L, Gessner BD, Alter G. Polysaccharide and conjugate vaccines to Streptococcus pneumoniae generate distinct humoral responses. Sci Transl Med 2022; 14:eabm4065. [PMID: 35921476 PMCID: PMC9885968 DOI: 10.1126/scitranslmed.abm4065] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Streptococcus pneumoniae is a major cause of community-acquired pneumonia, bacteremia, and meningitis in older adults worldwide. Two pneumococcal vaccines containing S. pneumoniae capsular polysaccharides are in current use: the polysaccharide vaccine PPSV23 and the glycoconjugate vaccine PCV13. In clinical trials, both vaccines elicit similar opsonophagocytic killing activity. In contrast to polysaccharide vaccines, conjugate vaccines have shown consistent efficacy against nasopharyngeal carriage and noninvasive pneumonia overall and for some prevalent individual serotypes. Given these different clinical profiles, it is crucial to understand the differential immunological responses induced by these two vaccines. Here, we used a high-throughput systems serology approach to profile the biophysical and functional features of serum antibodies induced by PCV13 and PPSV23 at 1 month and 1 year. In comparison with PPSV23, PCV13 induced higher titers across antibody isotypes; more durable antibody responses across immunoglobulin G (IgG), IgA, and IgM isotypes; and increased antigenic breadth. Although titers measured in opsonophagocytic activity (OPA) assays were similar between the two groups, confirming what was observed in clinical studies, serum samples from PCV13 vaccinees could induce additional non-OPA antibody-dependent functions, including monocyte phagocytosis and natural killer cell activation. In a multivariate modeling approach, distinct humoral profiles were demonstrated in each arm. Together, these results demonstrate that the glycoconjugate PCV13 vaccine induces an antigenically broader, more durable, polyfunctional antibody response. These findings may help explain the increased protection against S. pneumoniae colonization and noninvasive pneumonia and the longer duration of protection against invasive pneumococcal disease, mediated by PCV13.
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Affiliation(s)
- Leela R. L. Davies
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Deniz Cizmeci
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Wenyue Guo
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | | | | | | | | | | | - Luis Jodar
- Pfizer Vaccines, Collegeville, PA 19426, USA
| | | | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.,Corresponding author.
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21
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Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) accelerated development of messenger RNA (mRNA) vaccines, which have proven to be highly effective against COVID-19. However, antibody responses vary widely and wane over time. This study evaluated the range and kinetics of the primary antibody response to SARS-CoV-2 mRNA-based vaccination in parallel with the B cells that are involved in generating and maintaining this response. These include plasmablasts, the antibody-secreting cells that arise rapidly yet transiently following immunization, and memory B cells, a heterogeneous population that can provide long-lasting immunity. Our results show that the antibody response was tightly linked to early plasmablasts, while the cellular response was sustained by a distinct population of memory B cells. Messenger RNA (mRNA) vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are highly effective at inducing protective immunity. However, weak antibody responses are seen in some individuals, and cellular correlates of immunity remain poorly defined, especially for B cells. Here we used unbiased approaches to longitudinally dissect primary antibody, plasmablast, and memory B cell (MBC) responses to the two-dose mRNA-1273 vaccine in SARS-CoV-2–naive adults. Coordinated immunoglobulin A (IgA) and IgG antibody responses were preceded by bursts of spike-specific plasmablasts after both doses but earlier and more intensely after dose 2. While antibody and B cell cellular responses were generally robust, they also varied within the cohort and decreased over time after a dose-2 peak. Both antigen-nonspecific postvaccination plasmablast frequency after dose 1 and their spike-specific counterparts early after dose 2 correlated with subsequent antibody levels. This correlation between early plasmablasts and antibodies remained for titers measured at 6 months after vaccination. Several distinct antigen-specific MBC populations emerged postvaccination with varying kinetics, including two MBC populations that correlated with 2- and 6-month antibody titers. Both were IgG-expressing MBCs: one less mature, appearing as a correlate after the first dose, while the other MBC correlate showed a more mature and resting phenotype, emerging as a correlate later after dose 2. This latter MBC was also a major contributor to the sustained spike-specific MBC response observed at month 6. Thus, these plasmablasts and MBCs that emerged after both the first and second doses with distinct kinetics are potential determinants of the magnitude and durability of antibodies in response to mRNA-based vaccination.
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22
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Clonal structure, stability and dynamics of human memory B cells and circulating plasmablasts. Nat Immunol 2022; 23:1076-1085. [PMID: 35761085 PMCID: PMC9276532 DOI: 10.1038/s41590-022-01230-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/26/2022] [Indexed: 12/22/2022]
Abstract
Memory B cells persist for a lifetime and rapidly differentiate into antibody-producing plasmablasts and plasma cells upon antigen re-encounter. The clonal relationship and evolution of memory B cells and circulating plasmablasts is not well understood. Using single-cell sequencing combined with isolation of specific antibodies, we found that in two healthy donors, the memory B cell repertoire was dominated by large IgM, IgA and IgG2 clonal families, whereas IgG1 families, including those specific for recall antigens, were of small size. Analysis of multiyear samples demonstrated stability of memory B cell clonal families and revealed that a large fraction of recently generated plasmablasts was derived from long-term memory B cell families and was found recurrently. Collectively, this study provides a systematic description of the structure, stability and dynamics of the human memory B cell pool and suggests that memory B cells may be active at any time point in the generation of plasmablasts.
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23
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Wang Z, Cheng Z, Lu S, Chard Dunmall LS, Wang J, Guo Y, Wang Y. Characterization of the Intra-tumoral B Cell Immunoglobulin Repertoire Is of Prognostic Value for Esophageal Squamous Cell Carcinoma. Front Immunol 2022; 13:896627. [PMID: 35812448 PMCID: PMC9257635 DOI: 10.3389/fimmu.2022.896627] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/26/2022] [Indexed: 12/24/2022] Open
Abstract
Esophageal Squamous Cell carcinomas (ESCC) is a highly heterogeneous malignancy that is among the leading cause of cancer-related death worldwide. B cells play pivotal roles in the immune defense system and cancer progression and regression, yet the repertoire of tumor infiltrating B cells (TIBs) and its association with clinical outcome remains unexplored in ESCC. Here we collected bulk RNA-seq sequencing data from 119 ESCC tumors and matched adjacent normal samples to delineate the B cell repertoire. We found that ESCC is more heavily infiltrated by B cells and plasma cells compared to activated T cells. The immunoglobulin heavy chain variable region (IGHV) gene usage was remarkably biased and IGHV3-74 was under-represented in ESCC tumors. The TIBs showed a more oligoclonal profile along with widespread clonal expansion and IgG subclass switch events (CSRs). Survival analysis revealed several unexpected associations between tumor infiltrating B cells and prognosis. Higher levels of immunoglobulin expression (IGH), CD138 expression, IGH to MS4A1 ratio, CSR events and clone diversity are all associated with better survival. Notably, we found that the abundance of CD20-negative IgG2-producing plasma cells has a strong positive effect on overall survival with a hazard ratio (HR) of 0.40 (log-rank p: 0.002). Combing molecular subtyping, the IgG2-producing plasma cells could stratify high-risk patients more accurately with a HR of 0.253 (log-rank p: 0.0006). The direct link between protective B cell populations and ESCC prognosis provides biomarkers for high-risk patient selection and holds great promise for developing strategies for immunotherapy targeting B cells in ESCC patients.
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Affiliation(s)
- Zhizhong Wang
- National Center for International Research in Cell and Gene Therapy, Sino-British Research Centre for Molecular Oncology, State Key Laboratory of Esophageal Cancer Prevention Treatment, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Zhenguo Cheng
- National Center for International Research in Cell and Gene Therapy, Sino-British Research Centre for Molecular Oncology, State Key Laboratory of Esophageal Cancer Prevention Treatment, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
- Department of Pharmacology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Shuangshuang Lu
- National Center for International Research in Cell and Gene Therapy, Sino-British Research Centre for Molecular Oncology, State Key Laboratory of Esophageal Cancer Prevention Treatment, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Louisa S. Chard Dunmall
- Centre for Biomarkers Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Jun Wang
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Yongjun Guo
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
- *Correspondence: Yaohe Wang, ; Yongjun Guo,
| | - Yaohe Wang
- National Center for International Research in Cell and Gene Therapy, Sino-British Research Centre for Molecular Oncology, State Key Laboratory of Esophageal Cancer Prevention Treatment, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
- Centre for Biomarkers Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
- *Correspondence: Yaohe Wang, ; Yongjun Guo,
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24
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Higgins BW, Shuparski AG, Miller KB, Robinson AM, McHeyzer-Williams LJ, McHeyzer-Williams MG. Isotype-specific plasma cells express divergent transcriptional programs. Proc Natl Acad Sci U S A 2022; 119:e2121260119. [PMID: 35704755 PMCID: PMC9231473 DOI: 10.1073/pnas.2121260119] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 04/29/2022] [Indexed: 11/18/2022] Open
Abstract
Antibodies are produced across multiple isotypes with distinct properties that coordinate initial antigen clearance and confer long-term antigen-specific immune protection. Here, we interrogate the molecular programs of isotype-specific murine plasma cells (PC) following helper T cell-dependent immunization and within established steady-state immunity. We developed a single-cell-indexed and targeted molecular strategy to dissect conserved and divergent components of the rapid effector phase of antigen-specific IgM+ versus inflammation-modulating programs dictated by type 1 IgG2a/b+ PC differentiation. During antibody affinity maturation, the germinal center (GC) cycle imparts separable programs for post-GC type 2 inhibitory IgG1+ and type 1 inflammatory IgG2a/b+ PC to direct long-term cellular function. In the steady state, two subsets of IgM+ and separate IgG2b+ PC programs clearly segregate from splenic type 3 IgA+ PC programs that emphasize mucosal barrier protection. These diverse isotype-specific molecular pathways of PC differentiation control complementary modules of antigen clearance and immune protection that could be selectively targeted for immunotherapeutic applications and vaccine design.
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Affiliation(s)
- Brett W. Higgins
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Andrew G. Shuparski
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Karen B. Miller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037
| | - Amanda M. Robinson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037
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25
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Hopp RJ, Niebur HB. Persistent Hyper IgA as a Marker of Immune Deficiency: A Case Report. Antibodies (Basel) 2022; 11:antib11020030. [PMID: 35645203 PMCID: PMC9149891 DOI: 10.3390/antib11020030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/28/2022] [Accepted: 04/18/2022] [Indexed: 02/05/2023] Open
Abstract
An elevated IgA level obtained in a 10-year-old male a year after an episode of pneumococcal sepsis led to the discovery of a broad-based IgG-specific antibody deficiency syndrome. The specifics of the case and pertinent literature are presented, including a discussion of the hyper-IgD syndrome. An elevated IgA, greater than two standard deviations above the expected age range should prompt a complete workup for selective antibody deficiency syndrome and adds an additional associated marker of an indolent hyper-IgD syndrome in a different clinical circumstance, although the lack of antibody response to vaccines is atypical of the hyper-IgD syndrome.
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26
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Hoehn KB, Pybus OG, Kleinstein SH. Phylogenetic analysis of migration, differentiation, and class switching in B cells. PLoS Comput Biol 2022; 18:e1009885. [PMID: 35468128 PMCID: PMC9037912 DOI: 10.1371/journal.pcbi.1009885] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 01/31/2022] [Indexed: 11/20/2022] Open
Abstract
B cells undergo rapid mutation and selection for antibody binding affinity when producing antibodies capable of neutralizing pathogens. This evolutionary process can be intermixed with migration between tissues, differentiation between cellular subsets, and switching between functional isotypes. B cell receptor (BCR) sequence data has the potential to elucidate important information about these processes. However, there is currently no robust, generalizable framework for making such inferences from BCR sequence data. To address this, we develop three parsimony-based summary statistics to characterize migration, differentiation, and isotype switching along B cell phylogenetic trees. We use simulations to demonstrate the effectiveness of this approach. We then use this framework to infer patterns of cellular differentiation and isotype switching from high throughput BCR sequence datasets obtained from patients in a study of HIV infection and a study of food allergy. These methods are implemented in the R package dowser, available at https://dowser.readthedocs.io. B cells produce high affinity antibodies through an evolutionary process of mutation and selection during adaptive immune responses. Migration between tissues, differentiation to cellular subtypes, and switching between different antibody isotypes can be important factors in shaping the role B cells play in response to infection, autoimmune disease, and allergies. B cell receptor (BCR) sequence data has the potential to elucidate important information about these processes. However, there is currently no robust, generalizable framework for making such inferences from BCR sequence data. Here, we develop three parsimony-based summary statistics to characterize migration, differentiation, and isotype switching along B cell phylogenetic trees. We confirm the effectiveness of our approach using simulations and further apply our method to data from patients with HIV and allergy. Our methods are released in the R package dowser: https://dowser.readthedocs.io.
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Affiliation(s)
- Kenneth B. Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, United Kingdom
| | - Steven H. Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- * E-mail:
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27
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Delidakis G, Kim JE, George K, Georgiou G. Improving Antibody Therapeutics by Manipulating the Fc Domain: Immunological and Structural Considerations. Annu Rev Biomed Eng 2022; 24:249-274. [PMID: 35363537 PMCID: PMC9648538 DOI: 10.1146/annurev-bioeng-082721-024500] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Interactions between the crystallizable fragment (Fc) domain of antibodies and a plethora of cellular Fc receptors (FcRs) or soluble proteins form a critical link between humoral and innate immunity. In particular, the immunoglobulin G Fc domain is critical for the clearance of target cells by processes that include (a) cytotoxicity, phagocytosis, or complement lysis; (b) modulation of inflammation; (c) antigen presentation; (d) antibody-mediated receptor clustering; and (e) cytokine release. More than 30 Fc-engineered antibodies aimed primarily at tailoring these effects for optimal therapeutic outcomes are in clinical evaluation or have already been approved. Nonetheless, our understanding of how FcR engagement impacts various immune cell phenotypes is still largely incomplete. Recent insights into FcR biology coupled with advances in Fc:FcR structural analysis, Fc engineering, and mouse models that recapitulate human biology are helping to fill in existing knowledge gaps. These advances will provide a blueprint on how to fine-tune the Fc domain to achieve optimal therapeutic efficacy. Expected final online publication date for the Annual Review of Biomedical Engineering, Volume 24 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- George Delidakis
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA;
| | - Jin Eyun Kim
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Katia George
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA; .,Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA.,Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
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28
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Wu H, Zhou Z, Xie S, Yan R, Gong M, Tian X, Wang Z. Similarity measurements of B cell receptor repertoire in baseline mice showed spectrum convergence of IgM. BMC Immunol 2022; 23:11. [PMID: 35246036 PMCID: PMC8895918 DOI: 10.1186/s12865-022-00482-8] [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: 08/13/2021] [Accepted: 02/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The B cell receptor (BCR) repertoire is highly diverse among individuals. Poor similarity of the spectrum among inbred baseline mice may limit the ability to discriminate true signals from those involving specific experimental factors. The repertoire similarity of the baseline status lacks intensive measurements. RESULTS We measured the repertoire similarity of IgH in blood and spleen samples from untreated BALB/c and C57BL/6J mice to investigate the baseline status of the two inbred strains. The antibody pool was stratified by the isotype of IgA, IgG and IgM. Between individuals, the results showed better convergence of CDR3 and clonal lineage profiles in IgM than in IgA and IgG, and better robustness of somatic mutation networks in IgM than in IgA and IgG. It also showed that the CDR3 clonotypes and clonal lineages shared better in the spleen samples than in the blood samples. The animal batch differences were detected in CDR3 evenness, mutated clonotype proportions, and maximal network degrees. A cut-off of 95% identity in the CDR3 nucleotide sequences was suitable for clonal lineage establishment. CONCLUSIONS Our findings reveal a natural landscape of BCR repertoire similarities between baseline mice and provide a solid reference for designing studies of mouse BCR repertoires.
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Affiliation(s)
- Hongkai Wu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Zhichao Zhou
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Shi Xie
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Rong Yan
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Mingxing Gong
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xingui Tian
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China.
| | - Zhanhui Wang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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29
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Marquez S, Babrak L, Greiff V, Hoehn KB, Lees WD, Luning Prak ET, Miho E, Rosenfeld AM, Schramm CA, Stervbo U. Adaptive Immune Receptor Repertoire (AIRR) Community Guide to Repertoire Analysis. Methods Mol Biol 2022; 2453:297-316. [PMID: 35622333 PMCID: PMC9761518 DOI: 10.1007/978-1-0716-2115-8_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Adaptive immune receptor repertoires (AIRRs) are rich with information that can be mined for insights into the workings of the immune system. Gene usage, CDR3 properties, clonal lineage structure, and sequence diversity are all capable of revealing the dynamic immune response to perturbation by disease, vaccination, or other interventions. Here we focus on a conceptual introduction to the many aspects of repertoire analysis and orient the reader toward the uses and advantages of each. Along the way, we note some of the many software tools that have been developed for these investigations and link the ideas discussed to chapters on methods provided elsewhere in this volume.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Ulrik Stervbo
- Center for Translational Medicine, Immunology, and Transplantation, Medical Department I, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany. .,Immundiagnostik, Marien Hospital Herne, University Hospital of the Ruhr-University Bochum, Herne, Germany.
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30
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Spoerry C, Karlsson J, Aschtgen MS, Loh E. Neisseria meningitidis IgA1-specific serine protease exhibits novel cleavage activity against IgG3. Virulence 2021; 12:389-403. [PMID: 33459578 PMCID: PMC7834093 DOI: 10.1080/21505594.2021.1871822] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 11/16/2022] Open
Abstract
Neisseria meningitidis (meningococcus) is a common bacterial colonizer of the human nasopharynx but can occasionally cause very severe systemic infections with rapid onset. Meningococci are able to degrade IgA encountered during colonization of mucosal membranes using their IgA1-specific serine protease. During systemic infection, specific IgG can induce complement-mediated lysis of the bacterium. However, meningococcal immune evasion mechanisms in thwarting IgG remain undescribed. In this study, we report for the first time that the meningococcal IgA1-specific serine protease is able to degrade IgG3 in addition to IgA. The IgG3 heavy chain is specifically cleaved in the lower hinge region thereby separating the antigen binding part from its effector binding part. Through molecular characterization, we demonstrate that meningococcal IgA1-specific serine protease of cleavage type 1 degrades both IgG3 and IgA, whereas cleavage type 2 only degrades IgA. Epidemiological analysis of 7581 clinical meningococcal isolates shows a significant higher proportion of cleavage type 1 among isolates from invasive cases compared to carrier cases, regardless of serogroup. Notably, serogroup W cc11 which is an increasing cause of invasive meningococcal disease globally harbors almost exclusively cleavage type 1 protease. Our study also shows an increasing prevalence of meningococcal isolates encoding IgA1P cleavage type 1 compared to cleavage type 2 during the observed decade (2010-2019). Altogether, our work describes a novel mechanism of IgG3 degradation by meningococci and its association to invasive meningococcal disease.
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Affiliation(s)
- Christian Spoerry
- Department of Microbiology, Tumor, and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Jens Karlsson
- Department of Microbiology, Tumor, and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Marie-Stephanie Aschtgen
- Department of Microbiology, Tumor, and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Edmund Loh
- Department of Microbiology, Tumor, and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
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31
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Aksenova AY, Zhuk AS, Lada AG, Zotova IV, Stepchenkova EI, Kostroma II, Gritsaev SV, Pavlov YI. Genome Instability in Multiple Myeloma: Facts and Factors. Cancers (Basel) 2021; 13:5949. [PMID: 34885058 PMCID: PMC8656811 DOI: 10.3390/cancers13235949] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple myeloma (MM) is a malignant neoplasm of terminally differentiated immunoglobulin-producing B lymphocytes called plasma cells. MM is the second most common hematologic malignancy, and it poses a heavy economic and social burden because it remains incurable and confers a profound disability to patients. Despite current progress in MM treatment, the disease invariably recurs, even after the transplantation of autologous hematopoietic stem cells (ASCT). Biological processes leading to a pathological myeloma clone and the mechanisms of further evolution of the disease are far from complete understanding. Genetically, MM is a complex disease that demonstrates a high level of heterogeneity. Myeloma genomes carry numerous genetic changes, including structural genome variations and chromosomal gains and losses, and these changes occur in combinations with point mutations affecting various cellular pathways, including genome maintenance. MM genome instability in its extreme is manifested in mutation kataegis and complex genomic rearrangements: chromothripsis, templated insertions, and chromoplexy. Chemotherapeutic agents used to treat MM add another level of complexity because many of them exacerbate genome instability. Genome abnormalities are driver events and deciphering their mechanisms will help understand the causes of MM and play a pivotal role in developing new therapies.
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Affiliation(s)
- Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anna S. Zhuk
- International Laboratory “Computer Technologies”, ITMO University, 197101 St. Petersburg, Russia;
| | - Artem G. Lada
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA;
| | - Irina V. Zotova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (I.V.Z.); (E.I.S.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Ivan I. Kostroma
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Sergey V. Gritsaev
- Russian Research Institute of Hematology and Transfusiology, 191024 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Departments of Biochemistry and Molecular Biology, Microbiology and Pathology, Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
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32
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Khatri I, Diks AM, van den Akker EB, Oosten LEM, Zwaginga JJ, Reinders MJT, van Dongen JJM, Berkowska MA. Longitudinal Dynamics of Human B-Cell Response at the Single-Cell Level in Response to Tdap Vaccination. Vaccines (Basel) 2021; 9:1352. [PMID: 34835283 PMCID: PMC8617659 DOI: 10.3390/vaccines9111352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/08/2021] [Accepted: 11/13/2021] [Indexed: 01/28/2023] Open
Abstract
To mount an adequate immune response against pathogens, stepwise mutation and selection processes are crucial functions of the adaptive immune system. To better characterize a successful vaccination response, we performed longitudinal (days 0, 5, 7, 10, and 14 after Boostrix vaccination) analysis of the single-cell transcriptome as well as the B-cell receptor (BCR) repertoire (scBCR-rep) in plasma cells of an immunized donor and compared it with baseline B-cell characteristics as well as flow cytometry findings. Based on the flow cytometry knowledge and literature findings, we discriminated individual B-cell subsets in the transcriptomics data and traced over-time maturation of plasmablasts/plasma cells (PB/PCs) and identified the pathways associated with the plasma cell maturation. We observed that the repertoire in PB/PCs differed from the baseline B-cell repertoire e.g., regarding expansion of unique clones in post-vaccination visits, high usage of IGHG1 in expanded clones, increased class-switching events post-vaccination represented by clonotypes spanning multiple IGHC classes and positive selection of CDR3 sequences over time. Importantly, the Variable gene family-based clustering of BCRs represented a similar measure as the gene-based clustering, but certainly improved the clustering of BCRs, as BCRs from duplicated Variable gene families could be clustered together. Finally, we developed a query tool to dissect the immune response to the components of the Boostrix vaccine. Using this tool, we could identify the BCRs related to anti-tetanus and anti-pertussis toxoid BCRs. Collectively, we developed a bioinformatic workflow which allows description of the key features of an ongoing (longitudinal) immune response, such as activation of PB/PCs, Ig class switching, somatic hypermutation, and clonal expansion, all of which are hallmarks of antigen exposure, followed by mutation & selection processes.
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Affiliation(s)
- Indu Khatri
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (I.K.); (A.M.D.); (M.A.B.)
- Leiden Computational Biology Center, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands; (E.B.v.d.A.); (M.J.T.R.)
| | - Annieck M. Diks
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (I.K.); (A.M.D.); (M.A.B.)
| | - Erik B. van den Akker
- Leiden Computational Biology Center, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands; (E.B.v.d.A.); (M.J.T.R.)
- Department of Molecular Epidemiology, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands
| | - Liesbeth E. M. Oosten
- Department of Hematology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (L.E.M.O.); (J.J.Z.)
| | - Jaap Jan Zwaginga
- Department of Hematology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (L.E.M.O.); (J.J.Z.)
| | - Marcel J. T. Reinders
- Leiden Computational Biology Center, Leiden University Medical Center, 2333 ZC Leiden, The Netherlands; (E.B.v.d.A.); (M.J.T.R.)
- Delft Bioinformatics Lab, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Jacques J. M. van Dongen
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (I.K.); (A.M.D.); (M.A.B.)
| | - Magdalena A. Berkowska
- Department of Immunology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands; (I.K.); (A.M.D.); (M.A.B.)
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Ghraichy M, von Niederhäusern V, Kovaltsuk A, Galson JD, Deane CM, Trück J. Different B cell subpopulations show distinct patterns in their IgH repertoire metrics. eLife 2021; 10:73111. [PMID: 34661527 PMCID: PMC8560093 DOI: 10.7554/elife.73111] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/17/2021] [Indexed: 12/11/2022] Open
Abstract
Several human B cell subpopulations are recognised in the peripheral blood, which play distinct roles in the humoral immune response. These cells undergo developmental and maturational changes involving VDJ recombination, somatic hypermutation and class switch recombination, altogether shaping their immunoglobulin heavy chain (IgH) repertoire. Here, we sequenced the IgH repertoire of naïve, marginal zone, switched and plasma cells from 10 healthy adults along with matched unsorted and in silico separated CD19+ bulk B cells. Using advanced bioinformatic analysis and machine learning, we show that sorted B cell subpopulations are characterised by distinct repertoire characteristics on both the individual sequence and the repertoire level. Sorted subpopulations shared similar repertoire characteristics with their corresponding in silico separated subsets. Furthermore, certain IgH repertoire characteristics correlated with the position of the constant region on the IgH locus. Overall, this study provides unprecedented insight over mechanisms of B cell repertoire control in peripherally circulating B cell subpopulations.
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Affiliation(s)
- Marie Ghraichy
- Division of Immunology, University Children's Hospital and Children's Research Center, University of Zurich (UZH), Zurich, Switzerland
| | - Valentin von Niederhäusern
- Division of Immunology, University Children's Hospital and Children's Research Center, University of Zurich (UZH), Zurich, Switzerland
| | | | - Jacob D Galson
- Division of Immunology, University Children's Hospital and Children's Research Center, University of Zurich (UZH), Zurich, Switzerland.,Alchemab Therapeutics Ltd, London, United Kingdom
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Johannes Trück
- Division of Immunology, University Children's Hospital and Children's Research Center, University of Zurich (UZH), Zurich, Switzerland
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Sokolova MV, Hagen M, Bang H, Schett G, Rech J, Steffen U. IgA anti-citrullinated protein antibodies (IgA ACPA) are associated with flares during DMARD tapering in rheumatoid arthritis. Rheumatology (Oxford) 2021; 61:2124-2131. [PMID: 34508547 DOI: 10.1093/rheumatology/keab585] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/09/2021] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVES A substantial proportion of rheumatoid arthritis (RA) patients flare upon withdrawal of disease modifying anti-rheumatic drugs (DMARDs), thus the definition of prognostic markers is crucial. Anti-citrullinated protein antibody (ACPA)-positivity has been identified as a risk factor for flare. However, only the role of IgG is established in this context, while the role of IgA ACPA is poorly defined. We thus aimed to investigate the role of IgA ACPA in flare of RA. METHODS Serum levels of IgA1 and IgA2 ACPA at baseline and after 12 months were measured in 108 patients from the randomized controlled RETRO study. RA patients in stable remission for at least 6 months at study recruitment were assigned to either one of the DMARD tapering arms or to continuation of DMARDs. RESULTS In patients remaining in remission but not in the ones who flared, IgA2 ACPA levels and proportion of IgA2 in ACPA (IgA2%ACPA) significantly declined (median of 17.5%; p< 0.0001). This seemed to be independent of the treatment choice, as there was no difference in IgA2 ACPA dynamics between the study arms. IgA2% ACPA was associated with disease activity (DAS28) at flare (r = 0.36; p= 0.046). IgA and IgG ACPA showed a tendency towards independent contribution to the risk of flare with the highest risk if a patient had both antibody classes. CONCLUSION In this study, IgA ACPA was identified as a risk factor for flare in combination with IgG ACPA. IgA2 ACPA levels were associated with flare severity and declined in patients in stable remission.
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Affiliation(s)
- Maria V Sokolova
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany.,Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-Universität Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Melanie Hagen
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany.,Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-Universität Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | | | - Georg Schett
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany.,Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-Universität Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Juergen Rech
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany.,Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-Universität Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Ulrike Steffen
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-Universität Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany.,Deutsches Zentrum für Immuntherapie, Friedrich-Alexander-Universität Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
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Kardava L, Rachmaninoff N, Lau WW, Buckner CM, Trihemasava K, de Assis FL, Wang W, Zhang X, Wang Y, Chiang CI, Narpala S, Reger R, McCormack GE, Seamon CA, Childs RW, Suffredini AF, Strich JR, Chertow DS, Davey RT, Sneller MC, O’Connell S, Li Y, McDermott A, Chun TW, Fauci AS, Tsang JS, Moir S. Pre-vaccination and early B cell signatures predict antibody response to SARS-CoV-2 mRNA vaccine. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.07.06.21259528. [PMID: 34268520 PMCID: PMC8282109 DOI: 10.1101/2021.07.06.21259528] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
SARS-CoV-2 mRNA vaccines are highly effective, although weak antibody responses are seen in some individuals with correlates of immunity that remain poorly understood. Here we longitudinally dissected antibody, plasmablast, and memory B cell (MBC) responses to the two-dose Moderna mRNA vaccine in SARS-CoV-2-uninfected adults. Robust, coordinated IgA and IgG antibody responses were preceded by bursts of spike-specific plasmablasts after both doses, but earlier and more intensely after dose two. Distinct antigen-specific MBC populations also emerged post-vaccination with varying kinetics. We identified antigen non-specific pre-vaccination MBC and post-vaccination plasmablasts after dose one and their spike-specific counterparts early after dose two that correlated with subsequent antibody levels. These baseline and response signatures can thus provide early indicators of serological efficacy and explain response variability in the population.
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Affiliation(s)
- Lela Kardava
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Nicholas Rachmaninoff
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - William W. Lau
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
| | - Clarisa M. Buckner
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Krittin Trihemasava
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Felipe Lopes de Assis
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Wei Wang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Xiaozhen Zhang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Yimeng Wang
- Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | - Chi-I Chiang
- Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
| | | | - Robert Reger
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | - Genevieve E. McCormack
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Catherine A. Seamon
- Critical Care Medicine Department, National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA
| | - Richard W. Childs
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
- United States Public Health Service Commissioned Corps, Rockville, MD, USA
| | - Anthony F. Suffredini
- Critical Care Medicine Department, National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA
| | - Jeffrey R. Strich
- Critical Care Medicine Department, National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA
- United States Public Health Service Commissioned Corps, Rockville, MD, USA
| | - Daniel S. Chertow
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
- Critical Care Medicine Department, National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA
- United States Public Health Service Commissioned Corps, Rockville, MD, USA
| | - Richard T. Davey
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Michael C. Sneller
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | | | - Yuxing Li
- Institute for Bioscience and Biotechnology Research, Rockville, MD, USA
- Department of Microbiology and Immunology and Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Tae-Wook Chun
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Anthony S. Fauci
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - John S. Tsang
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA
| | - Susan Moir
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
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Zografou C, Vakrakou AG, Stathopoulos P. Short- and Long-Lived Autoantibody-Secreting Cells in Autoimmune Neurological Disorders. Front Immunol 2021; 12:686466. [PMID: 34220839 PMCID: PMC8248361 DOI: 10.3389/fimmu.2021.686466] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/28/2021] [Indexed: 12/24/2022] Open
Abstract
As B cells differentiate into antibody-secreting cells (ASCs), short-lived plasmablasts (SLPBs) are produced by a primary extrafollicular response, followed by the generation of memory B cells and long-lived plasma cells (LLPCs) in germinal centers (GCs). Generation of IgG4 antibodies is T helper type 2 (Th2) and IL-4, -13, and -10-driven and can occur parallel to IgE, in response to chronic stimulation by allergens and helminths. Although IgG4 antibodies are non-crosslinking and have limited ability to mobilize complement and cellular cytotoxicity, when self-tolerance is lost, they can disrupt ligand-receptor binding and cause a wide range of autoimmune disorders including neurological autoimmunity. In myasthenia gravis with predominantly IgG4 autoantibodies against muscle-specific kinase (MuSK), it has been observed that one-time CD20+ B cell depletion with rituximab commonly leads to long-term remission and a marked reduction in autoantibody titer, pointing to a short-lived nature of autoantibody-secreting cells. This is also observed in other predominantly IgG4 autoantibody-mediated neurological disorders, such as chronic inflammatory demyelinating polyneuropathy and autoimmune encephalitis with autoantibodies against the Ranvier paranode and juxtaparanode, respectively, and extends beyond neurological autoimmunity as well. Although IgG1 autoantibody-mediated neurological disorders can also respond well to rituximab induction therapy in combination with an autoantibody titer drop, remission tends to be less long-lasting and cases where titers are refractory tend to occur more often than in IgG4 autoimmunity. Moreover, presence of GC-like structures in the thymus of myasthenic patients with predominantly IgG1 autoantibodies against the acetylcholine receptor and in ovarian teratomas of autoimmune encephalitis patients with predominantly IgG1 autoantibodies against the N‐methyl‐d‐aspartate receptor (NMDAR) confers increased the ability to generate LLPCs. Here, we review available information on the short-and long-lived nature of ASCs in IgG1 and IgG4 autoantibody-mediated neurological disorders and highlight common mechanisms as well as differences, all of which can inform therapeutic strategies and personalized medical approaches.
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Affiliation(s)
- C Zografou
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - A G Vakrakou
- First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - P Stathopoulos
- First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, Greece
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Grönwall C, Liljefors L, Bang H, Hensvold AH, Hansson M, Mathsson-Alm L, Israelsson L, Joshua V, Svärd A, Stålesen R, Titcombe PJ, Steen J, Piccoli L, Sherina N, Clavel C, Svenungsson E, Gunnarsson I, Saevarsdottir S, Kastbom A, Serre G, Alfredsson L, Malmström V, Rönnelid J, Catrina AI, Lundberg K, Klareskog L. A Comprehensive Evaluation of the Relationship Between Different IgG and IgA Anti-Modified Protein Autoantibodies in Rheumatoid Arthritis. Front Immunol 2021; 12:627986. [PMID: 34093522 PMCID: PMC8173192 DOI: 10.3389/fimmu.2021.627986] [Citation(s) in RCA: 24] [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: 11/10/2020] [Accepted: 04/26/2021] [Indexed: 12/25/2022] Open
Abstract
Seropositive rheumatoid arthritis (RA) is characterized by the presence of rheumatoid factor (RF) and anti-citrullinated protein autoantibodies (ACPA) with different fine-specificities. Yet, other serum anti-modified protein autoantibodies (AMPA), e.g. anti-carbamylated (Carb), -acetylated (KAc), and malondialdehyde acetaldehyde (MAA) modified protein antibodies, have been described. In this comprehensive study, we analyze 30 different IgG and IgA AMPA reactivities to Cit, Carb, KAc, and MAA antigens detected by ELISA and autoantigen arrays in N=1985 newly diagnosed RA patients. Association with patient characteristics such as smoking and disease activity were explored. Carb and KAc reactivities by different assays were primarily seen in patients also positive for anti-citrulline reactivity. Modified vimentin (mod-Vim) peptides were used for direct comparison of different AMPA reactivities, revealing that IgA AMPA recognizing mod-Vim was mainly detected in subsets of patients with high IgG anti-Cit-Vim levels and a history of smoking. IgG reactivity to acetylation was mainly detected in a subset of patients with Cit and Carb reactivity. Anti-acetylated histone reactivity was RA-specific and associated with high anti-CCP2 IgG levels, multiple ACPA fine-specificities, and smoking status. This reactivity was also found to be present in CCP2+ RA-risk individuals without arthritis. Our data further demonstrate that IgG autoreactivity to MAA was increased in RA compared to controls with highest levels in CCP2+ RA, but was not RA-specific, and showed low correlation with other AMPA. Anti-MAA was instead associated with disease activity and was not significantly increased in CCP2+ individuals at risk of RA. Notably, RA patients could be subdivided into four different subsets based on their AMPA IgG and IgA reactivity profiles. Our serology results were complemented by screening of monoclonal antibodies derived from single B cells from RA patients for the same antigens as the RA cohort. Certain CCP2+ clones had Carb or Carb+KAc+ multireactivity, while such reactivities were not found in CCP2- clones. We conclude that autoantibodies exhibiting different patterns of ACPA fine-specificities as well as Carb and KAc reactivity are present in RA and may be derived from multireactive B-cell clones. Carb and KAc could be considered reactivities within the "Cit-umbrella" similar to ACPA fine-specificities, while MAA reactivity is distinctly different.
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Affiliation(s)
- Caroline Grönwall
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lisa Liljefors
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | - Aase H. Hensvold
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Center for Rheumatology, Academic Specialist Center, Stockholm Health Region, Stockholm, Sweden
- Rheumatology Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Monika Hansson
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Linda Mathsson-Alm
- Thermo Fisher Scientific, Immuno Diagnostics Division, Uppsala, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Lena Israelsson
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Vijay Joshua
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Svärd
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Center for Clinical Research Dalarna, Uppsala University, Uppsala, Sweden
| | - Ragnhild Stålesen
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Philip J. Titcombe
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- The Center for Immunology and Division of Rheumatic and Autoimmune Diseases, University of Minnesota Medical School, Minneapolis, MN, United States
| | - Johanna Steen
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Luca Piccoli
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Natalia Sherina
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Cyril Clavel
- Unité Différenciation Épithéliale et Autoimmunité Rhumatoïde, INSERM - Université de Toulouse, Toulouse, France
| | - Elisabet Svenungsson
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Rheumatology Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Iva Gunnarsson
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Rheumatology Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Saedis Saevarsdottir
- Department of Medicine Solna, Division of Clinical Epidemiology, Karolinska Institutet, Stockholm, Sweden
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Alf Kastbom
- Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Guy Serre
- Unité Différenciation Épithéliale et Autoimmunité Rhumatoïde, INSERM - Université de Toulouse, Toulouse, France
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm Health Region, Stockholm, Sweden
| | - Vivianne Malmström
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Johan Rönnelid
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Anca I. Catrina
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Center for Rheumatology, Academic Specialist Center, Stockholm Health Region, Stockholm, Sweden
- Rheumatology Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Karin Lundberg
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lars Klareskog
- Department of Medicine Solna, Division of Rheumatology, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Center for Rheumatology, Academic Specialist Center, Stockholm Health Region, Stockholm, Sweden
- Rheumatology Clinic, Karolinska University Hospital, Stockholm, Sweden
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Horns F, Dekker CL, Quake SR. Memory B Cell Activation, Broad Anti-influenza Antibodies, and Bystander Activation Revealed by Single-Cell Transcriptomics. Cell Rep 2021; 30:905-913.e6. [PMID: 31968262 PMCID: PMC7891556 DOI: 10.1016/j.celrep.2019.12.063] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 11/22/2019] [Accepted: 12/17/2019] [Indexed: 01/08/2023] Open
Abstract
Antibody memory protects humans from many diseases. Protective antibody memory responses require activation of transcriptional programs, cell proliferation, and production of antigen-specific antibodies, but how these aspects of the response are coordinated is poorly understood. We profile the molecular and cellular features of the antibody response to influenza vaccination by integrating single-cell transcriptomics, longitudinal antibody repertoire sequencing, and antibody binding measurements. Single-cell transcriptional profiling reveals a program of memory B cell activation characterized by CD11c and T-bet expression associated with clonal expansion and differentiation toward effector function. Vaccination elicits an antibody clone, which rapidly acquired broad high-affinity hemagglutinin binding during affinity maturation. Unexpectedly, many antibody clones elicited by vaccination do not bind vaccine, demonstrating non-specific activation of bystander antibodies by influenza vaccination. These results offer insight into how molecular recognition, transcriptional programs, and clonal proliferation are coordinated in the human B cell repertoire during memory recall. Antibody memory requires coordination of molecular recognition, gene expression programs, and clonal dynamics. Horns et al. study the human antibody memory response using single-cell and repertoire sequencing, revealing a transcriptional program of memory B cell activation, broadly binding anti-influenza antibodies, and widespread bystander activation of non-vaccine-binding antibodies after influenza vaccination.
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Affiliation(s)
- Felix Horns
- Biophysics Graduate Program, Stanford University, Stanford, CA 94305, USA
| | - Cornelia L Dekker
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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King HW, Orban N, Riches JC, Clear AJ, Warnes G, Teichmann SA, James LK. Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics. Sci Immunol 2021; 6:6/56/eabe6291. [PMID: 33579751 DOI: 10.1126/sciimmunol.abe6291] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/14/2021] [Indexed: 12/21/2022]
Abstract
Protective humoral memory forms in secondary lymphoid organs where B cells undergo affinity maturation and differentiation into memory or plasma cells. Here, we provide a comprehensive roadmap of human B cell maturation with single-cell transcriptomics matched with bulk and single-cell antibody repertoires to define gene expression, antibody repertoires, and clonal sharing of B cell states at single-cell resolution, including memory B cell heterogeneity that reflects diverse functional and signaling states. We reconstruct gene expression dynamics during B cell activation to reveal a pre-germinal center state primed to undergo class switch recombination and dissect how antibody class-dependent gene expression in germinal center and memory B cells is linked with a distinct transcriptional wiring with potential to influence their fate and function. Our analyses reveal the dynamic cellular states that shape human B cell-mediated immunity and highlight how antibody isotype may play a role during their antibody-based selection.
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Affiliation(s)
- Hamish W King
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London E1 2AT, UK. .,Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Nara Orban
- Barts Health Ear, Nose and Throat Service, Royal London Hospital, London E1 1BB, UK
| | - John C Riches
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK.,Francis Crick Institute, London NW1 1AT, UK
| | - Andrew J Clear
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Gary Warnes
- Flow Cytometry Core Facility, Blizard Institute, Queen Mary University of London, London E1 2AT, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 0EH, UK
| | - Louisa K James
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London E1 2AT, UK.
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40
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Izraelson M, Metsger M, Davydov AN, Shagina IA, Dronina MA, Obraztsova AS, Miskevich DA, Mamedov IZ, Volchkova LN, Nakonechnaya TO, Shugay M, Bolotin DA, Staroverov DB, Sharonov GV, Kondratyuk EY, Zagaynova EV, Lukyanov S, Shams I, Britanova OV, Chudakov DM. Distinct organization of adaptive immunity in the long-lived rodent Spalax galili. NATURE AGING 2021; 1:179-189. [PMID: 37118630 DOI: 10.1038/s43587-021-00029-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/08/2021] [Indexed: 04/30/2023]
Abstract
A balanced immune response is a cornerstone of healthy aging. Here, we uncover distinctive features of the long-lived blind mole-rat (Spalax spp.) adaptive immune system, relative to humans and mice. The T-cell repertoire remains diverse throughout the Spalax lifespan, suggesting a paucity of large long-lived clones of effector-memory T cells. Expression of master transcription factors of T-cell differentiation, as well as checkpoint and cytotoxicity genes, remains low as Spalax ages. The thymus shrinks as in mice and humans, while interleukin-7 and interleukin-7 receptor expression remains high, potentially reflecting the sustained homeostasis of naive T cells. With aging, immunoglobulin hypermutation level does not increase and the immunoglobulin-M repertoire remains diverse, suggesting shorter B-cell memory and sustained homeostasis of innate-like B cells. The Spalax adaptive immune system thus appears biased towards sustained functional and receptor diversity over specialized, long-lived effector-memory clones-a unique organizational strategy that potentially underlies this animal's extraordinary longevity and healthy aging.
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Affiliation(s)
- M Izraelson
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - M Metsger
- Central European Institute of Technology, Brno, Czech Republic
| | - A N Davydov
- Central European Institute of Technology, Brno, Czech Republic
| | - I A Shagina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - M A Dronina
- Institute of Evolution & Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - A S Obraztsova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - D A Miskevich
- Institute of Evolution & Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - I Z Mamedov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Central European Institute of Technology, Brno, Czech Republic
| | - L N Volchkova
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - T O Nakonechnaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - M Shugay
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - D A Bolotin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - D B Staroverov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - G V Sharonov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - E Y Kondratyuk
- Institute of Systematics and Ecology of Animals SB RAS, Novosibirsk, Russia
| | - E V Zagaynova
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - S Lukyanov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - I Shams
- Institute of Evolution & Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - O V Britanova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
| | - D M Chudakov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
- Privolzhsky Research Medical University, Nizhny Novgorod, Russia.
- Pirogov Russian National Research Medical University, Moscow, Russia.
- Central European Institute of Technology, Brno, Czech Republic.
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41
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Lindeman I, Zhou C, Eggesbø LM, Miao Z, Polak J, Lundin KE, Jahnsen J, Qiao SW, Iversen R, Sollid LM. Longevity, clonal relationship, and transcriptional program of celiac disease-specific plasma cells. J Exp Med 2021; 218:e20200852. [PMID: 33095260 PMCID: PMC7590513 DOI: 10.1084/jem.20200852] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/07/2020] [Accepted: 09/30/2020] [Indexed: 12/11/2022] Open
Abstract
Disease-specific plasma cells (PCs) reactive with transglutaminase 2 (TG2) or deamidated gluten peptides (DGPs) are abundant in celiac disease (CeD) gut lesions. Their contribution toward CeD pathogenesis is unclear. We assessed expression of markers associated with PC longevity in 15 untreated and 26 treated CeD patients in addition to 13 non-CeD controls and performed RNA sequencing with clonal inference and transcriptomic analysis of 3,251 single PCs. We observed antigen-dependent V-gene selection and stereotypic antibodies. Generation of recombinant DGP-specific antibodies revealed a key role of a heavy chain residue that displays polymorphism, suggesting that immunoglobulin gene polymorphisms may influence CeD-specific antibody responses. We identified transcriptional differences between CeD-specific and non-disease-specific PCs and between short-lived and long-lived PCs. The short-lived CD19+CD45+ phenotype dominated in untreated and short-term-treated CeD, in particular among disease-specific PCs but also in the general PC population. Thus, the disease lesion of untreated CeD is characterized by massive accumulation of short-lived PCs that are not only directed against disease-specific antigens.
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Affiliation(s)
- Ida Lindeman
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Chunyan Zhou
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, China
| | - Linn M. Eggesbø
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Zhichao Miao
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Translational Research Institute of Brain and Brain-Like Intelligence and Department of Anesthesiology, Shanghai Fourth People's Hospital (affiliated with Tongji University School of Medicine), Shanghai, China
| | - Justyna Polak
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Knut E.A. Lundin
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
- Department of Gastroenterology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Jørgen Jahnsen
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Shuo-Wang Qiao
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Rasmus Iversen
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Ludvig M. Sollid
- KG Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
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42
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Kim SI, Noh J, Kim S, Choi Y, Yoo DK, Lee Y, Lee H, Jung J, Kang CK, Song KH, Choe PG, Kim HB, Kim ES, Kim NJ, Seong MW, Park WB, Oh MD, Kwon S, Chung J. Stereotypic neutralizing V H antibodies against SARS-CoV-2 spike protein receptor binding domain in patients with COVID-19 and healthy individuals. Sci Transl Med 2021; 13:eabd6990. [PMID: 33397677 PMCID: PMC7875332 DOI: 10.1126/scitranslmed.abd6990] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/07/2020] [Accepted: 12/28/2020] [Indexed: 12/19/2022]
Abstract
Stereotypic antibody clonotypes exist in healthy individuals and may provide protective immunity against viral infections by neutralization. We observed that 13 of 17 patients with COVID-19 had stereotypic variable heavy chain (VH) antibody clonotypes directed against the receptor binding domain (RBD) of SARS-CoV-2 spike protein. These antibody clonotypes were composed of immunoglobulin heavy variable 3-53 (IGHV3-53) or IGHV3-66 and immunoglobulin heavy joining 6 (IGHJ6) genes. These clonotypes included IgM, IgG3, IgG1, IgA1, IgG2, and IgA2 subtypes and had minimal somatic mutations, which suggested swift class switching after SARS-CoV-2 infection. The different IGHV chains were paired with diverse light chains resulting in binding to the RBD of SARS-CoV-2 spike protein. Human antibodies specific for the RBD can neutralize SARS-CoV-2 by inhibiting entry into host cells. We observed that one of these stereotypic neutralizing antibodies could inhibit viral replication in vitro using a clinical isolate of SARS-CoV-2. We also found that these VH clonotypes existed in 6 of 10 healthy individuals, with IgM isotypes predominating. These findings suggest that stereotypic clonotypes can develop de novo from naïve B cells and not from memory B cells established from prior exposure to similar viruses. The expeditious and stereotypic expansion of these clonotypes may have occurred in patients infected with SARS-CoV-2 because they were already present.
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Affiliation(s)
- Sang Il Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Ischemic/Hypoxic Disease Institute, Seoul National University Medical Research Center, Seoul 03080, Republic of Korea
| | - Jinsung Noh
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Sujeong Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Younggeun Choi
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Duck Kyun Yoo
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Ischemic/Hypoxic Disease Institute, Seoul National University Medical Research Center, Seoul 03080, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Yonghee Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyunho Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Jongtak Jung
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Chang Kyung Kang
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Kyoung-Ho Song
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Pyoeng Gyun Choe
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Hong Bin Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Eu Suk Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Nam-Joong Kim
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Wan Beom Park
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Myoung-Don Oh
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, Republic of Korea.
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
- BK21+ Creative Research Engineer Development for IT, Seoul National University, Seoul 08826, Republic of Korea
- Biomedical Research Institute, Seoul National University Hospital, Seoul 03080, Republic of Korea
- Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul 08826, Republic of Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea.
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
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43
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Chu TH, Patz EF, Ackerman ME. Coming together at the hinges: Therapeutic prospects of IgG3. MAbs 2021; 13:1882028. [PMID: 33602056 PMCID: PMC7899677 DOI: 10.1080/19420862.2021.1882028] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/08/2021] [Accepted: 01/22/2021] [Indexed: 01/22/2023] Open
Abstract
The human IgG3 subclass is conspicuously absent among the formats for approved monoclonal antibody therapies and Fc fusion protein biologics. Concern about the potential for rapid degradation, reduced plasma half-life, and increased immunogenicity due to marked variation in allotypes has apparently outweighed the potential advantages of IgG3, which include high affinity for activating Fcγ receptors, effective complement fixation, and a long hinge that appears better suited for low abundance targets. This review aims to highlight distinguishing features of IgG3 and to explore its functional role in the immune response. We present studies of natural immunity and recombinant antibody therapies that elucidate key contributions of IgG3 and discuss historical roadblocks that no longer remain clearly relevant. Collectively, this body of evidence motivates thoughtful reconsideration of the clinical advancement of this distinctive antibody subclass for treatment of human diseases. Abbreviations: ADCC - Antibody-Dependent Cell-mediated CytotoxicityADE - Antibody-dependent enhancementAID - Activation-Induced Cytidine DeaminaseCH - Constant HeavyCHF - Complement factor HCSR - Class Switch RecombinationEM - Electron MicroscopyFab - Fragment, antigen bindingFc - Fragment, crystallizableFcRn - Neonatal Fc ReceptorFcγR - Fc gamma ReceptorHIV - Human Immunodeficiency VirusIg - ImmunoglobulinIgH - Immunoglobulin Heavy chain geneNHP - Non-Human Primate.
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Affiliation(s)
- Thach H. Chu
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
| | - Edward F. Patz
- Department of Radiology and Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC, USA
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44
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Galson JD, Schaetzle S, Bashford-Rogers RJM, Raybould MIJ, Kovaltsuk A, Kilpatrick GJ, Minter R, Finch DK, Dias J, James LK, Thomas G, Lee WYJ, Betley J, Cavlan O, Leech A, Deane CM, Seoane J, Caldas C, Pennington DJ, Pfeffer P, Osbourn J. Deep Sequencing of B Cell Receptor Repertoires From COVID-19 Patients Reveals Strong Convergent Immune Signatures. Front Immunol 2020; 11:605170. [PMID: 33384691 PMCID: PMC7769841 DOI: 10.3389/fimmu.2020.605170] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/16/2020] [Indexed: 12/14/2022] Open
Abstract
Deep sequencing of B cell receptor (BCR) heavy chains from a cohort of 31 COVID-19 patients from the UK reveals a stereotypical naive immune response to SARS-CoV-2 which is consistent across patients. Clonal expansion of the B cell population is also observed and may be the result of memory bystander effects. There was a strong convergent sequence signature across patients, and we identified 1,254 clonotypes convergent between at least four of the COVID-19 patients, but not present in healthy controls or individuals following seasonal influenza vaccination. A subset of the convergent clonotypes were homologous to known SARS and SARS-CoV-2 spike protein neutralizing antibodies. Convergence was also demonstrated across wide geographies by comparison of data sets between patients from UK, USA, and China, further validating the disease association and consistency of the stereotypical immune response even at the sequence level. These convergent clonotypes provide a resource to identify potential therapeutic and prophylactic antibodies and demonstrate the potential of BCR profiling as a tool to help understand patient responses.
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Affiliation(s)
| | | | | | - Matthew I. J. Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Aleksandr Kovaltsuk
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | | | - Ralph Minter
- Alchemab Therapeutics Ltd, London, United Kingdom
| | | | - Jorge Dias
- Alchemab Therapeutics Ltd, London, United Kingdom
| | - Louisa K. James
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Gavin Thomas
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Wing-Yiu Jason Lee
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Jason Betley
- Illumina, Inc., Illumina Centre, Cambridge, United Kingdom
| | | | - Alex Leech
- Alchemab Therapeutics Ltd, London, United Kingdom
| | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Joan Seoane
- Translational Research Program, Vall d’Hebron Institute of Oncology, Barcelona, Spain
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom
| | - Daniel J. Pennington
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Paul Pfeffer
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Jane Osbourn
- Alchemab Therapeutics Ltd, London, United Kingdom
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45
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Staats LAN, Pfeiffer H, Knopf J, Lindemann A, Fürst J, Kremer AE, Hackstein H, Neurath MF, Muñoz LE, Achenbach S, Leppkes M, Herrmann M, Schett G, Steffen U. IgA2 Antibodies against SARS-CoV-2 Correlate with NET Formation and Fatal Outcome in Severely Diseased COVID-19 Patients. Cells 2020; 9:E2676. [PMID: 33322797 PMCID: PMC7764693 DOI: 10.3390/cells9122676] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/01/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023] Open
Abstract
Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) leads to an adaptive immune response in the host and the formation of anti-SARS-CoV-2 specific antibodies. While IgG responses against SARS-CoV-2 have been characterized quite well, less is known about IgA. IgA2 activates immune cells and induces inflammation and neutrophil extracellular trap (NET) formation which may contribute to organ injury and fatal outcome in SARS-CoV-2-infected patients. SARS-CoV-2 spike protein specific antibody levels were measured in plasma samples of 15 noninfected controls and 82 SARS-CoV-2-infected patients with no or mild symptoms, moderate symptoms (hospitalization) or severe disease (intensive care unit, ICU). Antibody levels were compared to levels of C-reactive protein (CRP) and circulating extracellular DNA (ecDNA) as markers for general inflammation and NET formation, respectively. While levels of SARS-CoV-2-specific IgG were similar in all patient groups, IgA2 antibodies were restricted to severe disease and showed the strongest discrimination between nonfatal and fatal outcome in patients with severe SARS-CoV-2 infection. While anti-SARS-CoV-2 IgG and IgA2 levels correlated with CRP levels in severely diseased patients, only anti-SARS-CoV-2 IgA2 correlated with ecDNA. These data suggest that the formation of anti-SARS-CoV-2 IgA2 during SARS-CoV-2 infection is a marker for more severe disease related to NET formation and poor outcome.
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Affiliation(s)
- Léonie A. N. Staats
- Department of Internal Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (L.A.N.S.); (A.L.); (J.F.); (A.E.K.); (M.F.N.); (M.L.)
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany; (J.K.); (L.E.M.); (M.H.); (G.S.)
| | - Hella Pfeiffer
- Department of Transfusion Medicine and Haemostaseology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (H.P.); (H.H.); (S.A.)
| | - Jasmin Knopf
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany; (J.K.); (L.E.M.); (M.H.); (G.S.)
- Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Aylin Lindemann
- Department of Internal Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (L.A.N.S.); (A.L.); (J.F.); (A.E.K.); (M.F.N.); (M.L.)
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany; (J.K.); (L.E.M.); (M.H.); (G.S.)
| | - Julia Fürst
- Department of Internal Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (L.A.N.S.); (A.L.); (J.F.); (A.E.K.); (M.F.N.); (M.L.)
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany; (J.K.); (L.E.M.); (M.H.); (G.S.)
| | - Andreas E. Kremer
- Department of Internal Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (L.A.N.S.); (A.L.); (J.F.); (A.E.K.); (M.F.N.); (M.L.)
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany; (J.K.); (L.E.M.); (M.H.); (G.S.)
| | - Holger Hackstein
- Department of Transfusion Medicine and Haemostaseology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (H.P.); (H.H.); (S.A.)
| | - Markus F. Neurath
- Department of Internal Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (L.A.N.S.); (A.L.); (J.F.); (A.E.K.); (M.F.N.); (M.L.)
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany; (J.K.); (L.E.M.); (M.H.); (G.S.)
| | - Luis E. Muñoz
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany; (J.K.); (L.E.M.); (M.H.); (G.S.)
- Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Susanne Achenbach
- Department of Transfusion Medicine and Haemostaseology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (H.P.); (H.H.); (S.A.)
| | - Moritz Leppkes
- Department of Internal Medicine 1, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany; (L.A.N.S.); (A.L.); (J.F.); (A.E.K.); (M.F.N.); (M.L.)
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany; (J.K.); (L.E.M.); (M.H.); (G.S.)
| | - Martin Herrmann
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany; (J.K.); (L.E.M.); (M.H.); (G.S.)
- Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Georg Schett
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany; (J.K.); (L.E.M.); (M.H.); (G.S.)
- Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
| | - Ulrike Steffen
- Deutsches Zentrum Immuntherapie (DZI), 91054 Erlangen, Germany; (J.K.); (L.E.M.); (M.H.); (G.S.)
- Department of Internal Medicine 3, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91054 Erlangen, Germany
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46
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Scheepers C, Bekker V, Anthony C, Richardson SI, Oosthuysen B, Moyo T, Kgagudi P, Kitchin D, Nonyane M, York T, Mielke D, Mabvakure BM, Sheng Z, Lambson BE, Ismail A, Garrett NJ, Abdool Karim SS, Shapiro L, Williamson C, Morris L, Moore PL. Antibody Isotype Switching as a Mechanism to Counter HIV Neutralization Escape. Cell Rep 2020; 33:108430. [PMID: 33238131 PMCID: PMC7723817 DOI: 10.1016/j.celrep.2020.108430] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/18/2020] [Accepted: 11/02/2020] [Indexed: 02/04/2023] Open
Abstract
Neutralizing antibodies (nAbs) to highly variable viral pathogens show remarkable diversification during infection, resulting in an “arms race” between virus and host. Studies of nAb lineages have shown how somatic hypermutation (SHM) in immunoglobulin (Ig)-variable regions enables maturing antibodies to neutralize emerging viral escape variants. However, the Ig-constant region (which determines isotype) can also influence epitope recognition. Here, we use longitudinal deep sequencing of an HIV-directed nAb lineage, CAP88-CH06, and identify several co-circulating isotypes (IgG3, IgG1, IgA1, IgG2, and IgA2), some of which share identical variable regions. First, we show that IgG3 and IgA1 isotypes are better able to neutralize longitudinal autologous viruses and epitope mutants than can IgG1. Second, detrimental class-switch recombination (CSR) events that resulted in reduced neutralization can be rescued by further CSR, which we term “switch redemption.” Thus, CSR represents an additional immunological mechanism to counter viral escape from HIV-specific antibody responses. Scheepers et al. show within an HIV-specific antibody lineage that isotypes confer variable ability to neutralize emerging viral escape variants. This suggests that class switching, in addition to somatic hypermutation of immunoglobulin-variable regions, contributes to antibody maturation during infection.
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Affiliation(s)
- Cathrine Scheepers
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Valerie Bekker
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Colin Anthony
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7701, South Africa
| | - Simone I Richardson
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Brent Oosthuysen
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Thandeka Moyo
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Prudence Kgagudi
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Dale Kitchin
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Molati Nonyane
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Talita York
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7701, South Africa
| | - Dieter Mielke
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7701, South Africa
| | - Batsirai M Mabvakure
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Zizhang Sheng
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Brain Mind Behaviour Institute, Columbia University, New York, NY 10027, USA
| | - Bronwen E Lambson
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - Arshad Ismail
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Nigel J Garrett
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), KwaZulu-Natal 4013, South Africa
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), KwaZulu-Natal 4013, South Africa; Department of Epidemiology, Columbia University, New York, NY 10032, USA
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Brain Mind Behaviour Institute, Columbia University, New York, NY 10027, USA
| | - Carolyn Williamson
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7701, South Africa
| | - Lynn Morris
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2050, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), KwaZulu-Natal 4013, South Africa.
| | - Penny L Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2131, South Africa; Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg 2050, South Africa; Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7701, South Africa; Centre for the AIDS Programme of Research in South Africa (CAPRISA), KwaZulu-Natal 4013, South Africa.
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47
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Suprun M, Getts R, Grishina G, Tsuang A, Suárez‐Fariñas M, Sampson HA. Ovomucoid epitope-specific repertoire of IgE, IgG 4 , IgG 1 , IgA 1 , and IgD antibodies in egg-allergic children. Allergy 2020; 75:2633-2643. [PMID: 32391917 DOI: 10.1111/all.14357] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/24/2020] [Accepted: 04/08/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND Egg-white ovomucoid, that is, Gal d 1, is associated with IgE-mediated allergic reactions in most egg-allergic children. Epitope-specific IgE levels have been correlated with the severity of egg allergy, while emerging evidence suggests that other antibody isotypes (IgG1 , IgG4 , IgA, and IgD) may have a protective function; yet, their epitope-specific repertoires and associations with atopic comorbidities have not been studied. METHODS Bead-based epitope assay (BBEA) was used to quantitate the levels of epitope-specific (es)IgA, esIgE, esIgD, esIgG1 , and esIgG4 antibodies directed at 58 (15-mer) overlapping peptides, covering the entire sequence of ovomucoid, in plasma of 38 egg-allergic and 6 atopic children. Intraclass correlation (ICC) and coefficient of variation (CV) were used for the reliability assessment. The relationships across esIgs were evaluated using network analysis; linear and logistic regressions were used to compare groups based on egg allergy status and comorbidities. RESULTS BBEA had high reliability (ICC >0.75) and low variability (CV <20%) and could detect known IgE-binding epitopes. Egg-allergic children had lower esIgA1 (P = .010) and esIgG1 (P = .016) and higher esIgE (P < .001) and esIgD (P = .015) levels compared to the atopic controls. Interestingly, within the allergic group, children with higher esIgD had decreased odds of anaphylactic reactions (OR =0.48, P = .038). Network analysis identified most associations between esIgE with either esIgG4 or esIgD; indicating that IgE-secreting plasma cells could originate from either sequential isotype switch from antigen-experienced intermediate isotypes or directly from the IgD+ B cells. CONCLUSIONS Collectively, these data point toward a contribution of epitope-specific antibody repertoires to the pathogenesis of egg allergy.
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Affiliation(s)
- Maria Suprun
- Icahn School of Medicine at Mount Sinai New Yok NY USA
| | | | | | - Angela Tsuang
- Icahn School of Medicine at Mount Sinai New Yok NY USA
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48
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Bianchini R, Karagiannis SN, Jordakieva G, Jensen-Jarolim E. The Role of IgG4 in the Fine Tuning of Tolerance in IgE-Mediated Allergy and Cancer. Int J Mol Sci 2020; 21:ijms21145017. [PMID: 32708690 PMCID: PMC7404042 DOI: 10.3390/ijms21145017] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/09/2020] [Accepted: 07/10/2020] [Indexed: 12/24/2022] Open
Abstract
Among the four immunoglobulin G (IgG) subclasses, IgG4 is the least represented in serum of a healthy human and it is considered an “odd” antibody. The IgG4 antibody has unique structural features that affect its biological function. These include the ability to undergo antigen-binding fragment (Fab)-arm exchange, to create fragment crystallizable (Fc) – Fc binding with other IgG4 and other IgG subclass antibodies, have a unique affinity profile for Fc gamma receptors (FcγRs) and no binding to complement component C1q. Altogether, these characteristics support anti-inflammatory roles of IgG4 leading to immune tolerance. Under conditions of chronic antigenic stimulation and Th2-type inflammation, both tissue and serum IgG4 levels are increased. This review seeks to highlight how in allergen immunotherapy IgG4 can confer a protective role as a “blocking” antibody and safeguard from subsequent allergen exposure, while IgG4 can confer immunomodulatory functions to support malignancy. While Th2 conditions drive polarization of macrophages to the M2a subtype, chronic antigen stimulation drives B cell class switching to IgG4 to further support phenotypical macrophage changes towards an M2b-like state. M2b-like macrophages can secrete chemokine (C-C motif) ligand 1 (CCL1) and interleukin-10 (IL-10) to support regulatory cell recruitment and to further shape a tolerogenic microenvironment. Thereby, IgG4 have a Janus-faced role, favorable in allergy but detrimental in cancer.
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Affiliation(s)
- Rodolfo Bianchini
- The Interuniversity Messerli Research Institute of the University of Veterinary Medicine, Medical University of Vienna and University of Vienna, Veterinaerplatz 1, 1210 Vienna, Austria;
- Institute Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Division of Comparative Immunology and Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
| | - Sophia N. Karagiannis
- St. John’s Institute of Dermatology, School of Basic & Medical Biosciences, King’s College London, 9th Floor, Tower Wing, Guy’s Hospital, London SE1 9RT, UK;
- Breast Cancer Now Research Unit, School of Cancer & Pharmaceutical Sciences, King’s College London, Guy’s Cancer Centre, London SE1 9RT, UK
| | - Galateja Jordakieva
- Department of Physical Medicine, Rehabilitation and Occupational Medicine, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria;
| | - Erika Jensen-Jarolim
- The Interuniversity Messerli Research Institute of the University of Veterinary Medicine, Medical University of Vienna and University of Vienna, Veterinaerplatz 1, 1210 Vienna, Austria;
- Institute Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Division of Comparative Immunology and Oncology, Medical University of Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
- Correspondence:
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49
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Chen K, Magri G, Grasset EK, Cerutti A. Rethinking mucosal antibody responses: IgM, IgG and IgD join IgA. Nat Rev Immunol 2020; 20:427-441. [PMID: 32015473 PMCID: PMC10262260 DOI: 10.1038/s41577-019-0261-1] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2019] [Indexed: 02/08/2023]
Abstract
Humoral immune responses at mucosal surfaces have historically focused on IgA. Growing evidence highlights the complexity of IgA-inducing pathways and the functional impact of IgA on mucosal commensal bacteria. In the gut, IgA contributes to the establishment of a mutualistic host-microbiota relationship that is required to maintain homeostasis and prevent disease. This Review discusses how mucosal IgA responses occur in an increasingly complex humoral defence network that also encompasses IgM, IgG and IgD. Aside from integrating the protective functions of IgA, these hitherto neglected mucosal antibodies may strengthen the communication between mucosal and systemic immune compartments.
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Affiliation(s)
- Kang Chen
- Department of Obstetrics and Gynecology and Barbara Ann Karmanos Cancer Institute, Wayne State University, Detroit, MI, USA
| | - Giuliana Magri
- Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona Biomedical Research Park, Barcelona, Spain
| | - Emilie K Grasset
- The Immunology Institute, Department of Medicine, Mount Sinai School of Medicine, New York, NY, USA
- Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Andrea Cerutti
- Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), Barcelona Biomedical Research Park, Barcelona, Spain.
- The Immunology Institute, Department of Medicine, Mount Sinai School of Medicine, New York, NY, USA.
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona Biomedical Research Park, Barcelona, Spain.
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50
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Jia M, Liberatore RA, Guo Y, Chan KW, Pan R, Lu H, Waltari E, Mittler E, Chandran K, Finzi A, Kaufmann DE, Seaman MS, Ho DD, Shapiro L, Sheng Z, Kong XP, Bieniasz PD, Wu X. VSV-Displayed HIV-1 Envelope Identifies Broadly Neutralizing Antibodies Class-Switched to IgG and IgA. Cell Host Microbe 2020; 27:963-975.e5. [PMID: 32315598 PMCID: PMC7294236 DOI: 10.1016/j.chom.2020.03.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/27/2020] [Accepted: 03/26/2020] [Indexed: 12/25/2022]
Abstract
The HIV-1 envelope (Env) undergoes conformational changes during infection. Broadly neutralizing antibodies (bNAbs) are typically isolated by using soluble Env trimers, which do not capture all Env states. To address these limitations, we devised a vesicular stomatitis virus (VSV)-based probe to display membrane-embedded Env trimers and isolated five bNAbs from two chronically infected donors, M4008 and M1214. Donor B cell receptor (BCR) repertoires identified two bNAb lineages, M4008_N1 and M1214_N1, that class-switched to immunoglobulin G (IgG) and IgA. Variants of these bNAbs reconstituted as IgA demonstrated broadly neutralizing activity, and the IgA fraction of M1214 plasma conferred neutralization. M4008_N1 epitope mapping revealed a glycan-independent V3 epitope conferring tier 2 virus neutralization. A 4.86-Å-resolution cryogenic electron microscopy (cryo-EM) structure of M1214_N1 complexed with CH505 SOSIP revealed another elongated epitope, the V2V5 corridor, extending from V2 to V5. Overall, the VSVENV probe identified bNAb lineages with neutralizing IgG and IgA members targeting distinct sites of HIV-1 Env vulnerability. VSV-displayed HIV-1 envelope trimers identified five HIV-1 bNAbs BCR repertoires identified two bNAb lineages class-switched to both IgG and IgA The V3 crown-targeting bNAb M4008_N1 conferred tier 2 virus neutralization Cryo-EM structure of bNAb M1214_N1 with CH505 SOSIP defined a V2V5 corridor epitope
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Affiliation(s)
- Manxue Jia
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY 10016, USA
| | - Rachel A Liberatore
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10016, USA
| | - Yicheng Guo
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Kun-Wei Chan
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Ruimin Pan
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Hong Lu
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY 10016, USA
| | - Eric Waltari
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY 10016, USA
| | - Eva Mittler
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Kartik Chandran
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Andrés Finzi
- Centre de Recherche du CHUM and Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM and Université de Montréal, Montreal, QC H2X 0A9, Canada; Center for HIV-1/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, CA 92037, USA
| | - Michael S Seaman
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY 10016, USA
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zizhang Sheng
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Xiang-Peng Kong
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, New York, NY 10016, USA
| | - Xueling Wu
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY 10016, USA.
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