1
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Morgan DM, Zhang YJ, Kim JH, Murillo M, Singh S, Loschko J, Surendran N, Sekulovic O, Feng E, Shi S, Irvine DJ, Patil SU, Kanevsky I, Chorro L, Christopher Love J. Full-length single-cell BCR sequencing paired with RNA sequencing reveals convergent responses to pneumococcal vaccination. Commun Biol 2024; 7:1208. [PMID: 39341987 PMCID: PMC11438910 DOI: 10.1038/s42003-024-06823-0] [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: 06/13/2023] [Accepted: 09/02/2024] [Indexed: 10/01/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) can resolve transcriptional features from individual cells, but scRNA-seq techniques capable of resolving the variable regions of B cell receptors (BCRs) remain limited, especially from widely-used 3'-barcoded libraries. Here, we report a method that can recover paired, full-length variable region sequences of BCRs from 3'-barcoded scRNA-seq libraries. We first verify this method (B3E-seq) can produce accurate, full-length BCR sequences. We then apply this method to profile B cell responses elicited against the capsular polysaccharide of Streptococcus pneumoniae serotype 3 (ST3) by glycoconjugate vaccines in five infant rhesus macaques. We identify BCR features associated with specificity for the ST3 antigen which are present in multiple vaccinated monkeys, indicating a convergent response to vaccination. These results demonstrate the utility of our method to resolve key features of the B cell repertoire and profile antigen-specific responses elicited by vaccination.
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Affiliation(s)
- Duncan M Morgan
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemical Engineering, MIT, Cambridge, MA, USA
| | - Yiming J Zhang
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Jin-Hwan Kim
- Vaccine Research and Development Pfizer Inc. Pearl River, New York, NY, USA
| | - MaryAnn Murillo
- Vaccine Research and Development Pfizer Inc. Pearl River, New York, NY, USA
| | - Suddham Singh
- Vaccine Research and Development Pfizer Inc. Pearl River, New York, NY, USA
| | - Jakob Loschko
- Vaccine Research and Development Pfizer Inc. Pearl River, New York, NY, USA
- Deerfield Management, New York, NY, USA
| | - Naveen Surendran
- Vaccine Research and Development Pfizer Inc. Pearl River, New York, NY, USA
| | - Ognjen Sekulovic
- Vaccine Research and Development Pfizer Inc. Pearl River, New York, NY, USA
| | - Ellie Feng
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Shuting Shi
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Chemical Engineering, MIT, Cambridge, MA, USA
| | - Darrell J Irvine
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Materials Science and Engineering, MIT, Cambridge, MA, USA
| | - Sarita U Patil
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Isis Kanevsky
- Vaccine Research and Development Pfizer Inc. Pearl River, New York, NY, USA
| | - Laurent Chorro
- Vaccine Research and Development Pfizer Inc. Pearl River, New York, NY, USA
- Regeneron, Tarrytown, NY, USA
| | - J Christopher Love
- Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, USA.
- Department of Chemical Engineering, MIT, Cambridge, MA, USA.
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2
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Xu Z, Ismanto HS, Saputri DS, Haruna S, Sun G, Wilamowski J, Teraguchi S, Sengupta A, Li S, Standley DM. Robust detection of infectious disease, autoimmunity, and cancer from the paratope networks of adaptive immune receptors. Brief Bioinform 2024; 25:bbae431. [PMID: 39226888 PMCID: PMC11370640 DOI: 10.1093/bib/bbae431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/19/2024] [Accepted: 08/21/2024] [Indexed: 09/05/2024] Open
Abstract
Liquid biopsies based on peripheral blood offer a minimally invasive alternative to solid tissue biopsies for the detection of diseases, primarily cancers. However, such tests currently consider only the serum component of blood, overlooking a potentially rich source of biomarkers: adaptive immune receptors (AIRs) expressed on circulating B and T cells. Machine learning-based classifiers trained on AIRs have been reported to accurately identify not only cancers but also autoimmune and infectious diseases as well. However, when using the conventional "clonotype cluster" representation of AIRs, individuals within a disease or healthy cohort exhibit vastly different features, limiting the generalizability of these classifiers. This study aimed to address the challenge of classifying specific diseases from circulating B or T cells by developing a novel representation of AIRs based on similarity networks constructed from their antigen-binding regions (paratopes). Features based on this novel representation, paratope cluster occupancies (PCOs), significantly improved disease classification performance for infectious disease, autoimmune disease, and cancer. Under identical methodological conditions, classifiers trained on PCOs achieved a mean AUC of 0.893 when applied to new individuals, outperforming clonotype cluster-based classifiers (AUC 0.714) and the best-performing published classifier (AUC 0.777). Surprisingly, for cancer patients, we observed that "healthy-biased" AIRs were predicted to target known cancer-associated antigens at dramatically higher rates than healthy AIRs as a whole (Z scores >75), suggesting an overlooked reservoir of cancer-targeting immune cells that could be identified by PCOs.
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Affiliation(s)
- Zichang Xu
- Department of Systems Immunology, Immunology Frontier Research Institute (IFReC), Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Hendra S Ismanto
- Department of Systems Immunology, Immunology Frontier Research Institute (IFReC), Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Department of Genome Informatics, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Dianita S Saputri
- Department of Systems Immunology, Immunology Frontier Research Institute (IFReC), Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Department of Genome Informatics, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Soichiro Haruna
- Department of Genome Informatics, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Guanqun Sun
- School of information Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Jan Wilamowski
- Department of Genome Informatics, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Shunsuke Teraguchi
- Department of Genome Informatics, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Faculty of Data Science, Shiga University 1-1-1 Banba, Hikone, Shiga 522-8522, Japan
| | - Ayan Sengupta
- Cogent Labs, 3-2-1 Roppongi, Minato-ku, Tokyo 106-6122, Japan
| | - Songling Li
- Department of Systems Immunology, Immunology Frontier Research Institute (IFReC), Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Department of Genome Informatics, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Daron M Standley
- Department of Systems Immunology, Immunology Frontier Research Institute (IFReC), Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Department of Genome Informatics, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
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3
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Becerra JC, Hitchcock L, Vu K, Gach JS. Neutralizing the threat: harnessing broadly neutralizing antibodies against HIV-1 for treatment and prevention. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:207-220. [PMID: 38975023 PMCID: PMC11224682 DOI: 10.15698/mic2024.07.826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 05/06/2024] [Accepted: 05/15/2024] [Indexed: 07/09/2024]
Abstract
Broadly neutralizing antibodies (bnAbs) targeting the human immunodeficiency virus-1 (HIV-1) have played a crucial role in elucidating and characterizing neutralization-sensitive sites on the HIV-1 envelope spike and in informing vaccine development. Continual advancements in identifying more potent bnAbs, along with their capacity to trigger antibody-mediated effector functions, coupled with modifications to extend their half-life, position them as promising candidates for both HIV-1 treatment and prevention. While current pharmacological interventions have made significant progress in managing HIV-1 infection and enhancing quality of life, no definitive cure or vaccines have been developed thus far. Standard treatments involve daily oral anti-retroviral therapy, which, despite its efficacy, can lead to notable long-term side effects. Recent clinical trial data have demonstrated encouraging therapeutic and preventive potential for bnAb therapies in both HIV-1-infected individuals and those without the infection. This review provides an overview of the advancements in HIV-1-specific bnAbs and discusses the insights gathered from recent clinical trials regarding their application in treating and preventing HIV-1 infection.
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Affiliation(s)
- Juan C Becerra
- Department of Medicine, Division of Infectious Diseases, University of CaliforniaCA, Irvine, Irvine, 92697USA
| | - Lauren Hitchcock
- Department of Medicine, Division of Infectious Diseases, University of CaliforniaCA, Irvine, Irvine, 92697USA
| | - Khoa Vu
- Department of Medicine, Division of Infectious Diseases, University of CaliforniaCA, Irvine, Irvine, 92697USA
| | - Johannes S Gach
- Department of Medicine, Division of Infectious Diseases, University of CaliforniaCA, Irvine, Irvine, 92697USA
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4
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Foglierini M, Nortier P, Schelling R, Winiger RR, Jacquet P, O'Dell S, Demurtas D, Mpina M, Lweno O, Muller YD, Petrovas C, Daubenberger C, Perreau M, Doria-Rose NA, Gottardo R, Perez L. RAIN: machine learning-based identification for HIV-1 bNAbs. Nat Commun 2024; 15:5339. [PMID: 38914562 PMCID: PMC11196741 DOI: 10.1038/s41467-024-49676-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/17/2024] [Indexed: 06/26/2024] Open
Abstract
Broadly neutralizing antibodies (bNAbs) are promising candidates for the treatment and prevention of HIV-1 infections. Despite their critical importance, automatic detection of HIV-1 bNAbs from immune repertoires is still lacking. Here, we develop a straightforward computational method for the Rapid Automatic Identification of bNAbs (RAIN) based on machine learning methods. In contrast to other approaches, which use one-hot encoding amino acid sequences or structural alignment for prediction, RAIN uses a combination of selected sequence-based features for the accurate prediction of HIV-1 bNAbs. We demonstrate the performance of our approach on non-biased, experimentally obtained and sequenced BCR repertoires from HIV-1 immune donors. RAIN processing leads to the successful identification of distinct HIV-1 bNAbs targeting the CD4-binding site of the envelope glycoprotein. In addition, we validate the identified bNAbs using an in vitro neutralization assay and we solve the structure of one of them in complex with the soluble native-like heterotrimeric envelope glycoprotein by single-particle cryo-electron microscopy (cryo-EM). Overall, we propose a method to facilitate and accelerate HIV-1 bNAbs discovery from non-selected immune repertoires.
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Affiliation(s)
- Mathilde Foglierini
- Department of Medicine, Service of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Centre for Human Immunology, Lausanne, Switzerland
- Biomedical Data Science Centre, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Pauline Nortier
- Department of Medicine, Service of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Centre for Human Immunology, Lausanne, Switzerland
| | - Rachel Schelling
- Department of Medicine, Service of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Centre for Human Immunology, Lausanne, Switzerland
| | - Rahel R Winiger
- Department of Medicine, Service of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Centre for Human Immunology, Lausanne, Switzerland
| | - Philippe Jacquet
- Scientific Computing and Research Support Unit, University of Lausanne, Lausanne, Switzerland
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Davide Demurtas
- Interdisciplinary center of electron microscopy, CIME, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Omar Lweno
- Ifakara Health Institute, Bagamoyo, United Republic of Tanzania
| | - Yannick D Muller
- Department of Medicine, Service of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Centre for Human Immunology, Lausanne, Switzerland
| | - Constantinos Petrovas
- Department of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital, Lausanne, Switzerland
| | - Claudia Daubenberger
- Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Matthieu Perreau
- Department of Medicine, Service of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Raphael Gottardo
- Biomedical Data Science Centre, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Laurent Perez
- Department of Medicine, Service of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
- Centre for Human Immunology, Lausanne, Switzerland.
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5
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Zaslavsky ME, Craig E, Michuda JK, Sehgal N, Ram-Mohan N, Lee JY, Nguyen KD, Hoh RA, Pham TD, Röltgen K, Lam B, Parsons ES, Macwana SR, DeJager W, Drapeau EM, Roskin KM, Cunningham-Rundles C, Moody MA, Haynes BF, Goldman JD, Heath JR, Nadeau KC, Pinsky BA, Blish CA, Hensley SE, Jensen K, Meyer E, Balboni I, Utz PJ, Merrill JT, Guthridge JM, James JA, Yang S, Tibshirani R, Kundaje A, Boyd SD. Disease diagnostics using machine learning of immune receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2022.04.26.489314. [PMID: 35547855 PMCID: PMC9094102 DOI: 10.1101/2022.04.26.489314] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Clinical diagnosis typically incorporates physical examination, patient history, and various laboratory tests and imaging studies, but makes limited use of the human system's own record of antigen exposures encoded by receptors on B cells and T cells. We analyzed immune receptor datasets from 593 individuals to develop MAchine Learning for Immunological Diagnosis (Mal-ID) , an interpretive framework to screen for multiple illnesses simultaneously or precisely test for one condition. This approach detects specific infections, autoimmune disorders, vaccine responses, and disease severity differences. Human-interpretable features of the model recapitulate known immune responses to SARS-CoV-2, Influenza, and HIV, highlight antigen-specific receptors, and reveal distinct characteristics of Systemic Lupus Erythematosus and Type-1 Diabetes autoreactivity. This analysis framework has broad potential for scientific and clinical interpretation of human immune responses.
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6
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Perez L, Foglierini M. RAIN: a Machine Learning-based identification for HIV-1 bNAbs. RESEARCH SQUARE 2024:rs.3.rs-4023897. [PMID: 38903123 PMCID: PMC11188109 DOI: 10.21203/rs.3.rs-4023897/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Broadly neutralizing antibodies (bNAbs) are promising candidates for the treatment and prevention of HIV-1 infection. Despite their critical importance, automatic detection of HIV-1 bNAbs from immune repertoire is still lacking. Here, we developed a straightforward computational method for Rapid Automatic Identification of bNAbs (RAIN) based on Machine Learning methods. In contrast to other approaches using one-hot encoding amino acid sequences or structural alignment for prediction, RAIN uses a combination of selected sequence-based features for accurate prediction of HIV-1 bNAbs. We demonstrate the performance of our approach on non-biased, experimentally obtained sequenced BCR repertoires from HIV-1 immune donors. RAIN processing leads to the successful identification of novel HIV-1 bNAbs targeting the CD4-binding site of the envelope glycoprotein. In addition, we validate the identified bNAbs using in vitro neutralization assay and we solve the structure of one of them in complex with the soluble native-like heterotrimeric envelope glycoprotein by single-particle cryo-electron microscopy (cryo-EM). Overall, we propose a method to facilitate and accelerate HIV-1 bNAbs discovery from non-selected immune repertoires.
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Affiliation(s)
- Laurent Perez
- Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Mathilde Foglierini
- Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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7
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Balashova D, van Schaik BDC, Stratigopoulou M, Guikema JEJ, Caniels TG, Claireaux M, van Gils MJ, Musters A, Anang DC, de Vries N, Greiff V, van Kampen AHC. Systematic evaluation of B-cell clonal family inference approaches. BMC Immunol 2024; 25:13. [PMID: 38331731 PMCID: PMC11370117 DOI: 10.1186/s12865-024-00600-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
The reconstruction of clonal families (CFs) in B-cell receptor (BCR) repertoire analysis is a crucial step to understand the adaptive immune system and how it responds to antigens. The BCR repertoire of an individual is formed throughout life and is diverse due to several factors such as gene recombination and somatic hypermutation. The use of Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) using next generation sequencing enabled the generation of full BCR repertoires that also include rare CFs. The reconstruction of CFs from AIRR-seq data is challenging and several approaches have been developed to solve this problem. Currently, most methods use the heavy chain (HC) only, as it is more variable than the light chain (LC). CF reconstruction options include the definition of appropriate sequence similarity measures, the use of shared mutations among sequences, and the possibility of reconstruction without preliminary clustering based on V- and J-gene annotation. In this study, we aimed to systematically evaluate different approaches for CF reconstruction and to determine their impact on various outcome measures such as the number of CFs derived, the size of the CFs, and the accuracy of the reconstruction. The methods were compared to each other and to a method that groups sequences based on identical junction sequences and another method that only determines subclones. We found that after accounting for data set variability, in particular sequencing depth and mutation load, the reconstruction approach has an impact on part of the outcome measures, including the number of CFs. Simulations indicate that unique junctions and subclones should not be used as substitutes for CF and that more complex methods do not outperform simpler methods. Also, we conclude that different approaches differ in their ability to correctly reconstruct CFs when not considering the LC and to identify shared CFs. The results showed the effect of different approaches on the reconstruction of CFs and highlighted the importance of choosing an appropriate method.
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Affiliation(s)
- Daria Balashova
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Barbera D C van Schaik
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Maria Stratigopoulou
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, Netherlands
| | - Jeroen E J Guikema
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Pathology, Lymphoma and Myeloma Center Amsterdam, Meibergdreef 9, Amsterdam, Netherlands
| | - Tom G Caniels
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Mathieu Claireaux
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Marit J van Gils
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Anne Musters
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands
| | - Dornatien C Anang
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands
| | - Niek de Vries
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, Netherlands
- Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Antoine H C van Kampen
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, Netherlands.
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands.
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands.
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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8
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Griffith S, Muir L, Suchanek O, Hope J, Pade C, Gibbons JM, Tuong ZK, Fung A, Touizer E, Rees-Spear C, Nans A, Roustan C, Alguel Y, Fink D, Orkin C, Deayton J, Anderson J, Gupta RK, Doores KJ, Cherepanov P, McKnight Á, Clatworthy M, McCoy LE. Preservation of memory B cell homeostasis in an individual producing broadly neutralising antibodies against HIV-1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.05.578789. [PMID: 38370662 PMCID: PMC10871235 DOI: 10.1101/2024.02.05.578789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Immunological determinants favouring emergence of broadly neutralising antibodies are crucial to the development of HIV-1 vaccination strategies. Here, we combined RNAseq and B cell cloning approaches to isolate a broadly neutralising antibody (bnAb) ELC07 from an individual living with untreated HIV-1. Using single particle cryogenic electron microscopy (cryo-EM), we show that the antibody recognises a conformational epitope at the gp120-gp41 interface. ELC07 binds the closed state of the viral glycoprotein causing considerable perturbations to the gp41 trimer core structure. Phenotypic analysis of memory B cell subsets from the ELC07 bnAb donor revealed a lack of expected HIV-1-associated dysfunction, specifically no increase in CD21-/CD27- cells was observed whilst the resting memory (CD21+/CD27+) population appeared preserved despite uncontrolled HIV-1 viraemia. Moreover, single cell transcriptomes of memory B cells from this bnAb donor showed a resting memory phenotype irrespective of the epitope they targeted or their ability to neutralise diverse strains of HIV-1. Strikingly, single memory B cells from the ELC07 bnAb donor were transcriptionally similar to memory B cells from HIV-negative individuals. Our results demonstrate that potent bnAbs can arise without the HIV-1-induced dysregulation of the memory B cell compartment and suggest that sufficient levels of antigenic stimulation with a strategically designed immunogen could be effective in HIV-negative vaccine recipients.
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Affiliation(s)
- Sarah Griffith
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Luke Muir
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Ondrej Suchanek
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Joshua Hope
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Corinna Pade
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, UK
| | - Joseph M Gibbons
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, UK
| | - Zewen Kelvin Tuong
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - Audrey Fung
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Emma Touizer
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Chloe Rees-Spear
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Chloe Roustan
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Yilmaz Alguel
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Douglas Fink
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Chloe Orkin
- SHARE collaborative, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Jane Deayton
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, UK
| | - Jane Anderson
- Homerton University Hospital NHS Foundation, London, UK
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Katie J Doores
- Department of Infectious Diseases, School of Immunology & Microbial Sciences, King's College London, London, UK
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
- Department of Infectious Disease, St-Mary's Campus, Imperial College London, London, UK
| | - Áine McKnight
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, UK
| | - Menna Clatworthy
- Molecular Immunity Unit, Department of Medicine, Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
- Cellular Genetics, Wellcome Sanger Institute, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Cambridge, UK
| | - Laura E McCoy
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
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9
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Saputri DS, Ismanto HS, Nugraha DK, Xu Z, Horiguchi Y, Sakakibara S, Standley DM. Deciphering the antigen specificities of antibodies by clustering their complementarity determining region sequences. mSystems 2023; 8:e0072223. [PMID: 37975681 PMCID: PMC10734444 DOI: 10.1128/msystems.00722-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 10/06/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Determining antigen and epitope specificity is an essential step in the discovery of therapeutic antibodies as well as in the analysis adaptive immune responses to disease or vaccination. Despite extensive efforts, deciphering antigen specificity solely from BCR amino acid sequence remains a challenging task, requiring a combination of experimental and computational approaches. Here, we describe and experimentally validate a simple and straightforward approach for grouping antibodies that share antigen and epitope specificities based on their CDR sequence similarity. This approach allows us to identify the specificities of a large number of antibodies whose antigen targets are unknown, using a small fraction of antibodies with well-annotated binding specificities.
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Affiliation(s)
- Dianita S. Saputri
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Graduate School of Medicine, Osaka University, Suita, Japan
| | - Hendra S. Ismanto
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Dendi K. Nugraha
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Zichang Xu
- Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Yasuhiko Horiguchi
- Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
| | - Shuhei Sakakibara
- Immunology Frontier Research Center, Osaka University, Suita, Japan
- Graduate School of Medical Safety Management, Jikei University of Health Care Sciences, Osaka, Japan
| | - Daron M. Standley
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Graduate School of Medicine, Osaka University, Suita, Japan
- Immunology Frontier Research Center, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
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10
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Kreer C, Lupo C, Ercanoglu MS, Gieselmann L, Spisak N, Grossbach J, Schlotz M, Schommers P, Gruell H, Dold L, Beyer A, Nourmohammad A, Mora T, Walczak AM, Klein F. Probabilities of developing HIV-1 bNAb sequence features in uninfected and chronically infected individuals. Nat Commun 2023; 14:7137. [PMID: 37932288 PMCID: PMC10628170 DOI: 10.1038/s41467-023-42906-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 10/24/2023] [Indexed: 11/08/2023] Open
Abstract
HIV-1 broadly neutralizing antibodies (bNAbs) are able to suppress viremia and prevent infection. Their induction by vaccination is therefore a major goal. However, in contrast to antibodies that neutralize other pathogens, HIV-1-specific bNAbs frequently carry uncommon molecular characteristics that might prevent their induction. Here, we perform unbiased sequence analyses of B cell receptor repertoires from 57 uninfected and 46 chronically HIV-1- or HCV-infected individuals and learn probabilistic models to predict the likelihood of bNAb development. We formally show that lower probabilities for bNAbs are predictive of higher HIV-1 neutralization activity. Moreover, ranking bNAbs by their probabilities allows to identify highly potent antibodies with superior generation probabilities as preferential targets for vaccination approaches. Importantly, we find equal bNAb probabilities across infected and uninfected individuals. This implies that chronic infection is not a prerequisite for the generation of bNAbs, fostering the hope that HIV-1 vaccines can induce bNAb development in uninfected people.
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Affiliation(s)
- Christoph Kreer
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Cosimo Lupo
- Laboratoire de physique de l'Ecole normale supérieure, CNRS, PSL University, Sorbonne Université, and Université Paris Cité, 75005, Paris, France
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Roma I, 00185, Rome, Italy
| | - Meryem S Ercanoglu
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Lutz Gieselmann
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- German Center for Infection Research, Partner Site Bonn-Cologne, 50931, Cologne, Germany
| | - Natanael Spisak
- Laboratoire de physique de l'Ecole normale supérieure, CNRS, PSL University, Sorbonne Université, and Université Paris Cité, 75005, Paris, France
| | - Jan Grossbach
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases & Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, 50931, Cologne, Germany
| | - Maike Schlotz
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
| | - Philipp Schommers
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- German Center for Infection Research, Partner Site Bonn-Cologne, 50931, Cologne, Germany
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931, Cologne, Germany
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
| | - Leona Dold
- Department of Internal Medicine I, University Hospital of Bonn, Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Bonn, Germany
| | - Andreas Beyer
- Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases & Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, 50931, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931, Cologne, Germany
| | - Armita Nourmohammad
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077, Göttingen, Germany
- Department of Physics, University of Washington, 3910 15th Ave Northeast, Seattle, WA, 98195, USA
- Department of Applied Mathematics, University of Washington, 4182 W Stevens Way NE, Seattle, WA, 98105, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, 85 E Stevens Way NE, Seattle, WA, 98195, USA
- Fred Hutchinson Cancer Center, 1241 Eastlake Ave E, Seattle, WA, 98102, USA
| | - Thierry Mora
- Laboratoire de physique de l'Ecole normale supérieure, CNRS, PSL University, Sorbonne Université, and Université Paris Cité, 75005, Paris, France
| | - Aleksandra M Walczak
- Laboratoire de physique de l'Ecole normale supérieure, CNRS, PSL University, Sorbonne Université, and Université Paris Cité, 75005, Paris, France
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931, Cologne, Germany.
- German Center for Infection Research, Partner Site Bonn-Cologne, 50931, Cologne, Germany.
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931, Cologne, Germany.
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11
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Haynes BF, Wiehe K, Alam SM, Weissman D, Saunders KO. Progress with induction of HIV broadly neutralizing antibodies in the Duke Consortia for HIV/AIDS Vaccine Development. Curr Opin HIV AIDS 2023; 18:300-308. [PMID: 37751363 PMCID: PMC10552807 DOI: 10.1097/coh.0000000000000820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
PURPOSE OF REVIEW Design of an HIV vaccine that can induce broadly neutralizing antibodies (bnAbs) is a major goal. However, HIV bnAbs are not readily made by the immune system. Rather HIV bnAbs are disfavored by a number of virus and host factors. The purpose of the review is to discuss recent progress made in the design and use of immunogens capable of inducing HIV bnAbs in the Duke Consortia for HIV/AIDS Vaccine Development. RECENT FINDINGS New immunogens capable of binding with high affinity to unmutated common ancestors (UCAs) of bnAb B cell lineages have been designed and strategies for stabilization of HIV Env in its prefusion state are being developed. Success is starting to be translated from preclinical studies of UCA-targeting immunogens in animals, to success of initiating bnAb lineages in humans. SUMMARY Recent progress has been made in both immunogen design and in achieving bnAb B cell lineage induction in animal models and now in human clinical trials. With continued progress, a practical HIV/AIDS vaccine may be possible. However, host constraints on full bnAb maturation remain as potential roadblocks for full maturation of some types of bnAbs.
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Affiliation(s)
- Barton F. Haynes
- Duke Human Vaccine Institute, Departments of Medicine and Immunology
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - S. Munir Alam
- Duke Human Vaccine Institute, Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Drew Weissman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Departments of Surgery, Immunology and Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina, USA
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12
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Maliqi L, Friedrich N, Glögl M, Schmutz S, Schmidt D, Rusert P, Schanz M, Zaheri M, Pasin C, Niklaus C, Foulkes C, Reinberg T, Dreier B, Abela I, Peterhoff D, Hauser A, Kouyos RD, Günthard HF, van Gils MJ, Sanders RW, Wagner R, Plückthun A, Trkola A. Assessing immunogenicity barriers of the HIV-1 envelope trimer. NPJ Vaccines 2023; 8:148. [PMID: 37777519 PMCID: PMC10542815 DOI: 10.1038/s41541-023-00746-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/19/2023] [Indexed: 10/02/2023] Open
Abstract
Understanding the balance between epitope shielding and accessibility on HIV-1 envelope (Env) trimers is essential to guide immunogen selection for broadly neutralizing antibody (bnAb) based vaccines. To investigate the antigenic space of Env immunogens, we created a strategy based on synthetic, high diversity, Designed Ankyrin Repeat Protein (DARPin) libraries. We show that DARPin Antigenicity Analysis (DANA), a purely in vitro screening tool, has the capability to extrapolate relevant information of antigenic properties of Env immunogens. DANA screens of stabilized, soluble Env trimers revealed that stronger trimer stabilization led to the selection of highly mutated DARPins with length variations and framework mutations mirroring observations made for bnAbs. By mimicking heterotypic prime-boost immunization regimens, DANA may be used to select immunogen combinations that favor the selection of trimer-reactive binders. This positions DANA as a versatile strategy for distilling fundamental antigenic features of immunogens, complementary to preclinical immunogenicity testing.
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Affiliation(s)
- Liridona Maliqi
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Nikolas Friedrich
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Matthias Glögl
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Daniel Schmidt
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Peter Rusert
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Merle Schanz
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Chloé Pasin
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Cyrille Niklaus
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Caio Foulkes
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
| | - Thomas Reinberg
- Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Birgit Dreier
- Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Irene Abela
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - David Peterhoff
- Institute of Clinical Microbiology and Hygiene, University Hospital, Regensburg, Germany
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Alexandra Hauser
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Roger D Kouyos
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Huldrych F Günthard
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich (USZ), Zurich, Switzerland
| | - Marit J van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
- Department of Microbiology and Immunology, Weill Cornell Medical College, Cornell University, New York, USA
| | - Ralf Wagner
- Institute of Clinical Microbiology and Hygiene, University Hospital, Regensburg, Germany
- Institute of Medical Microbiology and Hygiene, Molecular Microbiology (Virology), University of Regensburg, Regensburg, Germany
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich (UZH), Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich (UZH), Zurich, Switzerland.
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13
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Singh A, Boggiano C, Eller MA, Maciel M, Marovich MA, Mehra VL, Mo AX, Singleton KL, Leitner WW. Optimizing the Immunogenicity of HIV Vaccines by Adjuvants - NIAID Workshop Report. Vaccine 2023; 41:4439-4446. [PMID: 37331838 DOI: 10.1016/j.vaccine.2023.06.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 05/11/2023] [Accepted: 06/06/2023] [Indexed: 06/20/2023]
Abstract
This report summarizes the highlights of a workshop convened by the National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), on April 4-5, 2022, to provide a discussion forum for sharing insights on the current status, key challenges, and next steps to advance the current landscape of promising adjuvants in preclinical and clinical human immunodeficiency virus (HIV) vaccine studies. A key goal was to solicit and share recommendations on scientific, regulatory, and operational guidelines for bridging the gaps in rational selection, access, and formulation of clinically relevant adjuvants for HIV vaccine candidates. The NIAID Vaccine Adjuvant Program working group remains committed to accentuate promising adjuvants and nurturing collaborations between adjuvant and HIV vaccine developers.
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Affiliation(s)
- Anjali Singh
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - César Boggiano
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael A Eller
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Milton Maciel
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mary A Marovich
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Vijay L Mehra
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Annie X Mo
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kentner L Singleton
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Wolfgang W Leitner
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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14
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Zhang X, Zhou Z. The Mechanism of bnAb Production and Its Application in Mutable Virus Broad-Spectrum Vaccines: Inspiration from HIV-1 Broad Neutralization Research. Vaccines (Basel) 2023; 11:1143. [PMID: 37514959 PMCID: PMC10384589 DOI: 10.3390/vaccines11071143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
Elite controllers among HIV-1-infected individuals have demonstrated a stronger ability to control the viral load in their bodies. Scientists have isolated antibodies with strong neutralizing ability from these individuals, which can neutralize HIV-1 variations; these are known as broadly neutralizing antibodies. The nucleic acid of some viruses will constantly mutate during replication (such as SARS-CoV-2), which will reduce the protective ability of the corresponding vaccines. The immune escape caused by this mutation is the most severe challenge faced by humans in the battle against the virus. Therefore, developing broad-spectrum vaccines that can induce broadly neutralizing antibodies against various viruses and their mutated strains is the best way to combat virus mutations. Exploring the mechanism by which the human immune system produces broadly neutralizing antibodies and its induction strategies is crucial in the design process of broad-spectrum vaccines.
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Affiliation(s)
- Xinyu Zhang
- Research Center for Infectious Diseases, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
- Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC) and WHO Collaborating Center for Standardization and Evaluation of Biologicals, No. 31 Huatuo Street, Daxing District, Beijing 102629, China
- College of Life Science, Jilin University, Changchun 130012, China
| | - Zehua Zhou
- Research Center for Infectious Diseases, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
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15
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Joyce C, Murrell S, Murrell B, Omorodion O, Ver LS, Carrico N, Bastidas R, Nedellec R, Bick M, Woehl J, Zhao F, Burns A, Barman S, Appel M, Ramos A, Wickramasinghe L, Eren K, Vollbrecht T, Smith DM, Kosakovsky Pond SL, McBride R, Worth C, Batista F, Sok D, Poignard P, Briney B, Wilson IA, Landais E, Burton DR. Antigen pressure from two founder viruses induces multiple insertions at a single antibody position to generate broadly neutralizing HIV antibodies. PLoS Pathog 2023; 19:e1011416. [PMID: 37384622 PMCID: PMC10309625 DOI: 10.1371/journal.ppat.1011416] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/10/2023] [Indexed: 07/01/2023] Open
Abstract
Vaccination strategies aimed at maturing broadly neutralizing antibodies (bnAbs) from naïve precursors are hindered by unusual features that characterize these Abs, including insertions and deletions (indels). Longitudinal studies of natural HIV infection cases shed light on the complex processes underlying bnAb development and have suggested a role for superinfection as a potential enhancer of neutralization breadth. Here we describe the development of a potent bnAb lineage that was elicited by two founder viruses to inform vaccine design. The V3-glycan targeting bnAb lineage (PC39-1) was isolated from subtype C-infected IAVI Protocol C elite neutralizer, donor PC39, and is defined by the presence of multiple independent insertions in CDRH1 that range from 1-11 amino acids in length. Memory B cell members of this lineage are predominantly atypical in phenotype yet also span the class-switched and antibody-secreting cell compartments. Development of neutralization breadth occurred concomitantly with extensive recombination between founder viruses before each virus separated into two distinct population "arms" that evolved independently to escape the PC39-1 lineage. Ab crystal structures show an extended CDRH1 that can help stabilize the CDRH3. Overall, these findings suggest that early exposure of the humoral system to multiple related Env molecules could promote the induction of bnAbs by focusing Ab responses to conserved epitopes.
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Affiliation(s)
- Collin Joyce
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
| | - Sasha Murrell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ben Murrell
- Department of Medicine, University of California San Diego, San Diego, California, United States of America
- Department of Microbiology, Tumor and Cell biology, Karolinska Institutet, Stockholm, Sweden
| | - Oluwarotimi Omorodion
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Lorena S. Ver
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI, New York, New York, United States of America
| | - Nancy Carrico
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI, New York, New York, United States of America
| | - Raiza Bastidas
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
| | - Rebecca Nedellec
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
| | - Michael Bick
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
| | - Jordan Woehl
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI, New York, New York, United States of America
| | - Fangzhu Zhao
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
| | - Alison Burns
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI, New York, New York, United States of America
| | - Shawn Barman
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI, New York, New York, United States of America
| | - Michael Appel
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI, New York, New York, United States of America
| | - Alejandra Ramos
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI, New York, New York, United States of America
| | - Lalinda Wickramasinghe
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI, New York, New York, United States of America
| | - Kemal Eren
- Department of Medicine, University of California San Diego, San Diego, California, United States of America
| | - Thomas Vollbrecht
- Department of Medicine, University of California San Diego, San Diego, California, United States of America
- Veterans Affairs San Diego Healthcare System, San Diego, California, United States of America
| | - Davey M. Smith
- Department of Medicine, University of California San Diego, San Diego, California, United States of America
| | - Sergei L. Kosakovsky Pond
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Ryan McBride
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Charli Worth
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California, United States of America
| | - Facundo Batista
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Devin Sok
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI, New York, New York, United States of America
| | | | - Pascal Poignard
- Institut de Biologie Structurale, Université Grenoble Alpes, Commissariat à l’Energie Atomique, Centre National de Recherche Scientifique and Centre Hospitalier Universitaire Grenoble Alpes, Grenoble, France
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- Center for Viral Systems Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Ian A. Wilson
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Elise Landais
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- IAVI, New York, New York, United States of America
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, United States of America
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, California, United States of America
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, California, United States of America
- Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, United States of America
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16
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Adeoye B, Nakiyingi L, Moreau Y, Nankya E, Olson AJ, Zhang M, Jacobson KR, Gupta A, Manabe YC, Hosseinipour MC, Kumwenda J, Sagar M. Mycobacterium tuberculosis disease associates with higher HIV-1-specific antibody responses. iScience 2023; 26:106631. [PMID: 37168567 PMCID: PMC10165194 DOI: 10.1016/j.isci.2023.106631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/14/2023] [Accepted: 04/04/2023] [Indexed: 05/13/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the most common infection among people with HIV (PWH). Mtb disease-associated inflammation could affect HIV-directed immune responses in PWH. We show that HIV antibodies are broader and more potent in PWH in the presence as compared to the absence of Mtb disease. With co-existing Mtb disease, the virus in PWH also encounters unique antibody selection pressure. The Mtb-linked HIV antibody enhancement associates with specific mediators important for B cell and antibody development. This Mtb humoral augmentation does not occur due to cross-reactivity, a generalized increase in all antibodies, or differences in duration or amount of antigen exposure. We speculate that the co-localization of Mtb and HIV in lymphatic tissues leads to the emergence of potent HIV antibodies. PWH's Mtb disease status has implications for the future use of HIV broadly neutralizing antibodies as prophylaxis or treatment and the induction of better humoral immunity.
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Affiliation(s)
- Bukola Adeoye
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Lydia Nakiyingi
- Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Yvetane Moreau
- Department of Medicine, Boston Medical Center, Boston, MA 02118, USA
| | - Ethel Nankya
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Alex J. Olson
- Department of Medicine, Boston Medical Center, Boston, MA 02118, USA
| | - Mo Zhang
- Department of Medicine, Boston Medical Center, Boston, MA 02118, USA
| | - Karen R. Jacobson
- Department of Medicine, Boston Medical Center, Boston, MA 02118, USA
| | - Amita Gupta
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yukari C. Manabe
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | | | - Manish Sagar
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Medicine, Boston Medical Center, Boston, MA 02118, USA
| | - AIDS Clinical Trials Group A5274 (REMEMBER) Study Team
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
- Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
- Department of Medicine, Boston Medical Center, Boston, MA 02118, USA
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- University of North Carolina School of Medicine, Chapel Hill, NC, USA
- University of Malawi College of Medicine, Blantyre, Malawi
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17
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Zhang Y, Li Q, Luo L, Duan C, Shen J, Wang Z. Application of germline antibody features to vaccine development, antibody discovery, antibody optimization and disease diagnosis. Biotechnol Adv 2023; 65:108143. [PMID: 37023966 DOI: 10.1016/j.biotechadv.2023.108143] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/26/2023] [Accepted: 03/29/2023] [Indexed: 04/08/2023]
Abstract
Although the efficacy and commercial success of vaccines and therapeutic antibodies have been tremendous, designing and discovering new drug candidates remains a labor-, time- and cost-intensive endeavor with high risks. The main challenges of vaccine development are inducing a strong immune response in broad populations and providing effective prevention against a group of highly variable pathogens. Meanwhile, antibody discovery faces several great obstacles, especially the blindness in antibody screening and the unpredictability of the developability and druggability of antibody drugs. These challenges are largely due to poorly understanding of germline antibodies and the antibody responses to pathogen invasions. Thanks to the recent developments in high-throughput sequencing and structural biology, we have gained insight into the germline immunoglobulin (Ig) genes and germline antibodies and then the germline antibody features associated with antigens and disease manifestation. In this review, we firstly outline the broad associations between germline antibodies and antigens. Moreover, we comprehensively review the recent applications of antigen-specific germline antibody features, physicochemical properties-associated germline antibody features, and disease manifestation-associated germline antibody features on vaccine development, antibody discovery, antibody optimization, and disease diagnosis. Lastly, we discuss the bottlenecks and perspectives of current and potential applications of germline antibody features in the biotechnology field.
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Affiliation(s)
- Yingjie Zhang
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Qing Li
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Liang Luo
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Changfei Duan
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China
| | - Zhanhui Wang
- National Key Laboratory of Veterinary Public Health Security, Beijing Key Laboratory of Detection Technology for Animal-Derived Food, College of Veterinary Medicine, China Agricultural University, 100193 Beijing, People's Republic of China.
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18
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Hao Q, Zhan C, Lian C, Luo S, Cao W, Wang B, Xie X, Ye X, Gui T, Voena C, Pighi C, Wang Y, Tian Y, Wang X, Dai P, Cai Y, Liu X, Ouyang S, Sun S, Hu Q, Liu J, Ye Y, Zhao J, Lu A, Wang JY, Huang C, Su B, Meng FL, Chiarle R, Pan-Hammarström Q, Yeap LS. DNA repair mechanisms that promote insertion-deletion events during immunoglobulin gene diversification. Sci Immunol 2023; 8:eade1167. [PMID: 36961908 PMCID: PMC10351598 DOI: 10.1126/sciimmunol.ade1167] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/01/2023] [Indexed: 03/26/2023]
Abstract
Insertions and deletions (indels) are low-frequency deleterious genomic DNA alterations. Despite their rarity, indels are common, and insertions leading to long complementarity-determining region 3 (CDR3) are vital for antigen-binding functions in broadly neutralizing and polyreactive antibodies targeting viruses. Because of challenges in detecting indels, the mechanism that generates indels during immunoglobulin diversification processes remains poorly understood. We carried out ultra-deep profiling of indels and systematically dissected the underlying mechanisms using passenger-immunoglobulin mouse models. We found that activation-induced cytidine deaminase-dependent ±1-base pair (bp) indels are the most prevalent indel events, biasing deleterious outcomes, whereas longer in-frame indels, especially insertions that can extend the CDR3 length, are rare outcomes. The ±1-bp indels are channeled by base excision repair, but longer indels require additional DNA-processing factors. Ectopic expression of a DNA exonuclease or perturbation of the balance of DNA polymerases can increase the frequency of longer indels, thus paving the way for models that can generate antibodies with long CDR3. Our study reveals the mechanisms that generate beneficial and deleterious indels during the process of antibody somatic hypermutation and has implications in understanding the detrimental genomic alterations in various conditions, including tumorigenesis.
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Affiliation(s)
- Qian Hao
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Chuanzong Zhan
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Chaoyang Lian
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Simin Luo
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Wenyi Cao
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Binbin Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Xia Xie
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences; 320 Yueyang Road, Shanghai 200031, China
| | - Xiaofei Ye
- Department of Biosciences and Nutrition, Karolinska Institutet; SE141-83, Huddinge, Stockholm, Sweden
- Present address: Kindstar Global Precision Medicine Institute, Wuhan, China and Kindstar Biotech, Wuhan, China
| | - Tuantuan Gui
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Claudia Voena
- Department of Molecular Biotechnology and Health Sciences, University of Torino; 10126 Torino, Italy
| | - Chiara Pighi
- Department of Molecular Biotechnology and Health Sciences, University of Torino; 10126 Torino, Italy
- Department of Pathology, Boston Children’s Hospital, and Harvard Medical School; Boston, MA 02115, USA
| | - Yanyan Wang
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences; 320 Yueyang Road, Shanghai 200031, China
| | - Ying Tian
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Xin Wang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Pengfei Dai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences; 320 Yueyang Road, Shanghai 200031, China
| | - Yanni Cai
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences; 320 Yueyang Road, Shanghai 200031, China
| | - Xiaojing Liu
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences; 320 Yueyang Road, Shanghai 200031, China
| | - Shengqun Ouyang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Shiqi Sun
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Qianwen Hu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Jun Liu
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Youqiong Ye
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Jingkun Zhao
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Aiguo Lu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ji-Yang Wang
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Department of Microbiology and Immunology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Chuanxin Huang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
| | - Bing Su
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Departments of Endocrinology and Gastroenterology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Jiao Tong University School of Medicine-Yale Institute for Immune Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai 200025
| | - Fei-Long Meng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences; 320 Yueyang Road, Shanghai 200031, China
| | - Roberto Chiarle
- Department of Molecular Biotechnology and Health Sciences, University of Torino; 10126 Torino, Italy
- Department of Pathology, Boston Children’s Hospital, and Harvard Medical School; Boston, MA 02115, USA
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet; SE141-83, Huddinge, Stockholm, Sweden
| | - Leng-Siew Yeap
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Department of Endocrinology and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine; 280 South Chongqing Road, Shanghai, 200025, China
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19
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García-Valiente R, Merino Tejero E, Stratigopoulou M, Balashova D, Jongejan A, Lashgari D, Pélissier A, Caniels TG, Claireaux MAF, Musters A, van Gils MJ, Rodríguez Martínez M, de Vries N, Meyer-Hermann M, Guikema JEJ, Hoefsloot H, van Kampen AHC. Understanding repertoire sequencing data through a multiscale computational model of the germinal center. NPJ Syst Biol Appl 2023; 9:8. [PMID: 36927990 PMCID: PMC10019394 DOI: 10.1038/s41540-023-00271-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Abstract
Sequencing of B-cell and T-cell immune receptor repertoires helps us to understand the adaptive immune response, although it only provides information about the clonotypes (lineages) and their frequencies and not about, for example, their affinity or antigen (Ag) specificity. To further characterize the identified clones, usually with special attention to the particularly abundant ones (dominant), additional time-consuming or expensive experiments are generally required. Here, we present an extension of a multiscale model of the germinal center (GC) that we previously developed to gain more insight in B-cell repertoires. We compare the extent that these simulated repertoires deviate from experimental repertoires established from single GCs, blood, or tissue. Our simulations show that there is a limited correlation between clonal abundance and affinity and that there is large affinity variability among same-ancestor (same-clone) subclones. Our simulations suggest that low-abundance clones and subclones, might also be of interest since they may have high affinity for the Ag. We show that the fraction of plasma cells (PCs) with high B-cell receptor (BcR) mRNA content in the GC does not significantly affect the number of dominant clones derived from single GCs by sequencing BcR mRNAs. Results from these simulations guide data interpretation and the design of follow-up experiments.
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Affiliation(s)
- Rodrigo García-Valiente
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Elena Merino Tejero
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Maria Stratigopoulou
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
| | - Daria Balashova
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Aldo Jongejan
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Danial Lashgari
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - Aurélien Pélissier
- IBM Research Zurich, 8803, Rüschlikon, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Tom G Caniels
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Mathieu A F Claireaux
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Anne Musters
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands
| | - Marit J van Gils
- Amsterdam UMC location University of Amsterdam, Medical Microbiology and Infection Prevention, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | | | - Niek de Vries
- Amsterdam UMC location University of Amsterdam, Experimental Immunology, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands
| | - Michael Meyer-Hermann
- Department for Systems Immunology and Braunschweig Integrated Centre of Systems Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jeroen E J Guikema
- Cancer Center Amsterdam, Amsterdam, The Netherlands
- Amsterdam UMC location University of Amsterdam, Pathology, Lymphoma and Myeloma Center Amsterdam, Meibergdreef 9, Amsterdam, The Netherlands
| | - Huub Hoefsloot
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Antoine H C van Kampen
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands.
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands.
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands.
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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20
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Haynes BF, Wiehe K, Borrow P, Saunders KO, Korber B, Wagh K, McMichael AJ, Kelsoe G, Hahn BH, Alt F, Shaw GM. Strategies for HIV-1 vaccines that induce broadly neutralizing antibodies. Nat Rev Immunol 2023; 23:142-158. [PMID: 35962033 PMCID: PMC9372928 DOI: 10.1038/s41577-022-00753-w] [Citation(s) in RCA: 131] [Impact Index Per Article: 131.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2022] [Indexed: 01/07/2023]
Abstract
After nearly four decades of research, a safe and effective HIV-1 vaccine remains elusive. There are many reasons why the development of a potent and durable HIV-1 vaccine is challenging, including the extraordinary genetic diversity of HIV-1 and its complex mechanisms of immune evasion. HIV-1 envelope glycoproteins are poorly recognized by the immune system, which means that potent broadly neutralizing antibodies (bnAbs) are only infrequently induced in the setting of HIV-1 infection or through vaccination. Thus, the biology of HIV-1-host interactions necessitates novel strategies for vaccine development to be designed to activate and expand rare bnAb-producing B cell lineages and to select for the acquisition of critical improbable bnAb mutations. Here we discuss strategies for the induction of potent and broad HIV-1 bnAbs and outline the steps that may be necessary for ultimate success.
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Affiliation(s)
- Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA.
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA.
- Department of Immunology, Duke University of School of Medicine, Durham, NC, USA.
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Bette Korber
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
- New Mexico Consortium, Los Alamos, NM, USA
| | - Kshitij Wagh
- T-6: Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, USA
- New Mexico Consortium, Los Alamos, NM, USA
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Immunology, Duke University of School of Medicine, Durham, NC, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Frederick Alt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA, USA
| | - George M Shaw
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
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21
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Gill K, Moore C, Nwogu O, Kroner JW, Chang WC, Stevens ML, kyzy AB, Biagini JM, Devonshire AL, Kottyan L, Schwartz JT, Assa’ad AH, Martin LJ, Andorf S, Hershey GKK, Roskin KM. B cell repertoire in children with skin barrier dysfunction supports altered IgE maturation associated with allergic food sensitization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526538. [PMID: 36778284 PMCID: PMC9915585 DOI: 10.1101/2023.02.01.526538] [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: 02/09/2023]
Abstract
The skin is a major immune organ and skin barrier dysfunction is a major risk factor for the development of the inappropriate immune response seen in allergic disease. Skin barrier disruption alters the landscape of antigens experienced by the immune system and the downstream impacts on the antibody repertoire remain poorly characterized, particularly for the IgE isotype responsible for allergic specificity and in early life, when allergic disease is developing. In this study, we sequenced antibody gene repertoires from a large and well-characterized cohort of children with atopic dermatitis and found that food sensitization was associated with lower mutation frequencies in the IgE compartment. This trend was abrogated in children living with pets during the first year of life. These results elucidate potential molecular mechanisms underlying the protective effects of pet ownership and non-antiseptic environs reported for allergic disease, and the hygiene hypothesis more broadly. We also observed increased IgE diversity and increased isotype-switching to the IgE isotype, suggesting that B cell development, particularly isotype-switching, is heavily altered in the those with food allergen sensitizations relative to those without food allergen sensitizations. Unlike for food antigens, aeroallergen sensitization exhibited no effect on IgE mutation or diversity. Consistent patterns of antibody rearrangement were associated with food allergen sensitization in subjects with atopic dermatitis. Thus, we propose the Immune Repertoire in Atopic Disease (IRAD) score, to quantify this repertoire shift and to aid clinically in patient diagnosis and risk stratification.
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Affiliation(s)
- Kirandeep Gill
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
| | - Carolina Moore
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
| | - Onyekachi Nwogu
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
| | - John W. Kroner
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
| | - Wan-Chi Chang
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
| | - Mariana L. Stevens
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
| | - Asel Baatyrbek kyzy
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
| | - Jocelyn M. Biagini
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine; Cincinnati, Ohio, USA
| | - Ashley L. Devonshire
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine; Cincinnati, Ohio, USA
| | - Leah Kottyan
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine; Cincinnati, Ohio, USA
| | - Justin T. Schwartz
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine; Cincinnati, Ohio, USA
| | - Amal H. Assa’ad
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine; Cincinnati, Ohio, USA
| | - Lisa J. Martin
- Division of Human Genetics, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine; Cincinnati, Ohio, USA
| | - Sandra Andorf
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Division of Allergy and Immunology, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Division of Biostatistics and Epidemiology, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine; Cincinnati, Ohio, USA
| | - Gurjit K. Khurana Hershey
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine; Cincinnati, Ohio, USA
| | - Krishna M. Roskin
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center; Cincinnati, Ohio, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine; Cincinnati, Ohio, USA
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22
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Goldman JD, Wang K, Röltgen K, Nielsen SCA, Roach JC, Naccache SN, Yang F, Wirz OF, Yost KE, Lee JY, Chun K, Wrin T, Petropoulos CJ, Lee I, Fallen S, Manner PM, Wallick JA, Algren HA, Murray KM, Hadlock J, Chen D, Dai CL, Yuan D, Su Y, Jeharajah J, Berrington WR, Pappas GP, Nyatsatsang ST, Greninger AL, Satpathy AT, Pauk JS, Boyd SD, Heath JR. Reinfection with SARS-CoV-2 and Waning Humoral Immunity: A Case Report. Vaccines (Basel) 2022; 11:5. [PMID: 36679852 PMCID: PMC9861578 DOI: 10.3390/vaccines11010005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Recovery from COVID-19 is associated with production of anti-SARS-CoV-2 antibodies, but it is uncertain whether these confer immunity. We describe viral RNA shedding duration in hospitalized patients and identify patients with recurrent shedding. We sequenced viruses from two distinct episodes of symptomatic COVID-19 separated by 144 days in a single patient, to conclusively describe reinfection with a different strain harboring the spike variant D614G. This case of reinfection was one of the first cases of reinfection reported in 2020. With antibody, B cell and T cell analytics, we show correlates of adaptive immunity at reinfection, including a differential response in neutralizing antibodies to a D614G pseudovirus. Finally, we discuss implications for vaccine programs and begin to define benchmarks for protection against reinfection from SARS-CoV-2.
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Affiliation(s)
- Jason D. Goldman
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA 98122, USA
- Providence St. Joseph Health, Renton, WA 98057, USA
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, WA 98195, USA
| | - Kai Wang
- Institute for Systems Biology, Seattle, WA 98103, USA
| | - Katharina Röltgen
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | | | | | | | - Fan Yang
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Oliver F. Wirz
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kathryn E. Yost
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Ji-Yeun Lee
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kelly Chun
- LabCorp Esoterix, Calabasas, CA 91301, USA
| | - Terri Wrin
- Monogram Biosciences, South San Francisco, CA 94080, USA
| | | | - Inyoul Lee
- Institute for Systems Biology, Seattle, WA 98103, USA
| | | | - Paula M. Manner
- Providence St. Joseph Health, Renton, WA 98057, USA
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98104, USA
| | - Julie A. Wallick
- Providence St. Joseph Health, Renton, WA 98057, USA
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98104, USA
| | - Heather A. Algren
- Providence St. Joseph Health, Renton, WA 98057, USA
- Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA 98104, USA
| | - Kim M. Murray
- Institute for Systems Biology, Seattle, WA 98103, USA
| | - Jennifer Hadlock
- Providence St. Joseph Health, Renton, WA 98057, USA
- Institute for Systems Biology, Seattle, WA 98103, USA
| | - Daniel Chen
- Institute for Systems Biology, Seattle, WA 98103, USA
| | | | - Dan Yuan
- Institute for Systems Biology, Seattle, WA 98103, USA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA 98103, USA
| | - Joshua Jeharajah
- Division of Infectious Diseases, Polyclinic, Seattle, WA 98104, USA
| | - William R. Berrington
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA 98122, USA
- Providence St. Joseph Health, Renton, WA 98057, USA
| | - George P. Pappas
- Division of Pulmonology and Critical Care Medicine, Swedish Medical Center, Seattle, WA 98104, USA
| | - Sonam T. Nyatsatsang
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA 98122, USA
- Providence St. Joseph Health, Renton, WA 98057, USA
| | - Alexander L. Greninger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98109, USA
- Vaccine and Infectious Disease Division, Fred Hutch, Seattle, DC 98109, USA
| | | | - John S. Pauk
- Division of Infectious Diseases, Swedish Medical Center, Seattle, WA 98122, USA
- Providence St. Joseph Health, Renton, WA 98057, USA
| | - Scott D. Boyd
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Sean N. Parker Center for Allergy and Asthma Research, Stanford, CA 94304, USA
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23
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Ismanto HS, Xu Z, Saputri DS, Wilamowski J, Li S, Nugraha DK, Horiguchi Y, Okada M, Arase H, Standley DM. Landscape of infection enhancing antibodies in COVID-19 and healthy donors. Comput Struct Biotechnol J 2022; 20:6033-6040. [PMCID: PMC9635252 DOI: 10.1016/j.csbj.2022.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/01/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Hendra S. Ismanto
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Zichang Xu
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Dianita S. Saputri
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Jan Wilamowski
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Songling Li
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Department of System Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan
| | - Dendi K. Nugraha
- Deparment of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Yasuhiko Horiguchi
- Deparment of Molecular Bacteriology, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan
| | - Masato Okada
- Deparment of Oncogene Research, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Department of Oncogene Research, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan
| | - Hisashi Arase
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Department of Immunochemistry, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan
| | - Daron M Standley
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Department of System Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Center for Infectious Disease Education and Research, Osaka University, Osaka 565-0871, Japan
- Corresponding author at: Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan.
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24
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Xu Z, Ismanto HS, Zhou H, Saputri DS, Sugihara F, Standley DM. Advances in antibody discovery from human BCR repertoires. FRONTIERS IN BIOINFORMATICS 2022; 2:1044975. [PMID: 36338807 PMCID: PMC9631452 DOI: 10.3389/fbinf.2022.1044975] [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: 09/15/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Antibodies make up an important and growing class of compounds used for the diagnosis or treatment of disease. While traditional antibody discovery utilized immunization of animals to generate lead compounds, technological innovations have made it possible to search for antibodies targeting a given antigen within the repertoires of B cells in humans. Here we group these innovations into four broad categories: cell sorting allows the collection of cells enriched in specificity to one or more antigens; BCR sequencing can be performed on bulk mRNA, genomic DNA or on paired (heavy-light) mRNA; BCR repertoire analysis generally involves clustering BCRs into specificity groups or more in-depth modeling of antibody-antigen interactions, such as antibody-specific epitope predictions; validation of antibody-antigen interactions requires expression of antibodies, followed by antigen binding assays or epitope mapping. Together with innovations in Deep learning these technologies will contribute to the future discovery of diagnostic and therapeutic antibodies directly from humans.
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Affiliation(s)
- Zichang Xu
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hendra S. Ismanto
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hao Zhou
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Dianita S. Saputri
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Fuminori Sugihara
- Core Instrumentation Facility, Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Daron M. Standley
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Department Systems Immunology, Immunology Frontier Research Center, Osaka University, Suita, Japan
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25
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Barnes CO, Schoofs T, Gnanapragasam PN, Golijanin J, Huey-Tubman KE, Gruell H, Schommers P, Suh-Toma N, Lee YE, Cetrulo Lorenzi JC, Piechocka-Trocha A, Scheid JF, West AP, Walker BD, Seaman MS, Klein F, Nussenzweig MC, Bjorkman PJ. A naturally arising broad and potent CD4-binding site antibody with low somatic mutation. SCIENCE ADVANCES 2022; 8:eabp8155. [PMID: 35960796 PMCID: PMC9374330 DOI: 10.1126/sciadv.abp8155] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 06/29/2022] [Indexed: 05/05/2023]
Abstract
The induction of broadly neutralizing antibodies (bNAbs) is a potential strategy for a vaccine against HIV-1. However, most bNAbs exhibit features such as unusually high somatic hypermutation, including insertions and deletions, which make their induction challenging. VRC01-class bNAbs not only exhibit extraordinary breadth and potency but also rank among the most highly somatically mutated bNAbs. Here, we describe a VRC01-class antibody isolated from a viremic controller, BG24, that is much less mutated than most relatives of its class while achieving comparable breadth and potency. A 3.8-Å x-ray crystal structure of a BG24-BG505 Env trimer complex revealed conserved contacts at the gp120 interface characteristic of the VRC01-class Abs, despite lacking common CDR3 sequence motifs. The existence of moderately mutated CD4-binding site (CD4bs) bNAbs such as BG24 provides a simpler blueprint for CD4bs antibody induction by a vaccine, raising the prospect that such an induction might be feasible with a germline-targeting approach.
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Affiliation(s)
- Christopher O. Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Till Schoofs
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, 50931 Cologne, Germany
| | | | - Jovana Golijanin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Kathryn E. Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Henning Gruell
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, 50931 Cologne, Germany
| | - Philipp Schommers
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, 50931 Cologne, Germany
- Department I of Internal Medicine, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
| | - Nina Suh-Toma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yu Erica Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Alicja Piechocka-Trocha
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02129, USA
| | - Johannes F. Scheid
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Bruce D. Walker
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02129, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital of Cologne, University of Cologne, 50931 Cologne, Germany
- German Center for Infection Research, partner site Bonn–Cologne, 50931 Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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26
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Ou BS, Saouaf OM, Baillet J, Appel EA. Sustained delivery approaches to improving adaptive immune responses. Adv Drug Deliv Rev 2022; 187:114401. [PMID: 35750115 DOI: 10.1016/j.addr.2022.114401] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 11/17/2022]
Abstract
The immune system is one of the most important, complex biological networks regulating and protecting human health. Its precise modulation can prevent deadly infections and fight cancer. Accordingly, prophylactic vaccines and cancer immunotherapies are some of the most powerful technologies to protect against potential dangers through training of the immune system. Upon immunization, activation and maturation of B and T cells of the adaptive immune system are necessary for development of proper humoral and cellular protection. Yet, the exquisite organization of the immune system requires spatiotemporal control over the exposure of immunomodulatory signals. For example, while the human immune system has evolved to develop immunity to natural pathogenic infections that often last for weeks, current prophylactic vaccination technologies only expose the immune system to immunomodulatory signals for hours to days. It has become clear that leveraging sustained release technologies to prolong immunogen and adjuvant exposure can increase the potency, durability, and quality of adaptive immune responses. Over the past several years, tremendous breakthroughs have been made in the design of novel biomaterials such as nanoparticles, microparticles, hydrogels, and microneedles that can precisely control and the presentation of immunomodulatory signals to the immune system. In this review, we discuss relevant sustained release strategies and their corresponding benefits to cellular and humoral responses.
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Affiliation(s)
- Ben S Ou
- Department of Bioengineering, Stanford University, Stanford 94305, USA
| | - Olivia M Saouaf
- Department of Materials Science & Engineering, Stanford University, Stanford 94305, USA
| | - Julie Baillet
- Department of Materials Science & Engineering, Stanford University, Stanford 94305, USA; University of Bordeaux, CNRS, Bordeaux INP, LCPO, UMR 5629, Pessac 33600, France
| | - Eric A Appel
- Department of Bioengineering, Stanford University, Stanford 94305, USA; Department of Materials Science & Engineering, Stanford University, Stanford 94305, USA; Department of Pediatrics (Endocrinology), Stanford University, Stanford 94305, USA; ChEM-H Institute, Stanford University, Stanford CA 94305, USA; Woods Institute for the Environment, Stanford University, Stanford, CA 94305, USA.
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27
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Contribution of rare mutational outcomes to broadly neutralizing antibodies. Acta Biochim Biophys Sin (Shanghai) 2022; 54:820-827. [PMID: 35713319 PMCID: PMC9828561 DOI: 10.3724/abbs.2022065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Antibodies are important immune molecules that are elicited by B cells to protect our bodies during viral infections or vaccinations. In humans, the antibody repertoire is diversified by programmed DNA lesion processes to ensure specific and high affinity binding to various antigens. Broadly neutralizing antibodies (bnAbs) are antibodies that have strong neutralizing activities against different variants of a virus. bnAbs such as anti-HIV bnAbs often have special characteristics including insertions and deletions, long complementarity determining region 3 (CDR3), and high frequencies of mutations, often at improbable sites of the variable regions. These unique features are rare mutational outcomes that are acquired during antibody diversification processes. In this review, we will discuss possible mechanisms that generate these rare antibody mutational outcomes. The understanding of the mechanisms that generate these rare mutational outcomes during antibody diversification will have implications in vaccine design strategies to elicit bnAbs.
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28
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Gonzales SJ, Clarke KN, Batugedara G, Garza R, Braddom AE, Reyes RA, Ssewanyana I, Garrison KC, Ippolito GC, Greenhouse B, Bol S, Bunnik EM. A Molecular Analysis of Memory B Cell and Antibody Responses Against Plasmodium falciparum Merozoite Surface Protein 1 in Children and Adults From Uganda. Front Immunol 2022; 13:809264. [PMID: 35720313 PMCID: PMC9201334 DOI: 10.3389/fimmu.2022.809264] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 05/05/2022] [Indexed: 01/18/2023] Open
Abstract
Memory B cells (MBCs) and plasma antibodies against Plasmodium falciparum (Pf) merozoite antigens are important components of the protective immune response against malaria. To gain understanding of how responses against Pf develop in these two arms of the humoral immune system, we evaluated MBC and antibody responses against the most abundant merozoite antigen, full-length Pf merozoite surface protein 1 (PfMSP1FL), in individuals from a region in Uganda with high Pf transmission. Our results showed that PfMSP1FL-specific B cells in adults with immunological protection against malaria were predominantly IgG+ classical MBCs, while children with incomplete protection mainly harbored IgM+ PfMSP1FL-specific classical MBCs. In contrast, anti-PfMSP1FL plasma IgM reactivity was minimal in both children and adults. Instead, both groups showed high plasma IgG reactivity against PfMSP1FL, with broadening of the response against non-3D7 strains in adults. The B cell receptors encoded by PfMSP1FL-specific IgG+ MBCs carried high levels of amino acid substitutions and recognized relatively conserved epitopes on the highly variable PfMSP1 protein. Proteomics analysis of PfMSP119-specific IgG in plasma of an adult revealed a limited repertoire of anti-MSP1 antibodies, most of which were IgG1 or IgG3. Similar to B cell receptors of PfMSP1FL-specific MBCs, anti-PfMSP119 IgGs had high levels of amino acid substitutions and their sequences were predominantly found in classical MBCs, not atypical MBCs. Collectively, these results showed evolution of the PfMSP1-specific humoral immune response with cumulative Pf exposure, with a shift from IgM+ to IgG+ B cell memory, diversification of B cells from germline, and stronger recognition of PfMSP1 variants by the plasma IgG repertoire.
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Affiliation(s)
- S. Jake Gonzales
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Kathleen N. Clarke
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Gayani Batugedara
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Rolando Garza
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Ashley E. Braddom
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Raphael A. Reyes
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Isaac Ssewanyana
- Infectious Disease Research Collaboration, Kampala, Uganda
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Kendra C. Garrison
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, United States
| | - Gregory C. Ippolito
- Department of Molecular Biosciences and Department of Oncology, Dell Medical School, University of Texas at Austin, Austin, TX, United States
| | - Bryan Greenhouse
- Department of Medicine, University of California San Francisco, San Francisco, CA, United States
| | - Sebastiaan Bol
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Evelien M. Bunnik
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
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29
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He WT, Musharrafieh R, Song G, Dueker K, Tse LV, Martinez DR, Schäfer A, Callaghan S, Yong P, Beutler N, Torres JL, Volk RM, Zhou P, Yuan M, Liu H, Anzanello F, Capozzola T, Parren M, Garcia E, Rawlings SA, Smith DM, Wilson IA, Safonova Y, Ward AB, Rogers TF, Baric RS, Gralinski LE, Burton DR, Andrabi R. Targeted isolation of diverse human protective broadly neutralizing antibodies against SARS-like viruses. Nat Immunol 2022; 23:960-970. [PMID: 35654851 PMCID: PMC10083051 DOI: 10.1038/s41590-022-01222-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/20/2022] [Indexed: 01/09/2023]
Abstract
The emergence of current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) and potential future spillovers of SARS-like coronaviruses into humans pose a major threat to human health and the global economy. Development of broadly effective coronavirus vaccines that can mitigate these threats is needed. Here, we utilized a targeted donor selection strategy to isolate a large panel of human broadly neutralizing antibodies (bnAbs) to sarbecoviruses. Many of these bnAbs are remarkably effective in neutralizing a diversity of sarbecoviruses and against most SARS-CoV-2 VOCs, including the Omicron variant. Neutralization breadth is achieved by bnAb binding to epitopes on a relatively conserved face of the receptor-binding domain (RBD). Consistent with targeting of conserved sites, select RBD bnAbs exhibited protective efficacy against diverse SARS-like coronaviruses in a prophylaxis challenge model in vivo. These bnAbs provide new opportunities and choices for next-generation antibody prophylactic and therapeutic applications and provide a molecular basis for effective design of pan-sarbecovirus vaccines.
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Affiliation(s)
- Wan-Ting He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
| | - Rami Musharrafieh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
| | - Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
| | - Katharina Dueker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
| | - Longping V Tse
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David R Martinez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sean Callaghan
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
| | - Peter Yong
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Reid M Volk
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Panpan Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Fabio Anzanello
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
| | - Tazio Capozzola
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
| | - Mara Parren
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Elijah Garcia
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Stephen A Rawlings
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Davey M Smith
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ian A Wilson
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Yana Safonova
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Andrew B Ward
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Thomas F Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Departments of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Lisa E Gralinski
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA.
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
- International AIDS Vaccine Initiative Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA.
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30
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Broadly neutralizing antibodies against HIV-1 and concepts for application. Curr Opin Virol 2022; 54:101211. [DOI: 10.1016/j.coviro.2022.101211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/22/2022] [Accepted: 02/27/2022] [Indexed: 12/21/2022]
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31
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Chang AJ, Baron S, Hoffman J, Hicar MD. Clonal expansion and markers of directed mutation of IGHV4-34 B cells in plasmablasts during Kawasaki disease. Mol Immunol 2022; 145:67-77. [PMID: 35303530 PMCID: PMC9166636 DOI: 10.1016/j.molimm.2022.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 02/18/2022] [Accepted: 03/06/2022] [Indexed: 11/26/2022]
Abstract
Kawasaki disease (KD) is the leading cause of acquired heart disease in children. The cause remains unknown; however, epidemiologic and demographic data support a single preceding infectious agent may lead to KD. A variety of pathophysiologic responses have been proposed, including direct invasion of the coronary arteries, a superantigen response, and a post-infectious autoimmune phenomenon. A role for B cell responses during KD are supported by numerous findings including B cell specific markers identified in genome wide association studies. We have recently published data showing children with KD have similar plasmablast (PB) responses to children with infections. Since during other infections, cells expressing antibodies against the preceding infection are enriched in PBs, we sought to explore the specific antibodies encoded by PBs during KD. In one child we see a massive expansion in IGHV4-34 utilizing antibodies, which has been associated with autoimmunity in the past. We further explored this expansion of IGHV4-34 utilization during the peripheral PB rise with next generation sequencing (NGS) analysis and utilizing newer techniques of chromium chip single cell separation (10x Genomics®). We also utilized peptide array screening to attempt to identify an antigen to the most prolific clones.
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Affiliation(s)
| | - Sarah Baron
- University at Buffalo, Department of Pediatrics, USA
| | | | - Mark D Hicar
- University at Buffalo, Department of Pediatrics, USA.
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32
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He WT, Musharrafieh R, Song G, Dueker K, Tse LV, Martinez DR, Schäfer A, Callaghan S, Yong P, Beutler N, Torres JL, Volk RM, Zhou P, Yuan M, Liu H, Anzanello F, Capozzola T, Parren M, Garcia E, Rawlings SA, Smith DM, Wilson IA, Safonova Y, Ward AB, Rogers TF, Baric RS, Gralinski LE, Burton DR, Andrabi R. Targeted isolation of panels of diverse human protective broadly neutralizing antibodies against SARS-like viruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2021.09.08.459480. [PMID: 35169804 PMCID: PMC8845431 DOI: 10.1101/2021.09.08.459480] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The emergence of current SARS-CoV-2 variants of concern (VOCs) and potential future spillovers of SARS-like coronaviruses into humans pose a major threat to human health and the global economy 1-7 . Development of broadly effective coronavirus vaccines that can mitigate these threats is needed 8, 9 . Notably, several recent studies have revealed that vaccination of recovered COVID-19 donors results in enhanced nAb responses compared to SARS-CoV-2 infection or vaccination alone 10-13 . Here, we utilized a targeted donor selection strategy to isolate a large panel of broadly neutralizing antibodies (bnAbs) to sarbecoviruses from two such donors. Many of the bnAbs are remarkably effective in neutralization against sarbecoviruses that use ACE2 for viral entry and a substantial fraction also show notable binding to non-ACE2-using sarbecoviruses. The bnAbs are equally effective against most SARS-CoV-2 VOCs and many neutralize the Omicron variant. Neutralization breadth is achieved by bnAb binding to epitopes on a relatively conserved face of the receptor binding domain (RBD) as opposed to strain-specific nAbs to the receptor binding site that are commonly elicited in SARS-CoV-2 infection and vaccination 14-18 . Consistent with targeting of conserved sites, select RBD bnAbs exhibited in vivo protective efficacy against diverse SARS-like coronaviruses in a prophylaxis challenge model. The generation of a large panel of potent bnAbs provides new opportunities and choices for next-generation antibody prophylactic and therapeutic applications and, importantly, provides a molecular basis for effective design of pan-sarbecovirus vaccines.
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Affiliation(s)
- Wan-ting He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rami Musharrafieh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ge Song
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Katharina Dueker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Longping V. Tse
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - David R. Martinez
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alexandra Schäfer
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sean Callaghan
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Peter Yong
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jonathan L. Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Reid M. Volk
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Panpan Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hejun Liu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Fabio Anzanello
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Tazio Capozzola
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mara Parren
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Elijah Garcia
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Stephen A. Rawlings
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Davey M. Smith
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Ian A. Wilson
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 9203
| | - Yana Safonova
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Andrew B. Ward
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Thomas F. Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Ralph S. Baric
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Departments of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lisa E. Gralinski
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dennis R. Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA 02139, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA 92037, USA
- Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, CA 92037, USA
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33
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Frazzini S, Amadori M, Turin L, Riva F. SARS CoV-2 infections in animals, two years into the pandemic. Arch Virol 2022; 167:2503-2517. [PMID: 36207554 PMCID: PMC9543933 DOI: 10.1007/s00705-022-05609-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 08/19/2022] [Indexed: 12/14/2022]
Abstract
In December 2019, several cases of pneumonia caused by a novel coronavirus, later identified as SARS-CoV-2, were detected in the Chinese city of Wuhan. Due to its rapid worldwide spread, on 11 March 2020 the World Health Organization declared a pandemic state. Since this new virus is genetically similar to the coronaviruses of bats, SARS-CoV-2 was hypothesized to have a zoonotic origin. Within a year of the appearance of SARS-CoV-2, several cases of infection were also reported in animals, suggesting human-to-animal and animal-to-animal transmission among mammals. Natural infection has been found in companion animals as well as captive animals such as lions, tigers, and gorillas. Among farm animals, so far, minks have been found to be susceptible to SARS-CoV-2 infection, whereas not all the relevant studies agree on the susceptibility of pigs. Experimental infections have documented the susceptibility to SARS-CoV-2 of further animal species, including mice, hamsters, cats, dogs, ferrets, raccoon dogs, cattle, and non-human primates. Experimental infections have proven crucial for clarifying the role of animals in transmission and developing models for viral pathogenesis and immunotherapy. On the whole, this review aims to update and critically revise the current information on natural and experimental SARS-CoV-2 infections in animals.
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Affiliation(s)
- Sara Frazzini
- Department of Veterinary Medicine (DIMEVET), University of Milan, Milan, Italy
| | | | - Lauretta Turin
- Department of Veterinary Medicine (DIMEVET), University of Milan, Milan, Italy
| | - Federica Riva
- Department of Veterinary Medicine (DIMEVET), University of Milan, Milan, Italy
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34
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Williams WB, Wiehe K, Saunders KO, Haynes BF. Strategies for induction of HIV-1 envelope-reactive broadly neutralizing antibodies. J Int AIDS Soc 2021; 24 Suppl 7:e25831. [PMID: 34806332 PMCID: PMC8606870 DOI: 10.1002/jia2.25831] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/23/2021] [Indexed: 12/30/2022] Open
Abstract
INTRODUCTION A primary focus of HIV-1 vaccine development is the activation of B cell receptors for naïve or precursor broadly neutralizing antibodies (bnAbs), followed by expansion and maturation of bnAb B cell lineage intermediates leading to highly affinity-matured bnAbs. HIV-1 envelope (Env) encodes epitopes for bnAbs of different specificities. Design of immunogens to induce bnAb precursors of different specificities and mature them into bnAb status is a goal for HIV-1 vaccine development. We review vaccine strategies for bnAb lineages development and highlight the immunological barriers that these strategies must overcome to generate bnAbs. METHODS We provide perspectives based on published research articles and reviews. DISCUSSION The recent Antibody Mediated Protection (AMP) trial that tested the protective efficacy of one HIV-1 Env bnAb specificity demonstrated that relatively high levels of long-lasting serum titers of multiple specificities of bnAbs will be required for protection from HIV-1 transmission. Current vaccine efforts for induction of bnAb lineages are focused on immunogens designed to expand naïve HIV-1 bnAb precursor B cells following the recent success of vaccine-induction of bnAb precursor B cells in macaques and humans. BnAb precursor B cells serve as templates for priming-immunogen design. However, design of boosting immunogens for bnAb maturation requires knowledge of the optimal immunogen design and immunological environment for bnAb B cell lineage affinity maturation. BnAb lineages acquire rare genetic changes as mutations during B cell maturation. Moreover, the immunological environment that supports bnAb development during HIV-1 infection is perturbed with an altered B cell repertoire and dysfunctional immunoregulatory controls, suggesting that in normal settings, bnAb development will be disfavoured. Thus, strategies for vaccine induction of bnAbs must circumvent immunological barriers for bnAb development that normally constrain bnAb B cell affinity maturation. CONCLUSIONS A fully protective HIV-1 vaccine needs to induce durable high titers of bnAbs that can be generated by a sequential set of Env immunogens for expansion and maturation of bnAb B cell lineages in a permitted immunological environment. Moreover, multiple specificities of bnAbs will be required to be sufficiently broad to prevent the escape of HIV-1 strains during transmission.
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Affiliation(s)
- Wilton B. Williams
- Human Vaccine InstituteDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of SurgeryDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Kevin Wiehe
- Human Vaccine InstituteDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Kevin O. Saunders
- Human Vaccine InstituteDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of SurgeryDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of ImmunologyDuke University School of MedicineDurhamNorth CarolinaUSA
| | - Barton F. Haynes
- Human Vaccine InstituteDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of MedicineDuke University School of MedicineDurhamNorth CarolinaUSA
- Department of ImmunologyDuke University School of MedicineDurhamNorth CarolinaUSA
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35
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Braddom AE, Bol S, Gonzales SJ, Reyes RA, Musinguzi K, Nankya F, Ssewanyana I, Greenhouse B, Bunnik EM. B Cell Receptor Repertoire Analysis in Malaria-Naive and Malaria-Experienced Individuals Reveals Unique Characteristics of Atypical Memory B Cells. mSphere 2021; 6:e0072621. [PMID: 34523978 PMCID: PMC8550134 DOI: 10.1128/msphere.00726-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 08/31/2021] [Indexed: 11/24/2022] Open
Abstract
Malaria, caused by parasites of the Plasmodium genus, is responsible for significant morbidity and mortality globally. Chronic Plasmodium falciparum exposure affects the B cell compartment, leading to the accumulation of atypical memory B cells (atMBCs). IgM-positive (IgM+) and IgG+ atMBCs have not been compared in-depth in the context of malaria, nor is it known if atMBCs in malaria-experienced individuals are different from phenotypically similar B cells in individuals with no known history of Plasmodium exposure. To address these questions, we characterized the B cell receptor (BCR) repertoire of naive B cells (NBCs), IgM+ and IgG+ classical MBCs (cMBCs), and IgM+ and IgG+ atMBCs from 13 malaria-naive American adults and 7 malaria-experienced Ugandan adults. Our results demonstrate that P. falciparum exposure mainly drives changes in atMBCs. In comparison to malaria-naive adults, the BCR repertoire of Plasmodium-exposed adults showed increased levels of somatic hypermutation in the heavy chain V region in IgM+ and IgG+ atMBCs, shorter heavy chain complementarity-determining region 3 (HCDR3) in IgG+ atMBCs, and increased usage of IGHV3-73 in IgG+ cMBCs and both IgM+ and IgG+ atMBCs. Irrespective of Plasmodium exposure, IgM+ atMBCs closely resembled NBCs, while IgG+ atMBCs resembled IgG+ cMBCs. Physicochemical properties of the HCDR3 seemed to be intrinsic to cell type and independent of malaria experience. The resemblance between atMBCs from Plasmodium-exposed and naive adults suggests similar differentiation pathways regardless of chronic antigen exposure. Moreover, these data demonstrate that IgM+ and IgG+ atMBCs are distinct populations that should be considered separately in future analyses. IMPORTANCE Malaria, caused by Plasmodium parasites, still contributes to a high global burden of disease, mainly in children under 5 years of age. Chronic and recurrent Plasmodium infections affect the development of B cell memory against the parasite and promote the accumulation of atypical memory B cells (atMBCs), which have an unclear function in the immune response. Understanding where these cells originate from and whether they are beneficial in the immune response to Plasmodium will help inform vaccination development efforts. We found differences in B cell receptor (BCR) properties of atMBCs between malaria-naive and malaria-experienced adults that are suggestive of divergent selection processes, resulting in more somatic hypermutation and differential immunoglobulin heavy chain V (IGHV) gene usage. Despite these differences, atMBCs from malaria-naive and malaria-experienced adults also showed many similarities in BCR characteristics, such as physicochemical properties of the HCDR3 region, suggesting that atMBCs undergo similar differentiation pathways in response to different pathogens. Our study provides new insights into the effects of malaria experience on the B cell compartment and the relationships between atMBCs and other B cell populations.
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Affiliation(s)
- Ashley E. Braddom
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Sebastiaan Bol
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - S. Jake Gonzales
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Raphael A. Reyes
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | | | | | - Isaac Ssewanyana
- Infectious Disease Research Collaboration, Kampala, Uganda
- London School of Hygiene and Tropical Medicine, London, UK
| | - Bryan Greenhouse
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Evelien M. Bunnik
- Department of Microbiology, Immunology and Molecular Genetics, Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
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36
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Zhang Y, Chen T, Zeng H, Yang X, Xu Q, Zhang Y, Chen Y, Wang M, Zhu Y, Lan C, Wang Q, Tang H, Zhang Y, Wang C, Xie W, Ma C, Guan J, Guo S, Chen S, Yang W, Wei L, Ren J, Yu X, Zhang Z. RAPID: A Rep-Seq Dataset Analysis Platform With an Integrated Antibody Database. Front Immunol 2021; 12:717496. [PMID: 34484220 PMCID: PMC8414647 DOI: 10.3389/fimmu.2021.717496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022] Open
Abstract
The antibody repertoire is a critical component of the adaptive immune system and is believed to reflect an individual’s immune history and current immune status. Delineating the antibody repertoire has advanced our understanding of humoral immunity, facilitated antibody discovery, and showed great potential for improving the diagnosis and treatment of disease. However, no tool to date has effectively integrated big Rep-seq data and prior knowledge of functional antibodies to elucidate the remarkably diverse antibody repertoire. We developed a Rep-seq dataset Analysis Platform with an Integrated antibody Database (RAPID; https://rapid.zzhlab.org/), a free and web-based tool that allows researchers to process and analyse Rep-seq datasets. RAPID consolidates 521 WHO-recognized therapeutic antibodies, 88,059 antigen- or disease-specific antibodies, and 306 million clones extracted from 2,449 human IGH Rep-seq datasets generated from individuals with 29 different health conditions. RAPID also integrates a standardized Rep-seq dataset analysis pipeline to enable users to upload and analyse their datasets. In the process, users can also select set of existing repertoires for comparison. RAPID automatically annotates clones based on integrated therapeutic and known antibodies, and users can easily query antibodies or repertoires based on sequence or optional keywords. With its powerful analysis functions and rich set of antibody and antibody repertoire information, RAPID will benefit researchers in adaptive immune studies.
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Affiliation(s)
- Yanfang Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China.,Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Tianjian Chen
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Huikun Zeng
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China.,Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiujia Yang
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China.,Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Qingxian Xu
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yanxia Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yuan Chen
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Minhui Wang
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Nephrology, Hainan General Hospital, Haikou, China.,Hainan Affiliated Hospital of Hainan Medical College, Haikou, China
| | - Yan Zhu
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Chunhong Lan
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Qilong Wang
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Haipei Tang
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yan Zhang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Chengrui Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wenxi Xie
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Cuiyu Ma
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Junjie Guan
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Shixin Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Sen Chen
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wei Yang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
| | - Jian Ren
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xueqing Yu
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Division of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhenhai Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.,Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China.,Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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37
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Mu Z, Wiehe K, Saunders KO, Henderson R, Cain DW, Parks R, Martik D, Mansouri K, Edwards RJ, Newman A, Lu X, Xia SM, Bonsignori M, Montefiori D, Han Q, Venkatayogi S, Evangelous T, Wang Y, Rountree W, Tam Y, Barbosa C, Alam SM, Williams WB, Pardi N, Weissman D, Haynes BF. Ability of nucleoside-modified mRNA to encode HIV-1 envelope trimer nanoparticles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.08.09.455714. [PMID: 34401876 PMCID: PMC8366792 DOI: 10.1101/2021.08.09.455714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The success of nucleoside-modified mRNAs in lipid nanoparticles (mRNA-LNP) as COVID-19 vaccines heralded a new era of vaccine development. For HIV-1, multivalent envelope (Env) trimer protein nanoparticles are superior immunogens compared to trimers alone for priming of broadly neutralizing antibody (bnAb) B cell lineages. The successful expression of complex multivalent nanoparticle immunogens with mRNAs has not been demonstrated. Here we show that mRNAs can encode antigenic Env trimers on ferritin nanoparticles that initiate bnAb precursor B cell expansion and induce serum autologous tier 2 neutralizing activity in bnAb precursor VH + VL knock-in mice. Next generation sequencing demonstrated acquisition of critical mutations, and monoclonal antibodies that neutralized heterologous HIV-1 isolates were isolated. Thus, mRNA-LNP can encode complex immunogens and are of use in design of germline-targeting and sequential boosting immunogens for HIV-1 vaccine development.
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Affiliation(s)
- Zekun Mu
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kevin O. Saunders
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Rory Henderson
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Derek W. Cain
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Diana Martik
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Katayoun Mansouri
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert J. Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amanda Newman
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Xiaozhi Lu
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Shi-Mao Xia
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
- Current Address: Translational Immunobiology Unit, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, US
| | - David Montefiori
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Qifeng Han
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sravani Venkatayogi
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Tyler Evangelous
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yunfei Wang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wes Rountree
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | | | | | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wilton B. Williams
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Norbert Pardi
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Drew Weissman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Barton F. Haynes
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
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38
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Williams WB, Meyerhoff RR, Edwards RJ, Li H, Manne K, Nicely NI, Henderson R, Zhou Y, Janowska K, Mansouri K, Gobeil S, Evangelous T, Hora B, Berry M, Abuahmad AY, Sprenz J, Deyton M, Stalls V, Kopp M, Hsu AL, Borgnia MJ, Stewart-Jones GBE, Lee MS, Bronkema N, Moody MA, Wiehe K, Bradley T, Alam SM, Parks RJ, Foulger A, Oguin T, Sempowski GD, Bonsignori M, LaBranche CC, Montefiori DC, Seaman M, Santra S, Perfect J, Francica JR, Lynn GM, Aussedat B, Walkowicz WE, Laga R, Kelsoe G, Saunders KO, Fera D, Kwong PD, Seder RA, Bartesaghi A, Shaw GM, Acharya P, Haynes BF. Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies. Cell 2021; 184:2955-2972.e25. [PMID: 34019795 PMCID: PMC8135257 DOI: 10.1016/j.cell.2021.04.042] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/22/2021] [Accepted: 04/23/2021] [Indexed: 01/03/2023]
Abstract
Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) as a model antigen. 2G12 is a broadly neutralizing Ab (bnAb) that targets a conserved glycan patch on Env of geographically diverse HIV-1 strains using a unique heavy-chain (VH) domain-swapped architecture that results in fragment antigen-binding (Fab) dimerization. Here, we describe HIV-1 Env Fab-dimerized glycan (FDG)-reactive bnAbs without VH-swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques. FDG Abs also recognized cell-surface glycans on diverse pathogens, including yeast and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike. FDG precursors were expanded by glycan-bearing immunogens in macaques and were abundant in HIV-1-naive humans. Moreover, FDG precursors were predominately mutated IgM+IgD+CD27+, thus suggesting that they originated from a pool of antigen-experienced IgM+ or marginal zone B cells.
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Affiliation(s)
- Wilton B Williams
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA.
| | - R Ryan Meyerhoff
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - R J Edwards
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Hui Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kartik Manne
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | | | - Rory Henderson
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Ye Zhou
- Department of Computer Science, Duke University, Durham, NC 27708, USA
| | | | | | | | | | - Bhavna Hora
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | | | | | | | | | | | - Megan Kopp
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Allen L Hsu
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, NIEHS, NIH, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
| | | | - Matthew S Lee
- Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Naomi Bronkema
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA
| | - M Anthony Moody
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA; Department of Pediatrics, Duke University, Durham, NC 27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Todd Bradley
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - S Munir Alam
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | | | | | - Thomas Oguin
- Duke Human Vaccine Institute, Durham, NC 27710, USA
| | - Gregory D Sempowski
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Mattia Bonsignori
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Michael Seaman
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Sampa Santra
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - John Perfect
- Department of Medicine, Duke University, Durham, NC 27710, USA
| | | | - Geoffrey M Lynn
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA; Avidea Technologies, Inc., Baltimore, MD, USA
| | | | | | - Richard Laga
- Institute of Macromolecular Chemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Garnett Kelsoe
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA
| | - Daniela Fera
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA
| | - Peter D Kwong
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Robert A Seder
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Alberto Bartesaghi
- Department of Computer Science, Duke University, Durham, NC 27708, USA; Department of Biochemistry, Duke University, Durham, NC 27705, USA; Department of Electrical and Computer Engineering, Duke University, Durham, NC 27708, USA
| | - George M Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Surgery, Duke University, Durham, NC 27710, USA.
| | - Barton F Haynes
- Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA; Department of Immunology, Duke University, Durham, NC 27710, USA.
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39
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Cizmeci D, Lofano G, Rossignol E, Dugast AS, Kim D, Cavet G, Nguyen N, Tan YC, Seaman MS, Alter G, Julg B. Distinct clonal evolution of B-cells in HIV controllers with neutralizing antibody breadth. eLife 2021; 10:62648. [PMID: 33843586 PMCID: PMC8041465 DOI: 10.7554/elife.62648] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 04/02/2021] [Indexed: 01/16/2023] Open
Abstract
A minor subset of individuals infected with HIV-1 develop antibody neutralization breadth during the natural course of the infection, often linked to chronic, high-level viremia. Despite significant efforts, vaccination strategies have been unable to induce similar neutralization breadth and the mechanisms underlying neutralizing antibody induction remain largely elusive. Broadly neutralizing antibody responses can also be found in individuals who control HIV to low and even undetectable plasma levels in the absence of antiretroviral therapy, suggesting that high antigen exposure is not a strict requirement for neutralization breadth. We therefore performed an analysis of paired heavy and light chain B-cell receptor (BCR) repertoires in 12,591 HIV-1 envelope-specific single memory B-cells to determine alterations in the BCR immunoglobulin gene repertoire and B-cell clonal expansions that associate with neutralizing antibody breadth in 22 HIV controllers. We found that the frequency of genomic mutations in IGHV and IGLV was directly correlated with serum neutralization breadth. The repertoire of the most mutated antibodies was dominated by a small number of large clones with evolutionary signatures suggesting that these clones had reached peak affinity maturation. These data demonstrate that even in the setting of low plasma HIV antigenemia, similar to what a vaccine can potentially achieve, BCR selection for extended somatic hypermutation and clonal evolution can occur in some individuals suggesting that host-specific factors might be involved that could be targeted with future vaccine strategies.
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Affiliation(s)
- Deniz Cizmeci
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | - Giuseppe Lofano
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | - Evan Rossignol
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | | | | | - Guy Cavet
- Atreca Inc, Redwood City, United States
| | | | | | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, United States
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
| | - Boris Julg
- Ragon Institute of MGH, MIT and Harvard, Cambridge, United States
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40
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Townsley SM, Donofrio GC, Jian N, Leggat DJ, Dussupt V, Mendez-Rivera L, Eller LA, Cofer L, Choe M, Ehrenberg PK, Geretz A, Gift S, Grande R, Lee A, Peterson C, Piechowiak MB, Slike BM, Tran U, Joyce MG, Georgiev IS, Rolland M, Thomas R, Tovanabutra S, Doria-Rose NA, Polonis VR, Mascola JR, McDermott AB, Michael NL, Robb ML, Krebs SJ. B cell engagement with HIV-1 founder virus envelope predicts development of broadly neutralizing antibodies. Cell Host Microbe 2021; 29:564-578.e9. [PMID: 33662277 DOI: 10.1016/j.chom.2021.01.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 12/08/2020] [Accepted: 01/27/2021] [Indexed: 12/22/2022]
Abstract
Determining which immunological mechanisms contribute to the development of broad neutralizing antibodies (bNAbs) during HIV-1 infection is a major goal to inform vaccine design. Using samples from a longitudinal HIV-1 acute infection cohort, we found key B cell determinants within the first 14-43 days of viremia that predict the development of bNAbs years later. Individuals who develop neutralization breadth had significantly higher B cell engagement with the autologous founder HIV envelope (Env) within 1 month of initial viremia. A higher frequency of founder-Env-specific naive B cells was associated with increased B cell activation and differentiation and predictive of bNAb development. These data demonstrate that the initial B cell interaction with the founder HIV Env is important for the development of broadly neutralizing antibodies and provide evidence that events within HIV acute infection lead to downstream functional outcomes.
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Affiliation(s)
- Samantha M Townsley
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Gina C Donofrio
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Ningbo Jian
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - David J Leggat
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Vincent Dussupt
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Letzibeth Mendez-Rivera
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Leigh Anne Eller
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Lauryn Cofer
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Misook Choe
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA; Emerging Infectious Diseases Branch, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Philip K Ehrenberg
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Aviva Geretz
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Syna Gift
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Rebecca Grande
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Anna Lee
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Caroline Peterson
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA; Emerging Infectious Diseases Branch, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Mary Bryson Piechowiak
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Bonnie M Slike
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Ursula Tran
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - M Gordon Joyce
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA; Emerging Infectious Diseases Branch, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Ivelin S Georgiev
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Morgane Rolland
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | | | - Victoria R Polonis
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - John R Mascola
- Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | | | - Nelson L Michael
- Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Merlin L Robb
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Shelly J Krebs
- U.S. Military HIV Research Program, Center of Infectious Disease Research, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA.
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41
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Forgacs D, Abreu RB, Sautto GA, Kirchenbaum GA, Drabek E, Williamson KS, Kim D, Emerling DE, Ross TM. Convergent antibody evolution and clonotype expansion following influenza virus vaccination. PLoS One 2021; 16:e0247253. [PMID: 33617543 PMCID: PMC7899375 DOI: 10.1371/journal.pone.0247253] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/03/2021] [Indexed: 12/14/2022] Open
Abstract
Recent advances in high-throughput single cell sequencing have opened up new avenues into the investigation of B cell receptor (BCR) repertoires. In this study, PBMCs were collected from 17 human participants vaccinated with the split-inactivated influenza virus vaccine during the 2016-2017 influenza season. A combination of Immune Repertoire Capture (IRCTM) technology and IgG sequencing was performed on ~7,800 plasmablast (PB) cells and preferential IgG heavy-light chain pairings were investigated. In some participants, a single expanded clonotype accounted for ~22% of their PB BCR repertoire. Approximately 60% (10/17) of participants experienced convergent evolution, possessing public PBs that were elicited independently in multiple participants. Binding profiles of one private and three public PBs confirmed they were all subtype-specific, cross-reactive hemagglutinin (HA) head-directed antibodies. Collectively, this high-resolution antibody repertoire analysis demonstrated the impact evolution can have on BCRs in response to influenza virus vaccination, which can guide future universal influenza prophylactic approaches.
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Affiliation(s)
- David Forgacs
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
| | - Rodrigo B. Abreu
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
| | - Giuseppe A. Sautto
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
| | - Greg A. Kirchenbaum
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
| | - Elliott Drabek
- Atreca, Inc., South San Francisco, CA, United States of America
| | | | - Dongkyoon Kim
- Atreca, Inc., South San Francisco, CA, United States of America
| | | | - Ted M. Ross
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States of America
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States of America
- * E-mail:
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42
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Raybould MIJ, Rees AR, Deane CM. Current strategies for detecting functional convergence across B-cell receptor repertoires. MAbs 2021; 13:1996732. [PMID: 34781829 PMCID: PMC8604390 DOI: 10.1080/19420862.2021.1996732] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 10/10/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022] Open
Abstract
Convergence across B-cell receptor (BCR) and antibody repertoires has become instrumental in prioritizing candidates in recent rapid therapeutic antibody discovery campaigns. It has also increased our understanding of the immune system, providing evidence for the preferential selection of BCRs to particular (immunodominant) epitopes post vaccination/infection. These important implications for both drug discovery and immunology mean that it is essential to consider the optimal way to combine experimental and computational technology when probing BCR repertoires for convergence signatures. Here, we discuss the theoretical basis for observing BCR repertoire functional convergence and explore factors of study design that can impact functional signal. We also review the computational arsenal available to detect antibodies with similar functional properties, highlighting opportunities enabled by recent clustering algorithms that exploit structural similarities between BCRs. Finally, we suggest future areas of development that should increase the power of BCR repertoire functional clustering.
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Affiliation(s)
- Matthew I. J. Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
| | | | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, UK
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Guthmiller JJ, Lan LYL, Fernández-Quintero ML, Han J, Utset HA, Bitar DJ, Hamel NJ, Stovicek O, Li L, Tepora M, Henry C, Neu KE, Dugan HL, Borowska MT, Chen YQ, Liu STH, Stamper CT, Zheng NY, Huang M, Palm AKE, García-Sastre A, Nachbagauer R, Palese P, Coughlan L, Krammer F, Ward AB, Liedl KR, Wilson PC. Polyreactive Broadly Neutralizing B cells Are Selected to Provide Defense against Pandemic Threat Influenza Viruses. Immunity 2020; 53:1230-1244.e5. [PMID: 33096040 PMCID: PMC7772752 DOI: 10.1016/j.immuni.2020.10.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/14/2020] [Accepted: 10/07/2020] [Indexed: 12/19/2022]
Abstract
Polyreactivity is the ability of a single antibody to bind to multiple molecularly distinct antigens and is a common feature of antibodies induced upon pathogen exposure. However, little is known about the role of polyreactivity during anti-influenza virus antibody responses. By analyzing more than 500 monoclonal antibodies (mAbs) derived from B cells induced by numerous influenza virus vaccines and infections, we found mAbs targeting conserved neutralizing influenza virus hemagglutinin epitopes were polyreactive. Polyreactive mAbs were preferentially induced by novel viral exposures due to their broad viral binding breadth. Polyreactivity augmented mAb viral binding strength by increasing antibody flexibility, allowing for adaption to imperfectly conserved epitopes. Lastly, we found affinity-matured polyreactive B cells were typically derived from germline polyreactive B cells that were preferentially selected to participate in B cell responses over time. Together, our data reveal that polyreactivity is a beneficial feature of antibodies targeting conserved epitopes.
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Affiliation(s)
- Jenna J Guthmiller
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Linda Yu-Ling Lan
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Monica L Fernández-Quintero
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Henry A Utset
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Dalia J Bitar
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Natalie J Hamel
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Olivia Stovicek
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Lei Li
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Micah Tepora
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Carole Henry
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Karlynn E Neu
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Haley L Dugan
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Marta T Borowska
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Yao-Qing Chen
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Sean T H Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Nai-Ying Zheng
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Min Huang
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Anna-Karin E Palm
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Raffael Nachbagauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lynda Coughlan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Microbiology and Immunology and Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Klaus R Liedl
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.
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44
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Li J, Xue H, Ma Q, He X, Ma L, Shi B, Sun S, Yao X. Heterogeneity of CD4 +CD25 +Foxp3 +Treg TCR β CDR3 Repertoire Based on the Differences of Symbiotic Microorganisms in the Gut of Mice. Front Cell Dev Biol 2020; 8:576445. [PMID: 32984355 PMCID: PMC7490519 DOI: 10.3389/fcell.2020.576445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/13/2020] [Indexed: 12/12/2022] Open
Abstract
Gut microbes play a crucial role in the occurrence and development of autoimmune diseases. The diversity of intestinal microorganisms affected by the living environment, regulate the immune function of peripheral immune organs and local tissues. In the study, the diversity of intestinal microorganisms of Germ-free (GF), Specific Pathogen-free (SPF), and Clean (CL) BALB/c mice were conducted by 16S rDNA sequencing. High-throughput sequencing technology was used to analysis the composition and characterization of TCR β chain CDR3 repertoires in Regulatory T cells (Treg) in intestine and spleen of GF, SPF, and CL mice, so as to investigate the effects of differential composition of intestinal microorganisms on the CD4+CD25+Foxp3+Treg TCR β CDR3 repertoire of intestine and spleen. We observed that GF, SPF, and CL mice have different gut microorganism composition, and the abundance and quantity of microorganisms are positively correlated with the level of feeding environment. Interestingly, incomplete structure of spleen and small intestine in GF mice was found. Moreover, a significant difference in the usage of high frequency unique CDR3 amino acid sequences was detected in the intestinal Treg TCRβ CDR3 repertoire among GF, SPF and CL mice, and there were a greater heterogeneity in the usage frequency of TRBV, TRBJ, and TRBV-TRBJ combinations gene segments. However, the effect of different feeding environment on the mice Treg TCRβ CDR3 repertoire of spleen was weak, implying that the different composition of intestinal microbiota may primarily affect the diversity of the local Treg TCRβ CDR3 repertoire and does not alter the overall properties of the circulating immune system. These results provide basic data to further analyze the mechanism of gut microbes regulating the intestinal mucosal immune system.
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Affiliation(s)
- Jun Li
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Huaijuan Xue
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Qingqing Ma
- Department of Laboratory Medicine, Guizhou Aerospace Hospital, Zunyi, China
| | - Xiaoyan He
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Long Ma
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Bin Shi
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Suhong Sun
- Department of Breast Surgery, The Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Xinsheng Yao
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
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45
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Agazio A, Cimons J, Shotts KM, Guo K, Santiago ML, Pelanda R, Torres RM. Histone H2A-Reactive B Cells Are Functionally Anergic in Healthy Mice With Potential to Provide Humoral Protection Against HIV-1. Front Immunol 2020; 11:1565. [PMID: 32849530 PMCID: PMC7396680 DOI: 10.3389/fimmu.2020.01565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/15/2020] [Indexed: 11/13/2022] Open
Abstract
Peripheral tolerance is essential for silencing weakly autoreactive B cells that have escaped central tolerance, but it is unclear why these potentially pathogenic B cells are retained rather than being eliminated entirely. Release from peripheral tolerance restraint can occur under certain circumstances (i.e., strong TLR stimulus), that are present during infection. In this regard, we hypothesized that autoreactive B cells could function as a reserve population that can be activated to contribute to the humoral immune response, particularly with pathogens, such as HIV-1, that exploit immune tolerance to avoid host defense. In this study, we identify a population of autoreactive B cells with the potential to neutralize HIV-1 and experimentally release them from the functional restrictions of peripheral tolerance. We have previously identified murine monoclonal antibodies that displayed autoreactivity against histone H2A and neutralized HIV-1 in vitro. Here, we identify additional H2A-reactive IgM monoclonal antibodies and demonstrate that they are both autoreactive and polyreactive with self and foreign antigens and are able to neutralize multiple clades of tier 2 HIV-1. Flow cytometric analysis of H2A-reactive B cells in naïve wildtype mice revealed that these B cells are present in peripheral B cell populations and we further document that murine H2A-reactive B cells are restrained by peripheral tolerance mechanisms. Specifically, we show endogenous H2A-reactive B cells display increased expression of the inhibitory mediators CD5 and phosphatase and tensin homolog (PTEN) phosphatase and fail to mobilize calcium upon immunoreceptor stimulation; all characterized markers of anergy. Moreover, we show that toll-like receptor stimulation or provision of CD4 T cell help induces the in vitro production of H2A-reactive antibodies, breaking tolerance. Thus, we have identified a novel poly/autoreactive B cell population that has the potential to neutralize HIV-1 but is silenced by immune tolerance.
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Affiliation(s)
- Amanda Agazio
- Department of Immunology & Microbiology, University of Colorado, Aurora, CO, United States
| | - Jennifer Cimons
- Department of Immunology & Microbiology, University of Colorado, Aurora, CO, United States
| | - Kristin M. Shotts
- Department of Immunology & Microbiology, University of Colorado, Aurora, CO, United States
| | - Kejun Guo
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, CO, United States
| | - Mario L. Santiago
- Department of Medicine, Division of Infectious Diseases, School of Medicine, University of Colorado, Aurora, CO, United States
| | - Roberta Pelanda
- Department of Immunology & Microbiology, University of Colorado, Aurora, CO, United States
| | - Raul M. Torres
- Department of Immunology & Microbiology, University of Colorado, Aurora, CO, United States
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46
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Moyo T, Kitchin D, Moore PL. Targeting the N332-supersite of the HIV-1 envelope for vaccine design. Expert Opin Ther Targets 2020; 24:499-509. [PMID: 32340497 DOI: 10.1080/14728222.2020.1752183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introduction: Broadly neutralizing antibodies (bNAbs) that are able to target diverse global viruses are widely believed to be crucial for an HIV-1 vaccine. Several conserved targets recognized by these antibodies have been identified on the HIV-1 envelope glycoprotein. One such target that shows particular promise for vaccination is the N332-supersite.Areas covered: This review describes the potential of the N332-supersite epitope as an immunogen design platform. We discuss the structure of the epitope and the bNAbs that target it, emphasizing their diverse modes of binding. Furthermore, the successes and limitations of recent N332-supersite immunization studies are discussed.Expert opinion: During HIV-1 infection, some of the broadest and most potent bNAbs target the N332-supersite. Furthermore, some of these antibodies require less affinity maturation than the high levels typical of many bNAbs, making these potentially more achievable vaccine targets. In addition, bNAbs bind this epitope with multiple angles of approach and glycan dependencies, perhaps increasing the probability of eliciting such responses by vaccination. Animal studies have shown that N332-supersite bNAb precursors can be activated by novel immunogens. While follow-up studies must establish whether boosting strategies can drive the maturation of bNAbs from these precursors, the development of targeted N332-supersite immunogens expands our arsenal of potential HIV-1 vaccine candidates.
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Affiliation(s)
- Thandeka Moyo
- Centre for HIV-1 and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Dale Kitchin
- Centre for HIV-1 and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Penny L Moore
- Centre for HIV-1 and STIs, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.,Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu Natal, Durban, South Africa
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47
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Dimitrov JD. Harnessing the Therapeutic Potential of 'Rogue' Antibodies. Trends Pharmacol Sci 2020; 41:409-417. [PMID: 32334839 DOI: 10.1016/j.tips.2020.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/23/2020] [Accepted: 03/26/2020] [Indexed: 12/23/2022]
Abstract
Therapeutic antibodies have revolutionized modern medicine. At present, antibodies are successfully used for treatment of diverse human diseases, ranging from cancer to viral infections. All clinically approved antibodies rely on highly specific recognition of their target antigen. Antigen-binding promiscuity, binding to autoantigens, and propensity for self-binding (homophilic interaction) are highly undesirable characteristics of antibody drug candidates. Nevertheless, the immune system of all healthy individuals constantly produces and uses large quantities of antibodies that can be classified as inappropriate for development as drugs. Here, I provide arguments that antibodies with 'aberrant' properties have therapeutic potential. They could be useful in certain complex pathological conditions, thus enriching our armamentarium for treatment of human diseases.
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Affiliation(s)
- Jordan D Dimitrov
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, F-75006 Paris, France.
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48
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Burke MJ, Stockley PG, Boyes J. Broadly Neutralizing Bovine Antibodies: Highly Effective New Tools against Evasive Pathogens? Viruses 2020; 12:v12040473. [PMID: 32331321 PMCID: PMC7232318 DOI: 10.3390/v12040473] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 04/16/2020] [Accepted: 04/21/2020] [Indexed: 02/07/2023] Open
Abstract
Potent antibody-mediated neutralization is critical for an organism to combat the vast array of pathogens it will face during its lifetime. Due to the potential genetic diversity of some viruses, such as HIV-1 and influenza, standard neutralizing antibodies are often ineffective or easily evaded as their targets are masked or rapidly mutated. This has thwarted efforts to both prevent and treat HIV-1 infections and means that entirely new formulations are required to vaccinate against influenza each year. However, some rare antibodies isolated from infected individuals confer broad and potent neutralization. A subset of these broadly neutralizing antibodies possesses a long complementarity-determining 3 region of the immunoglobulin heavy chain (CDR H3). This feature generates unique antigen binding site configurations that can engage conserved but otherwise inaccessible epitope targets thus neutralizing many viral variants. Remarkably, ultralong CDR H3s are a common feature of the cow antibody repertoire and are encoded by a single variable, diversity, joining (VDJ) recombination that is extensively diversified prior to antigen exposure. Recently, it was shown that cows rapidly generate a broadly neutralizing response upon exposure to HIV-1 and this is primarily mediated by these novel ultralong antibody types. This review summarises the current knowledge of these unusual CDR H3 structures and discusses their known and potential future uses.
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Affiliation(s)
- Matthew J. Burke
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; (M.J.B.); (P.G.S.)
| | - Peter G. Stockley
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; (M.J.B.); (P.G.S.)
- Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Joan Boyes
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK; (M.J.B.); (P.G.S.)
- Correspondence:
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49
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Roskin K, Spearman P. HIV-1 Broadly Neutralizing Antibodies Take the Road Less Traveled, and That Makes All the Difference. Cell Host Microbe 2020; 27:487-488. [PMID: 32272069 DOI: 10.1016/j.chom.2020.03.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Broadly neutralizing antibodies (bnAbs) against HIV-1 provide critical insights into co-evolution between the virus and human B cell responses. In this issue of Cell Host & Microbe, Shen et al. (2020) describe a rare mutation in an antibody lineage targeting the fusion peptide of HIV-1 envelope creating a critical bifurcation, with only one path leading to bnAb development.
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Affiliation(s)
- Krishnan Roskin
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center and the University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Paul Spearman
- Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center and the University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH 45229, USA.
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