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Lê Quý K, Chernigovskaya M, Stensland M, Singh S, Leem J, Revale S, Yadin DA, Nice FL, Povall C, Minns DH, Galson JD, Nyman TA, Snapkow I, Greiff V. Benchmarking and integrating human B-cell receptor genomic and antibody proteomic profiling. NPJ Syst Biol Appl 2024; 10:73. [PMID: 38997321 PMCID: PMC11245537 DOI: 10.1038/s41540-024-00402-z] [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: 11/02/2023] [Accepted: 07/01/2024] [Indexed: 07/14/2024] Open
Abstract
Immunoglobulins (Ig), which exist either as B-cell receptors (BCR) on the surface of B cells or as antibodies when secreted, play a key role in the recognition and response to antigenic threats. The capability to jointly characterize the BCR and antibody repertoire is crucial for understanding human adaptive immunity. From peripheral blood, bulk BCR sequencing (bulkBCR-seq) currently provides the highest sampling depth, single-cell BCR sequencing (scBCR-seq) allows for paired chain characterization, and antibody peptide sequencing by tandem mass spectrometry (Ab-seq) provides information on the composition of secreted antibodies in the serum. Yet, it has not been benchmarked to what extent the datasets generated by these three technologies overlap and complement each other. To address this question, we isolated peripheral blood B cells from healthy human donors and sequenced BCRs at bulk and single-cell levels, in addition to utilizing publicly available sequencing data. Integrated analysis was performed on these datasets, resolved by replicates and across individuals. Simultaneously, serum antibodies were isolated, digested with multiple proteases, and analyzed with Ab-seq. Systems immunology analysis showed high concordance in repertoire features between bulk and scBCR-seq within individuals, especially when replicates were utilized. In addition, Ab-seq identified clonotype-specific peptides using both bulk and scBCR-seq library references, demonstrating the feasibility of combining scBCR-seq and Ab-seq for reconstructing paired-chain Ig sequences from the serum antibody repertoire. Collectively, our work serves as a proof-of-principle for combining bulk sequencing, single-cell sequencing, and mass spectrometry as complementary methods towards capturing humoral immunity in its entirety.
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Grants
- The Leona M. and Harry B. Helmsley Charitable Trust (#2019PG-T1D011, to VG), UiO World-Leading Research Community (to VG), UiO: LifeScience Convergence Environment Immunolingo (to VG), EU Horizon 2020 iReceptorplus (#825821) (to VG), a Norwegian Cancer Society Grant (#215817, to VG), Research Council of Norway projects (#300740, (#311341, #331890 to VG), a Research Council of Norway IKTPLUSS project (#311341, to VG). This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 101007799 (Inno4Vac). This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA (to VG).
- Mass spectrometry-based proteomic analyses were performed by the Proteomics Core Facility, Department of Immunology, University of Oslo/Oslo University Hospital, which is supported by the Core Facilities program of the South-Eastern Norway Regional Health Authority. This core facility is also a member of the National Network of Advanced Proteomics Infrastructure (NAPI), which is funded by the Research Council of Norway INFRASTRUKTUR-program (project number: 295910).
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Affiliation(s)
- Khang Lê Quý
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Maria Chernigovskaya
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Maria Stensland
- Proteomics Core Facility, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Sachin Singh
- Proteomics Core Facility, University of Oslo and Oslo University Hospital, Oslo, Norway
| | | | | | | | | | | | | | | | - Tuula A Nyman
- Proteomics Core Facility, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Igor Snapkow
- Department of Chemical Toxicology, Norwegian Institute of Public Health, Oslo, Norway
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
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2
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Dunlap G, Wagner A, Meednu N, Wang R, Zhang F, Ekabe JC, Jonsson AH, Wei K, Sakaue S, Nathan A, Bykerk VP, Donlin LT, Goodman SM, Firestein GS, Boyle DL, Holers VM, Moreland LW, Tabechian D, Pitzalis C, Filer A, Raychaudhuri S, Brenner MB, Thakar J, McDavid A, Rao DA, Anolik JH. Clonal associations between lymphocyte subsets and functional states in rheumatoid arthritis synovium. Nat Commun 2024; 15:4991. [PMID: 38862501 PMCID: PMC11167034 DOI: 10.1038/s41467-024-49186-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 05/20/2024] [Indexed: 06/13/2024] Open
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease involving antigen-specific T and B cells. Here, we perform single-cell RNA and repertoire sequencing on paired synovial tissue and blood samples from 12 seropositive RA patients. We identify clonally expanded CD4 + T cells, including CCL5+ cells and T peripheral helper (Tph) cells, which show a prominent transcriptomic signature of recent activation and effector function. CD8 + T cells show higher oligoclonality than CD4 + T cells, with the largest synovial clones enriched in GZMK+ cells. CD8 + T cells with possibly virus-reactive TCRs are distributed across transcriptomic clusters. In the B cell compartment, NR4A1+ activated B cells, and plasma cells are enriched in the synovium and demonstrate substantial clonal expansion. We identify synovial plasma cells that share BCRs with synovial ABC, memory, and activated B cells. Receptor-ligand analysis predicted IFNG and TNFRSF members as mediators of synovial Tph-B cell interactions. Together, these results reveal clonal relationships between functionally distinct lymphocyte populations that infiltrate the synovium of patients with RA.
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Grants
- UH2 AR067685 NIAMS NIH HHS
- UM2 AR067678 NIAMS NIH HHS
- K08 AR081412 NIAMS NIH HHS
- UH2 AR067681 NIAMS NIH HHS
- UH2 AR067688 NIAMS NIH HHS
- UH2 AR067689 NIAMS NIH HHS
- UH2 AR067690 NIAMS NIH HHS
- UH2 AR067677 NIAMS NIH HHS
- UH2 AR067694 NIAMS NIH HHS
- UH2 AR067679 NIAMS NIH HHS
- UH2 AR067676 NIAMS NIH HHS
- UH2 AR067691 NIAMS NIH HHS
- Funding for AMP RA/SLE work was provided through grants from the National Institutes of Health (UH2-AR067676, UH2-AR067677, UH2-AR067679, UH2-AR067681, UH2-AR067685, UH2-AR067688, UH2-AR067689, UH2-AR067690, UH2-AR067691, UH2-AR067694, and UM2-AR067678).
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Affiliation(s)
- Garrett Dunlap
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Aaron Wagner
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Nida Meednu
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center, Rochester, NY, USA
| | - Ruoqiao Wang
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Fan Zhang
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Rheumatology and the Center for Health Artificial Intelligence, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jabea Cyril Ekabe
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center, Rochester, NY, USA
| | - Anna Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Saori Sakaue
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aparna Nathan
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vivian P Bykerk
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Laura T Donlin
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Susan M Goodman
- Hospital for Special Surgery, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Gary S Firestein
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego;, La Jolla, CA, USA
| | - David L Boyle
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego;, La Jolla, CA, USA
| | - V Michael Holers
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Larry W Moreland
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Darren Tabechian
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center, Rochester, NY, USA
| | - Costantino Pitzalis
- Centre for Experimental Medicine & Rheumatology, EULAR Centre of Excellence, William Harvey Research Institute, Queen Mary University of London, London, UK
- Barts Health NHS Trust, Barts Biomedical Research Centre (BRC), National Institute for Health and Care Research (NIHR), London, UK
- Department of Biomedical Sciences, Humanitas University and Humanitas Research Hospital, Milan, Italy
| | - Andrew Filer
- Rheumatology Research Group, Institute for Inflammation and Ageing, University of Birmingham, NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
- Birmingham Tissue Analytics, Institute of Translational Medicine, University of Birmingham, Birmingham, UK
- NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital, Birmingham, UK
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael B Brenner
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Juilee Thakar
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Andrew McDavid
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Jennifer H Anolik
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center, Rochester, NY, USA.
- Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA.
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3
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Joshi VR, Claiborne DT, Pack ML, Power KA, Newman RM, Batorsky R, Bean DJ, Goroff MS, Lingwood D, Seaman MS, Rosenberg E, Allen TM. A VRC13-like bNAb response is associated with complex escape pathways in HIV-1 envelope. J Virol 2024; 98:e0172023. [PMID: 38412036 PMCID: PMC10949433 DOI: 10.1128/jvi.01720-23] [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: 11/13/2023] [Accepted: 02/07/2024] [Indexed: 02/29/2024] Open
Abstract
The rational design of HIV-1 immunogens to trigger the development of broadly neutralizing antibodies (bNAbs) requires understanding the viral evolutionary pathways influencing this process. An acute HIV-1-infected individual exhibiting >50% plasma neutralization breadth developed neutralizing antibody specificities against the CD4-binding site (CD4bs) and V1V2 regions of Env gp120. Comparison of pseudoviruses derived from early and late autologous env sequences demonstrated the development of >2 log resistance to VRC13 but not to other CD4bs-specific bNAbs. Mapping studies indicated that the V3 and CD4-binding loops of Env gp120 contributed significantly to developing resistance to the autologous neutralizing response and that the CD4-binding loop (CD4BL) specifically was responsible for the developing resistance to VRC13. Tracking viral evolution during the development of this cross-neutralizing CD4bs response identified amino acid substitutions arising at only 4 of 11 known VRC13 contact sites (K282, T283, K421, and V471). However, each of these mutations was external to the V3 and CD4BL regions conferring resistance to VRC13 and was transient in nature. Rather, complete resistance to VRC13 was achieved through the cooperative expression of a cluster of single amino acid changes within and immediately adjacent to the CD4BL, including a T359I substitution, exchange of a potential N-linked glycosylation (PNLG) site to residue S362 from N363, and a P369L substitution. Collectively, our data characterize complex HIV-1 env evolution in an individual developing resistance to a VRC13-like neutralizing antibody response and identify novel VRC13-associated escape mutations that may be important to inducing VRC13-like bNAbs for lineage-based immunogens.IMPORTANCEThe pursuit of eliciting broadly neutralizing antibodies (bNAbs) through vaccination and their use as therapeutics remains a significant focus in the effort to eradicate HIV-1. Key to our understanding of this approach is a more extensive understanding of bNAb contact sites and susceptible escape mutations in HIV-1 envelope (env). We identified a broad neutralizer exhibiting VRC13-like responses, a non-germline restricted class of CD4-binding site antibody distinct from the well-studied VRC01-class. Through longitudinal envelope sequencing and Env-pseudotyped neutralization assays, we characterized a complex escape pathway requiring the cooperative evolution of four amino acid changes to confer complete resistance to VRC13. This suggests that VRC13-class bNAbs may be refractory to rapid escape and attractive for therapeutic applications. Furthermore, the identification of longitudinal viral changes concomitant with the development of neutralization breadth may help identify the viral intermediates needed for the maturation of VRC13-like responses and the design of lineage-based immunogens.
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Affiliation(s)
- Vinita R. Joshi
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Virology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Daniel T. Claiborne
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Melissa L. Pack
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Karen A. Power
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ruchi M. Newman
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rebecca Batorsky
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - David J. Bean
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Matthew S. Goroff
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Daniel Lingwood
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Eric Rosenberg
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Todd M. Allen
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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4
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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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5
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Monson N, Smith C, Greenberg H, Plumb P, Guzman A, Tse K, Chen D, Zhang W, Morgan M, Speed H, Powell C, Batra S, Cowell L, Christley S, Vernino S, Blackburn K, Greenberg B. VH2+ Antigen-Experienced B Cells in the Cerebrospinal Fluid Are Expanded and Enriched in Pediatric Anti-NMDA Receptor Encephalitis. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1332-1339. [PMID: 37712756 PMCID: PMC10593502 DOI: 10.4049/jimmunol.2300156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 08/17/2023] [Indexed: 09/16/2023]
Abstract
Pediatric and adult autoimmune encephalitis (AE) are often associated with Abs to the NR1 subunit of the N-methyl-d-aspartate (NMDA) receptor (NMDAR). Very little is known regarding the cerebrospinal fluid humoral immune profile and Ab genetics associated with pediatric anti-NMDAR-AE. Using a combination of cellular, molecular, and immunogenetics tools, we collected cerebrospinal fluid from pediatric subjects and generated 1) flow cytometry data to calculate the frequency of B cell subtypes in the cerebrospinal fluid of pediatric subjects with anti-NMDAR-AE and controls, 2) a panel of recombinant human Abs from a pediatric case of anti-NMDAR-AE that was refractory to treatment, and 3) a detailed analysis of the Ab genes that bound the NR1 subunit of the NMDAR. Ag-experienced B cells including memory cells, plasmablasts, and Ab-secreting cells were expanded in the pediatric anti-NMDAR-AE cohort, but not in the controls. These Ag-experienced B cells in the cerebrospinal fluid of a pediatric case of NMDAR-AE that was refractory to treatment had expanded use of variable H chain family 2 (VH2) genes with high somatic hypermutation that all bound to the NR1 subunit of the NMDAR. A CDR3 motif was identified in this refractory case that likely drove early stage activation and expansion of naive B cells to Ab-secreting cells, facilitating autoimmunity associated with pediatric anti-NMDAR-AE through the production of Abs that bind NR1. These features of humoral immune responses in the cerebrospinal fluid of pediatric anti-NMDAR-AE patients may be relevant for clinical diagnosis and treatment.
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Affiliation(s)
- Nancy Monson
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX
| | - Chad Smith
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Hannah Greenberg
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Patricia Plumb
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Alyssa Guzman
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Key Tse
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Ding Chen
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Wei Zhang
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Miles Morgan
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Haley Speed
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Craig Powell
- Department of Neurobiology, Civitan International Research Center, University of Alabama Marnix E. Heersink School of Medicine, Birmingham, AL
| | - Sushobhna Batra
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Lindsay Cowell
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX
| | - Scott Christley
- Department of Population and Data Sciences, UT Southwestern Medical Center, Dallas, TX
| | - Steve Vernino
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
| | - Kyle Blackburn
- Department of Neurology, UT Southwestern Medical Center, Dallas, TX
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6
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Böttcher L, Wald S, Chou T. Mathematical Characterization of Private and Public Immune Receptor Sequences. Bull Math Biol 2023; 85:102. [PMID: 37707621 PMCID: PMC10501991 DOI: 10.1007/s11538-023-01190-z] [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: 04/11/2023] [Accepted: 07/26/2023] [Indexed: 09/15/2023]
Abstract
Diverse T and B cell repertoires play an important role in mounting effective immune responses against a wide range of pathogens and malignant cells. The number of unique T and B cell clones is characterized by T and B cell receptors (TCRs and BCRs), respectively. Although receptor sequences are generated probabilistically by recombination processes, clinical studies found a high degree of sharing of TCRs and BCRs among different individuals. In this work, we use a general probabilistic model for T/B cell receptor clone abundances to define "publicness" or "privateness" and information-theoretic measures for comparing the frequency of sampled sequences observed across different individuals. We derive mathematical formulae to quantify the mean and the variances of clone richness and overlap. Our results can be used to evaluate the effect of different sampling protocols on abundances of clones within an individual as well as the commonality of clones across individuals. Using synthetic and empirical TCR amino acid sequence data, we perform simulations to study expected clonal commonalities across multiple individuals. Based on our formulae, we compare these simulated results with the analytically predicted mean and variances of the repertoire overlap. Complementing the results on simulated repertoires, we derive explicit expressions for the richness and its uncertainty for specific, single-parameter truncated power-law probability distributions. Finally, the information loss associated with grouping together certain receptor sequences, as is done in spectratyping, is also evaluated. Our approach can be, in principle, applied under more general and mechanistically realistic clone generation models.
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Affiliation(s)
- Lucas Böttcher
- Department of Computational Science and Philosophy, Frankfurt School of Finance and Management, 60322 Frankfurt am Main, Germany
- Department of Computational Medicine, University of California, Los Angeles, 621 Charles E. Young Dr. S., Los Angeles, 90095-1766 CA USA
- Department of Medicine, University of Florida, Gainesville, 32610 FL USA
| | - Sascha Wald
- Statistical Physics Group, Centre for Fluid and Complex Systems, Coventry University, Priory Street, Coventry, CV1 5FB UK
| | - Tom Chou
- Department of Computational Medicine, University of California, Los Angeles, 621 Charles E. Young Dr. S., Los Angeles, 90095-1766 CA USA
- Department of Mathematics, University of California, Los Angeles, 520 Portola Plaza, Los Angeles, 90095-1555 CA USA
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7
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Wu Z, Gao S, Gao Q, Patel BA, Groarke EM, Feng X, Manley AL, Li H, Ospina Cardona D, Kajigaya S, Alemu L, Quinones Raffo D, Ombrello AK, Ferrada MA, Grayson PC, Calvo KR, Kastner DL, Beck DB, Young NS. Early activation of inflammatory pathways in UBA1-mutated hematopoietic stem and progenitor cells in VEXAS. Cell Rep Med 2023; 4:101160. [PMID: 37586319 PMCID: PMC10439277 DOI: 10.1016/j.xcrm.2023.101160] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 04/18/2023] [Accepted: 07/21/2023] [Indexed: 08/18/2023]
Abstract
VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome is a pleiotropic, severe autoinflammatory disease caused by somatic mutations in the ubiquitin-like modifier activating enzyme 1 (UBA1) gene. To elucidate VEXAS pathophysiology, we performed transcriptome sequencing of single bone marrow mononuclear cells and hematopoietic stem and progenitor cells (HSPCs) from VEXAS patients. HSPCs are biased toward myeloid (granulocytic) differentiation, and against lymphoid differentiation in VEXAS. Activation of multiple inflammatory pathways (interferons and tumor necrosis factor alpha) occurs ontogenically early in primitive hematopoietic cells and particularly in the myeloid lineage in VEXAS, and inflammation is prominent in UBA1-mutated cells. Dysregulation in protein degradation likely leads to higher stress response in VEXAS HSPCs, which positively correlates with inflammation. TCR usage is restricted and there are increased cytotoxicity and IFN-γ signaling in T cells. In VEXAS syndrome, both aberrant inflammation and myeloid predominance appear intrinsic to hematopoietic stem cells mutated in UBA1.
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Affiliation(s)
- Zhijie Wu
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Shouguo Gao
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Qingyan Gao
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bhavisha A Patel
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Emma M Groarke
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xingmin Feng
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ash Lee Manley
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Haoran Li
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniela Ospina Cardona
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Division of Rheumatology, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA; Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lemlem Alemu
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Diego Quinones Raffo
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amanda K Ombrello
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marcela A Ferrada
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter C Grayson
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katherine R Calvo
- Hematology Section, Department of Laboratory Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel L Kastner
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David B Beck
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Division of Rheumatology, Department of Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA; Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, NY 10016, USA.
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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8
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Sutherland C, Cowan GJM. AIRRSHIP: simulating human B cell receptor repertoire sequences. Bioinformatics 2023; 39:btad365. [PMID: 37279738 PMCID: PMC10272706 DOI: 10.1093/bioinformatics/btad365] [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: 01/31/2023] [Revised: 05/05/2023] [Accepted: 06/02/2023] [Indexed: 06/08/2023] Open
Abstract
SUMMARY Adaptive Immune Receptor Repertoire Sequencing is a rapidly developing field that has advanced understanding of the role of the adaptive immune system in health and disease. Numerous tools have been developed to analyse the complex data produced by this technique but work to compare their accuracy and reliability has been limited. Thorough, systematic assessment of their performance is dependent on the ability to produce high quality simulated datasets with known ground truth. We have developed AIRRSHIP, a flexible and fast Python package that produces synthetic human B cell receptor sequences. AIRRSHIP uses a comprehensive set of reference data to replicate key mechanisms in the immunoglobulin recombination process, with a particular focus on junctional complexity. Repertoires generated by AIRRSHIP are highly similar to published data and all steps in the sequence generation process are recorded. These data can be used to not only determine the accuracy of repertoire analysis tools but can also, by tuning of the large number of user-controllable parameters, give insight into factors that contribute to inaccuracies in results. AVAILABILITY AND IMPLEMENTATION AIRRSHIP is implemented in Python. It is available via https://github.com/Cowanlab/airrship and on PyPI at https://pypi.org/project/airrship/. Documentation can be found at https://airrship.readthedocs.io/.
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Affiliation(s)
- Catherine Sutherland
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, United Kingdom
| | - Graeme J M Cowan
- Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3FL, United Kingdom
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9
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Dunlap G, Wagner A, Meednu N, Zhang F, Jonsson AH, Wei K, Sakaue S, Nathan A, Bykerk VP, Donlin LT, Goodman SM, Firestein GS, Boyle DL, Holers VM, Moreland LW, Tabechian D, Pitzalis C, Filer A, Raychaudhuri S, Brenner MB, McDavid A, Rao DA, Anolik JH. Clonal associations of lymphocyte subsets and functional states revealed by single cell antigen receptor profiling of T and B cells in rheumatoid arthritis synovium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.18.533282. [PMID: 36993527 PMCID: PMC10055242 DOI: 10.1101/2023.03.18.533282] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Rheumatoid arthritis (RA) is an autoimmune disease initiated by antigen-specific T cells and B cells, which promote synovial inflammation through a complex set of interactions with innate immune and stromal cells. To better understand the phenotypes and clonal relationships of synovial T and B cells, we performed single-cell RNA and repertoire sequencing on paired synovial tissue and peripheral blood samples from 12 donors with seropositive RA ranging from early to chronic disease. Paired transcriptomic-repertoire analyses highlighted 3 clonally distinct CD4 T cells populations that were enriched in RA synovium: T peripheral helper (Tph) and T follicular helper (Tfh) cells, CCL5+ T cells, and T regulatory cells (Tregs). Among these cells, Tph cells showed a unique transcriptomic signature of recent T cell receptor (TCR) activation, and clonally expanded Tph cells expressed an elevated transcriptomic effector signature compared to non-expanded Tph cells. CD8 T cells showed higher oligoclonality than CD4 T cells, and the largest CD8 T cell clones in synovium were highly enriched in GZMK+ cells. TCR analyses revealed CD8 T cells with likely viral-reactive TCRs distributed across transcriptomic clusters and definitively identified MAIT cells in synovium, which showed transcriptomic features of TCR activation. Among B cells, non-naive B cells including age-associated B cells (ABC), NR4A1+ activated B cells, and plasma cells, were enriched in synovium and had higher somatic hypermutation rates compared to blood B cells. Synovial B cells demonstrated substantial clonal expansion, with ABC, memory, and activated B cells clonally linked to synovial plasma cells. Together, these results reveal clonal relationships between functionally distinct lymphocyte populations that infiltrate RA synovium.
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Affiliation(s)
- Garrett Dunlap
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School; Boston, MA, USA
| | - Aaron Wagner
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry; Rochester, NY, USA
| | - Nida Meednu
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center; Rochester, NY, USA
| | - Fan Zhang
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School; Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital; Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital; Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, USA
- Division of Rheumatology and the Center for Health Artificial Intelligence, University of Colorado School of Medicine; Aurora, CO, USA
| | - A Helena Jonsson
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School; Boston, MA, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School; Boston, MA, USA
| | - Saori Sakaue
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School; Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital; Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital; Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, USA
| | - Aparna Nathan
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School; Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital; Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital; Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, USA
| | - Vivian P Bykerk
- Hospital for Special Surgery; New York, NY, USA
- Weill Cornell Medicine; New York, NY, USA
| | - Laura T Donlin
- Hospital for Special Surgery; New York, NY, USA
- Weill Cornell Medicine; New York, NY, USA
| | - Susan M Goodman
- Hospital for Special Surgery; New York, NY, USA
- Weill Cornell Medicine; New York, NY, USA
| | - Gary S Firestein
- Division of Rheumatology, Allergy, and Immunology, University of California, San Diego; La Jolla, CA, USA
| | - David L Boyle
- Division of Rheumatology, Allergy, and Immunology, University of California, San Diego; La Jolla, CA, USA
| | - V Michael Holers
- Division of Rheumatology, University of Colorado School of Medicine; Aurora, CO, USA
| | - Larry W Moreland
- Division of Rheumatology, University of Colorado School of Medicine; Aurora, CO, USA
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh School of Medicine; Pittsburgh, PA, USA
| | - Darren Tabechian
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center; Rochester, NY, USA
| | - Costantino Pitzalis
- Centre for Experimental Medicine & Rheumatology, William Harvey Research Institute, Queen Mary University of London; London, UK
| | - Andrew Filer
- Rheumatology Research Group, Institute for Inflammation and Ageing, University of Birmingham, NIHR Birmingham Biomedical Research Center and Clinical Research Facility, University of Birmingham, Queen Elizabeth Hospital; Birmingham, UK
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School; Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital; Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital; Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, USA
- Versus Arthritis Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester; Manchester, UK
| | - Michael B Brenner
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School; Boston, MA, USA
| | - Andrew McDavid
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry; Rochester, NY, USA
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital and Harvard Medical School; Boston, MA, USA
| | - Jennifer H Anolik
- Division of Allergy, Immunology and Rheumatology, University of Rochester Medical Center; Rochester, NY, USA
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10
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Dacon C, Peng L, Lin TH, Tucker C, Lee CCD, Cong Y, Wang L, Purser L, Cooper AJR, Williams JK, Pyo CW, Yuan M, Kosik I, Hu Z, Zhao M, Mohan D, Peterson M, Skinner J, Dixit S, Kollins E, Huzella L, Perry D, Byrum R, Lembirik S, Murphy M, Zhang Y, Yang ES, Chen M, Leung K, Weinberg RS, Pegu A, Geraghty DE, Davidson E, Doranz BJ, Douagi I, Moir S, Yewdell JW, Schmaljohn C, Crompton PD, Mascola JR, Holbrook MR, Nemazee D, Wilson IA, Tan J. Rare, convergent antibodies targeting the stem helix broadly neutralize diverse betacoronaviruses. Cell Host Microbe 2023; 31:97-111.e12. [PMID: 36347257 PMCID: PMC9639329 DOI: 10.1016/j.chom.2022.10.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/04/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022]
Abstract
Humanity has faced three recent outbreaks of novel betacoronaviruses, emphasizing the need to develop approaches that broadly target coronaviruses. Here, we identify 55 monoclonal antibodies from COVID-19 convalescent donors that bind diverse betacoronavirus spike proteins. Most antibodies targeted an S2 epitope that included the K814 residue and were non-neutralizing. However, 11 antibodies targeting the stem helix neutralized betacoronaviruses from different lineages. Eight antibodies in this group, including the six broadest and most potent neutralizers, were encoded by IGHV1-46 and IGKV3-20. Crystal structures of three antibodies of this class at 1.5-1.75-Å resolution revealed a conserved mode of binding. COV89-22 neutralized SARS-CoV-2 variants of concern including Omicron BA.4/5 and limited disease in Syrian hamsters. Collectively, these findings identify a class of IGHV1-46/IGKV3-20 antibodies that broadly neutralize betacoronaviruses by targeting the stem helix but indicate these antibodies constitute a small fraction of the broadly reactive antibody response to betacoronaviruses after SARS-CoV-2 infection.
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Affiliation(s)
- Cherrelle Dacon
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ting-Hui Lin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Courtney Tucker
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | - Chang-Chun D Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yu Cong
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren Purser
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Andrew J R Cooper
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | | | - Chul-Woo Pyo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ivan Kosik
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhe Hu
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ming Zhao
- Protein Chemistry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Divya Mohan
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Mary Peterson
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Jeff Skinner
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Saurabh Dixit
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Erin Kollins
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Louis Huzella
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Donna Perry
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Russell Byrum
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Sanae Lembirik
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Michael Murphy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rona S Weinberg
- New York Blood Center, Lindsley F. Kimball Research Institute, New York, NY 10065, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | | | - Iyadh Douagi
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Susan Moir
- B Cell Immunology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan W Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Connie Schmaljohn
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Peter D Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael R Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joshua Tan
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA.
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11
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Pennell M, Rodriguez OL, Watson CT, Greiff V. The evolutionary and functional significance of germline immunoglobulin gene variation. Trends Immunol 2023; 44:7-21. [PMID: 36470826 DOI: 10.1016/j.it.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/07/2022] [Indexed: 12/04/2022]
Abstract
The recombination between immunoglobulin (IG) gene segments determines an individual's naïve antibody repertoire and, consequently, (auto)antigen recognition. Emerging evidence suggests that mammalian IG germline variation impacts humoral immune responses associated with vaccination, infection, and autoimmunity - from the molecular level of epitope specificity, up to profound changes in the architecture of antibody repertoires. These links between IG germline variants and immunophenotype raise the question on the evolutionary causes and consequences of diversity within IG loci. We discuss why the extreme diversity in IG loci remains a mystery, why resolving this is important for the design of more effective vaccines and therapeutics, and how recent evidence from multiple lines of inquiry may help us do so.
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Affiliation(s)
- Matt Pennell
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA; Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
| | - Oscar L Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
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12
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Robert PA, Akbar R, Frank R, Pavlović M, Widrich M, Snapkov I, Slabodkin A, Chernigovskaya M, Scheffer L, Smorodina E, Rawat P, Mehta BB, Vu MH, Mathisen IF, Prósz A, Abram K, Olar A, Miho E, Haug DTT, Lund-Johansen F, Hochreiter S, Haff IH, Klambauer G, Sandve GK, Greiff V. Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for antibody specificity prediction. NATURE COMPUTATIONAL SCIENCE 2022; 2:845-865. [PMID: 38177393 DOI: 10.1038/s43588-022-00372-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/09/2022] [Indexed: 01/06/2024]
Abstract
Machine learning (ML) is a key technology for accurate prediction of antibody-antigen binding. Two orthogonal problems hinder the application of ML to antibody-specificity prediction and the benchmarking thereof: the lack of a unified ML formalization of immunological antibody-specificity prediction problems and the unavailability of large-scale synthetic datasets to benchmark real-world relevant ML methods and dataset design. Here we developed the Absolut! software suite that enables parameter-based unconstrained generation of synthetic lattice-based three-dimensional antibody-antigen-binding structures with ground-truth access to conformational paratope, epitope and affinity. We formalized common immunological antibody-specificity prediction problems as ML tasks and confirmed that for both sequence- and structure-based tasks, accuracy-based rankings of ML methods trained on experimental data hold for ML methods trained on Absolut!-generated data. The Absolut! framework has the potential to enable real-world relevant development and benchmarking of ML strategies for biotherapeutics design.
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Affiliation(s)
- Philippe A Robert
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
| | - Rahmad Akbar
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Robert Frank
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | | | - Michael Widrich
- ELLIS Unit Linz and LIT AI Lab, Institute for Machine Learning, Johannes Kepler University Linz, Linz, Austria
| | - Igor Snapkov
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Andrei Slabodkin
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Maria Chernigovskaya
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | | | - Eva Smorodina
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Puneet Rawat
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Brij Bhushan Mehta
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Mai Ha Vu
- Department of Linguistics and Scandinavian Studies, University of Oslo, Oslo, Norway
| | | | - Aurél Prósz
- Danish Cancer Society Research Center, Translational Cancer Genomics, Copenhagen, Denmark
| | - Krzysztof Abram
- The Novo Nordisk Foundation Center for Biosustainability, Autoflow, DTU Biosustain and IT University of Copenhagen, Copenhagen, Denmark
| | - Alex Olar
- Department of Complex Systems in Physics, Eötvös Loránd University, Budapest, Hungary
| | - Enkelejda Miho
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
- aiNET GmbH, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | | | - Sepp Hochreiter
- ELLIS Unit Linz and LIT AI Lab, Institute for Machine Learning, Johannes Kepler University Linz, Linz, Austria
- Institute of Advanced Research in Artificial Intelligence (IARAI), Vienna, Austria
| | | | - Günter Klambauer
- ELLIS Unit Linz and LIT AI Lab, Institute for Machine Learning, Johannes Kepler University Linz, Linz, Austria
| | | | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
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13
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Wang Z, Muecksch F, Muenn F, Cho A, Zong S, Raspe R, Ramos V, Johnson B, Ben Tanfous T, DaSilva J, Bednarski E, Guzman-Cardozo C, Turroja M, Millard KG, Tober-Lau P, Hillus D, Yao KH, Shimeliovich I, Dizon J, Kaczynska A, Jankovic M, Gazumyan A, Oliveira TY, Caskey M, Bieniasz PD, Hatziioannou T, Kurth F, Sander LE, Nussenzweig MC, Gaebler C. Humoral immunity to SARS-CoV-2 elicited by combination COVID-19 vaccination regimens. J Exp Med 2022; 219:e20220826. [PMID: 36006380 PMCID: PMC9418484 DOI: 10.1084/jem.20220826] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/19/2022] [Accepted: 07/13/2022] [Indexed: 11/04/2022] Open
Abstract
The SARS-CoV-2 pandemic prompted a global vaccination effort and the development of numerous COVID-19 vaccines at an unprecedented scale and pace. As a result, current COVID-19 vaccination regimens comprise diverse vaccine modalities, immunogen combinations, and dosing intervals. Here, we compare vaccine-specific antibody and memory B cell responses following two-dose mRNA, single-dose Ad26.COV.2S, and two-dose ChAdOx1, or combination ChAdOx1/mRNA vaccination. Plasma-neutralizing activity, as well as the magnitude, clonal composition, and antibody maturation of the RBD-specific memory B cell compartments, showed substantial differences between the vaccination regimens. While individual monoclonal antibodies derived from memory B cells exhibited similar binding affinities and neutralizing potency against Wuhan-Hu-1 SARS-CoV-2, there were significant differences in epitope specificity and neutralizing breadth against viral variants of concern. Although the ChAdOx1 vaccine was inferior to mRNA and Ad26.COV.2S in several respects, biochemical and structural analyses revealed enrichment in a subgroup of memory B cell neutralizing antibodies with distinct RBD-binding properties resulting in remarkable potency and breadth.
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Affiliation(s)
- Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY
| | - Friederike Muenn
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Shuai Zong
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Raphael Raspe
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Brianna Johnson
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Tarek Ben Tanfous
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Justin DaSilva
- Laboratory of Retrovirology, The Rockefeller University, New York, NY
| | - Eva Bednarski
- Laboratory of Retrovirology, The Rockefeller University, New York, NY
| | | | - Martina Turroja
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Katrina G. Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Pinkus Tober-Lau
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - David Hillus
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Kai-Hui Yao
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Irina Shimeliovich
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Juan Dizon
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Anna Kaczynska
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Mila Jankovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Thiago Y. Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY
| | | | - Florian Kurth
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Berlin, Germany
| | - Leif Erik Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
- Department of Infectious Diseases and Respiratory Medicine, Charité–Universitätsmedizin Berlin, Berlin, Germany
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14
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Koraichi MB, Touzel MP, Mazzolini A, Mora T, Walczak AM. NoisET: Noise Learning and Expansion Detection of T-Cell Receptors. J Phys Chem A 2022; 126:7407-7414. [PMID: 36178325 DOI: 10.1021/acs.jpca.2c05002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-throughput sequencing of T- and B-cell receptors makes it possible to track immune repertoires across time, in different tissues, in acute and chronic diseases and in healthy individuals. However, quantitative comparison between repertoires is confounded by variability in the read count of each receptor clonotype due to sampling, library preparation, and expression noise. We review methods for accounting for both biological and experimental noise and present an easy-to-use python package NoisET that implements and generalizes a previously developed Bayesian method. It can be used to learn experimental noise models for repertoire sequencing from replicates, and to detect responding clones following a stimulus. We test the package on different repertoire sequencing technologies and data sets. We review how such approaches have been used to identify responding clonotypes in vaccination and disease data. Availability: NoisET is freely available to use with source code at github.com/statbiophys/NoisET.
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Affiliation(s)
- Meriem Bensouda Koraichi
- Laboratoire de physique de l' École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris75005, France
| | | | - Andrea Mazzolini
- Laboratoire de physique de l' École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris75005, France
| | - Thierry Mora
- Laboratoire de physique de l' École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris75005, France
| | - Aleksandra M Walczak
- Laboratoire de physique de l' École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris75005, France
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15
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Sangesland M, Torrents de la Peña A, Boyoglu-Barnum S, Ronsard L, Mohamed FAN, Moreno TB, Barnes RM, Rohrer D, Lonberg N, Ghebremichael M, Kanekiyo M, Ward A, Lingwood D. Allelic polymorphism controls autoreactivity and vaccine elicitation of human broadly neutralizing antibodies against influenza virus. Immunity 2022; 55:1693-1709.e8. [PMID: 35952670 PMCID: PMC9474600 DOI: 10.1016/j.immuni.2022.07.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/08/2022] [Accepted: 07/13/2022] [Indexed: 01/18/2023]
Abstract
Human broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin stalk of group 1 influenza A viruses (IAVs) are biased for IGHV1-69 alleles that use phenylalanine (F54) but not leucine (L54) within their CDRH2 loops. Despite this, we demonstrated that both alleles encode for human IAV bnAbs that employ structurally convergent modes of contact to the same epitope. To resolve differences in lineage expandability, we compared F54 versus L54 as substrate within humanized mice, where antibodies develop with human-like CDRH3 diversity but are restricted to single VH genes. While both alleles encoded for bnAb precursors, only F54 IGHV1-69 supported elicitation of heterosubtypic serum bnAbs following immunization with a stalk-only nanoparticle vaccine. L54 IGHV1-69 was unproductive, co-encoding for anergic B cells and autoreactive stalk antibodies that were cleared from B cell memory. Moreover, human stalk antibodies also demonstrated L54-dependent autoreactivity. Therefore, IGHV1-69 polymorphism, which is skewed ethnically, gates tolerance and vaccine expandability of influenza bnAbs.
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Affiliation(s)
- Maya Sangesland
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Alba Torrents de la Peña
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892-3005, USA
| | - Larance Ronsard
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Faez Amokrane Nait Mohamed
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Thalia Bracamonte Moreno
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Ralston M Barnes
- Bristol-Myers Squibb, 700 Bay Rd, Redwood City, CA 94063-2478, USA
| | - Daniel Rohrer
- Bristol-Myers Squibb, 700 Bay Rd, Redwood City, CA 94063-2478, USA
| | - Nils Lonberg
- Bristol-Myers Squibb, 700 Bay Rd, Redwood City, CA 94063-2478, USA
| | - Musie Ghebremichael
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 40 Convent Drive, Bethesda, MD 20892-3005, USA
| | - Andrew Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel Lingwood
- The Ragon Institute of Massachusetts General Hospital, The Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
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16
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Abstract
Antibodies and T cell receptors (TCRs) are the fundamental building blocks of adaptive immunity. Repertoire-scale functionality derives from their epitope-binding properties, just as macroscopic properties like temperature derive from microscopic molecular properties. However, most approaches to repertoire-scale measurement, including sequence diversity and entropy, are not based on antibody or TCR function in this way. Thus, they potentially overlook key features of immunological function. Here we present a framework that describes repertoires in terms of the epitope-binding properties of their constituent antibodies and TCRs, based on analysis of thousands of antibody-antigen and TCR-peptide-major-histocompatibility-complex binding interactions and over 400 high-throughput repertoires. We show that repertoires consist of loose overlapping classes of antibodies and TCRs with similar binding properties. We demonstrate the potential of this framework to distinguish specific responses vs. bystander activation in influenza vaccinees, stratify cytomegalovirus (CMV)-infected cohorts, and identify potential immunological "super-agers." Classes add a valuable dimension to the assessment of immune function.
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17
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Cho A, Muecksch F, Wang Z, Ben Tanfous T, DaSilva J, Raspe R, Johnson B, Bednarski E, Ramos V, Schaefer-Babajew D, Shimeliovich I, Dizon JP, Yao KH, Schmidt F, Millard KG, Turroja M, Jankovic M, Oliveira TY, Gazumyan A, Gaebler C, Caskey M, Hatziioannou T, Bieniasz PD, Nussenzweig MC. Antibody evolution to SARS-CoV-2 after single-dose Ad26.COV2.S vaccine in humans. J Exp Med 2022; 219:e20220732. [PMID: 35776090 PMCID: PMC9253517 DOI: 10.1084/jem.20220732] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/30/2022] [Accepted: 06/17/2022] [Indexed: 01/25/2023] Open
Abstract
The single-dose Ad.26.COV.2 (Janssen) vaccine elicits lower levels of neutralizing antibodies and shows more limited efficacy in protection against infection than either of the two available mRNA vaccines. In addition, Ad.26.COV.2 has been less effective in protection against severe disease during the Omicron surge. Here, we examined the memory B cell response to single-dose Ad.26.COV.2 vaccination. Compared with mRNA vaccines, Ad.26.COV.2 recipients had significantly lower numbers of RBD-specific memory B cells 1.5 or 6 mo after vaccination. Despite the lower numbers, the overall quality of the memory B cell responses appears to be similar, such that memory antibodies elicited by both vaccine types show comparable neutralizing potency against SARS-CoV-2 Wuhan-Hu-1, Delta, and Omicron BA.1 variants. The data help explain why boosting Ad.26.COV.2 vaccine recipients with mRNA vaccines is effective and why the Ad26.COV2.S vaccine can maintain some protective efficacy against severe disease during the Omicron surge.
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Affiliation(s)
- Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Tarek Ben Tanfous
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Justin DaSilva
- Laboratory of Retrovirology, The Rockefeller University, New York, NY
| | - Raphael Raspe
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Brianna Johnson
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Eva Bednarski
- Laboratory of Retrovirology, The Rockefeller University, New York, NY
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | | | - Irina Shimeliovich
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Juan P. Dizon
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Kai-Hui Yao
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY
| | - Katrina G. Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Martina Turroja
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Mila Jankovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Thiago Y. Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | | | - Paul D. Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
- Howard Hughes Medical Institute, Chevy Chase, MD
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18
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Andreani T, Slot LM, Gabillard S, Strübing C, Reimertz C, Yaligara V, Bakker AM, Olfati-Saber R, Toes REM, Scherer HU, Augé F, Šimaitė D. Benchmarking computational methods for B-cell receptor reconstruction from single-cell RNA-seq data. NAR Genom Bioinform 2022; 4:lqac049. [PMID: 35855325 PMCID: PMC9278041 DOI: 10.1093/nargab/lqac049] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/30/2022] [Accepted: 06/21/2022] [Indexed: 11/12/2022] Open
Abstract
Multiple methods have recently been developed to reconstruct full-length B-cell receptors (BCRs) from single-cell RNA sequencing (scRNA-seq) data. This need emerged from the expansion of scRNA-seq techniques, the increasing interest in antibody-based drug development and the importance of BCR repertoire changes in cancer and autoimmune disease progression. However, a comprehensive assessment of performance-influencing factors such as the sequencing depth, read length or number of somatic hypermutations (SHMs) as well as guidance regarding the choice of methodology is still lacking. In this work, we evaluated the ability of six available methods to reconstruct full-length BCRs using one simulated and three experimental SMART-seq datasets. In addition, we validated that the BCRs assembled in silico recognize their intended targets when expressed as monoclonal antibodies. We observed that methods such as BALDR, BASIC and BRACER showed the best overall performance across the tested datasets and conditions, whereas only BASIC demonstrated acceptable results on very short read libraries. Furthermore, the de novo assembly-based methods BRACER and BALDR were the most accurate in reconstructing BCRs harboring different degrees of SHMs in the variable domain, while TRUST4, MiXCR and BASIC were the fastest. Finally, we propose guidelines to select the best method based on the given data characteristics.
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Affiliation(s)
- Tommaso Andreani
- AI & Deep Analytics—Omics Data Science, Sanofi , Frankfurt am Main 65926, Germany
| | - Linda M Slot
- Department of Rheumatology, Leiden University Medical Center , 2333 RC Leiden, The Netherlands
| | | | - Carsten Strübing
- Immunology & Inflammation Research, Sanofi , Frankfurt am Main 65926, Germany
| | - Claus Reimertz
- Immunology & Inflammation Research, Sanofi , Frankfurt am Main 65926, Germany
| | - Veeranagouda Yaligara
- Molecular Biology & Genomics, Translational Science Unit, Sanofi , Chilly-Mazarin 91385, France
| | - Aleida M Bakker
- Department of Rheumatology, Leiden University Medical Center , 2333 RC Leiden, The Netherlands
| | | | - René E M Toes
- Department of Rheumatology, Leiden University Medical Center , 2333 RC Leiden, The Netherlands
| | - Hans U Scherer
- Department of Rheumatology, Leiden University Medical Center , 2333 RC Leiden, The Netherlands
| | - Franck Augé
- AI & Deep Analytics—Omics Data Science, Sanofi , Paris 91385, France
| | - Deimantė Šimaitė
- AI & Deep Analytics—Omics Data Science, Sanofi , Frankfurt am Main 65926, Germany
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19
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Wang Z, Muecksch F, Cho A, Gaebler C, Hoffmann HH, Ramos V, Zong S, Cipolla M, Johnson B, Schmidt F, DaSilva J, Bednarski E, Ben Tanfous T, Raspe R, Yao K, Lee YE, Chen T, Turroja M, Milard KG, Dizon J, Kaczynska A, Gazumyan A, Oliveira TY, Rice CM, Caskey M, Bieniasz PD, Hatziioannou T, Barnes CO, Nussenzweig MC. Analysis of memory B cells identifies conserved neutralizing epitopes on the N-terminal domain of variant SARS-Cov-2 spike proteins. Immunity 2022; 55:998-1012.e8. [PMID: 35447092 PMCID: PMC8986478 DOI: 10.1016/j.immuni.2022.04.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/15/2022] [Accepted: 04/01/2022] [Indexed: 11/17/2022]
Abstract
SARS-CoV-2 infection or vaccination produces neutralizing antibody responses that contribute to better clinical outcomes. The receptor-binding domain (RBD) and the N-terminal domain (NTD) of the spike trimer (S) constitute the two major neutralizing targets for antibodies. Here, we use NTD-specific probes to capture anti-NTD memory B cells in a longitudinal cohort of infected individuals, some of whom were vaccinated. We found 6 complementation groups of neutralizing antibodies. 58% targeted epitopes outside the NTD supersite, 58% neutralized either Gamma or Omicron, and 14% were broad neutralizers that also neutralized Omicron. Structural characterization revealed that broadly active antibodies targeted three epitopes outside the NTD supersite including a class that recognized both the NTD and SD2 domain. Rapid recruitment of memory B cells producing these antibodies into the plasma cell compartment upon re-infection likely contributes to the relatively benign course of subsequent infections with SARS-CoV-2 variants, including Omicron.
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Affiliation(s)
- Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Shuai Zong
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Briana Johnson
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Justin DaSilva
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Eva Bednarski
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Tarek Ben Tanfous
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Raphael Raspe
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Kaihui Yao
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Yu E Lee
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Teresia Chen
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Martina Turroja
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Katrina G Milard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Juan Dizon
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Kaczynska
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | | | - Christopher O Barnes
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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20
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Lupo C, Spisak N, Walczak AM, Mora T. Learning the statistics and landscape of somatic mutation-induced insertions and deletions in antibodies. PLoS Comput Biol 2022; 18:e1010167. [PMID: 35653375 PMCID: PMC9197026 DOI: 10.1371/journal.pcbi.1010167] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 06/14/2022] [Accepted: 05/05/2022] [Indexed: 11/25/2022] Open
Abstract
Affinity maturation is crucial for improving the binding affinity of antibodies to antigens. This process is mainly driven by point substitutions caused by somatic hypermutations of the immunoglobulin gene. It also includes deletions and insertions of genomic material known as indels. While the landscape of point substitutions has been extensively studied, a detailed statistical description of indels is still lacking. Here we present a probabilistic inference tool to learn the statistics of indels from repertoire sequencing data, which overcomes the pitfalls and biases of standard annotation methods. The model includes antibody-specific maturation ages to account for variable mutational loads in the repertoire. After validation on synthetic data, we applied our tool to a large dataset of human immunoglobulin heavy chains. The inferred model allows us to identify universal statistical features of indels in heavy chains. We report distinct insertion and deletion hotspots, and show that the distribution of lengths of indels follows a geometric distribution, which puts constraints on future mechanistic models of the hypermutation process. Affinity maturation of B cell receptors is an important mechanism by which our body designs neutralizing antibodies to defend us against pathogens, including broadly neutralizing antibodies, which target a wide range of variants of the same pathogen. Such antibodies often contain key insertions and deletions to the germline gene, or “indels”, which are caused by somatic hypermutations. However, the mechanism, frequency and role of these indels are still elusive. We designed a computational method based on a probabilistic framework to infer the characteristics of this mutational process from high-throughput antibody sequencing experiments. Applied to human data, our approach provides a comprehensive quantitative description of insertions and deletions, opening avenues for better understanding the process of affinity maturation and the design of vaccines for eliciting a broad antibody response.
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Affiliation(s)
- Cosimo Lupo
- Laboratoire de physique de l’École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris, France
| | - Natanael Spisak
- Laboratoire de physique de l’École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris, France
| | - Aleksandra M. Walczak
- Laboratoire de physique de l’École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris, France
- * E-mail: (AMW); (TM)
| | - Thierry Mora
- Laboratoire de physique de l’École normale supérieure, CNRS, PSL University, Sorbonne Université, and Université de Paris, Paris, France
- * E-mail: (AMW); (TM)
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21
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Zhang Z, Chang WY, Wang K, Yang Y, Wang X, Yao C, Wu T, Wang L, Wang T. Interpreting the B-cell receptor repertoire with single-cell gene expression using Benisse. NAT MACH INTELL 2022. [DOI: 10.1038/s42256-022-00492-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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22
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Khetan R, Curtis R, Deane CM, Hadsund JT, Kar U, Krawczyk K, Kuroda D, Robinson SA, Sormanni P, Tsumoto K, Warwicker J, Martin ACR. Current advances in biopharmaceutical informatics: guidelines, impact and challenges in the computational developability assessment of antibody therapeutics. MAbs 2022; 14:2020082. [PMID: 35104168 PMCID: PMC8812776 DOI: 10.1080/19420862.2021.2020082] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Therapeutic monoclonal antibodies and their derivatives are key components of clinical pipelines in the global biopharmaceutical industry. The availability of large datasets of antibody sequences, structures, and biophysical properties is increasingly enabling the development of predictive models and computational tools for the "developability assessment" of antibody drug candidates. Here, we provide an overview of the antibody informatics tools applicable to the prediction of developability issues such as stability, aggregation, immunogenicity, and chemical degradation. We further evaluate the opportunities and challenges of using biopharmaceutical informatics for drug discovery and optimization. Finally, we discuss the potential of developability guidelines based on in silico metrics that can be used for the assessment of antibody stability and manufacturability.
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Affiliation(s)
- Rahul Khetan
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Robin Curtis
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | | | | | - Uddipan Kar
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | | | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.,Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | | | - Pietro Sormanni
- Chemistry of Health, Yusuf Hamied Department of Chemistry, University of Cambridge
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.,Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.,The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jim Warwicker
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Andrew C R Martin
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
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23
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Wang Z, Muecksch F, Cho A, Gaebler C, Hoffmann HH, Ramos V, Zong S, Cipolla M, Johnson B, Schmidt F, DaSilva J, Bednarski E, Tanfous TB, Raspe R, Yao K, Lee YE, Chen T, Turroja M, Milard KG, Dizon J, Kaczynska A, Gazumyan A, Oliveira TY, Rice CM, Caskey M, Bieniasz PD, Hatziioannou T, Barnes CO, Nussenzweig MC. Conserved Neutralizing Epitopes on the N-Terminal Domain of Variant SARS-CoV-2 Spike Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022. [PMID: 35132412 PMCID: PMC8820657 DOI: 10.1101/2022.02.01.478695] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
SARS-CoV-2 infection or vaccination produces neutralizing antibody responses that contribute to better clinical outcomes. The receptor binding domain (RBD) and the N-terminal domain (NTD) of the spike trimer (S) constitute the two major neutralizing targets for the antibody system. Neutralizing antibodies targeting the RBD bind to several different sites on this domain. In contrast, most neutralizing antibodies to NTD characterized to date bind to a single supersite, however these antibodies were obtained by methods that were not NTD specific. Here we use NTD specific probes to focus on anti-NTD memory B cells in a cohort of pre-omicron infected individuals some of which were also vaccinated. Of 275 NTD binding antibodies tested 103 neutralized at least one of three tested strains: Wuhan-Hu-1, Gamma, or PMS20, a synthetic variant which is extensively mutated in the NTD supersite. Among the 43 neutralizing antibodies that were further characterized, we found 6 complementation groups based on competition binding experiments. 58% targeted epitopes outside the NTD supersite, and 58% neutralized either Gamma or Omicron, but only 14% were broad neutralizers. Three of the broad neutralizers were characterized structurally. C1520 and C1791 recognize epitopes on opposite faces of the NTD with a distinct binding pose relative to previously described antibodies allowing for greater potency and cross-reactivity with 7 different variants including Beta, Delta, Gamma and Omicron. Antibody C1717 represents a previously uncharacterized class of NTD-directed antibodies that recognizes the viral membrane proximal side of the NTD and SD2 domain, leading to cross-neutralization of Beta, Gamma and Omicron. We conclude SARS-CoV-2 infection and/or Wuhan-Hu-1 mRNA vaccination produces a diverse collection of memory B cells that produce anti-NTD antibodies some of which can neutralize variants of concern. Rapid recruitment of these cells into the antibody secreting plasma cell compartment upon re-infection likely contributes to the relatively benign course of subsequent infections with SARS-CoV-2 variants including omicron.
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Affiliation(s)
- Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Shuai Zong
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Briana Johnson
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Justin DaSilva
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Eva Bednarski
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Tarek Ben Tanfous
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Raphael Raspe
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Kaihui Yao
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Yu E Lee
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Teresia Chen
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Martina Turroja
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Katrina G Milard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Juan Dizon
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Kaczynska
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA.,Howard Hughes Medical Institute
| | | | - Christopher O Barnes
- Department of Biology, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.,Howard Hughes Medical Institute
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24
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NGS Analysis of Clonality and Minimal Residual Disease in a Patient with Concurrent Richter's Transformation and CLL/SLL. Case Rep Hematol 2022; 2021:9740281. [PMID: 34992887 PMCID: PMC8727142 DOI: 10.1155/2021/9740281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 11/08/2021] [Accepted: 11/27/2021] [Indexed: 11/18/2022] Open
Abstract
B-cell lymphomas are neoplastic proliferations of clonal B lymphocytes. Clonality is generally determined by PCR amplification of VDJ rearrangements in the IgH heavy chain or VJ rearrangements in Igκ/Igλ light chain genes followed by capillary electrophoresis. More recently, next-generation sequencing (NGS) has been used to detect clonality in B-cell lymphomas because of the exponential amount of information that is obtained beyond just detecting a clonal population. The additional information obtained is useful for diagnostic confirmation, prognosis assessment, and response to therapy. In this study, we utilized NGS analysis to characterize two histologically distinct lymphomas (DLBCL and CLL/SLL) that were detected contemporaneously in an asymptomatic patient. NGS analysis showed that the same VDJ rearrangement was present in nodal (DLBCL) and marrow (CLL/SLL) biopsies confirming that the DLBCL resulted from Richter's transformation of a subclinical CLL/SLL. The V region of the rearrangement remained unmutated without somatic hypermutation. In silico analysis showed that the HCDR3 sequence was heterogeneous and not stereotypic. Minimal residual disease analysis by NGS showed that the tumor clone decreased by 2.84 logs in the bone marrow after R-CHOP therapy. However, a small number of tumor cells were still detected in the peripheral blood after R-CHOP therapy. Subsequent allogeneic transplantation was successful in eradicating the tumor clone and achieving deep molecular remission. We show that NGS analysis facilitated clinical management in our patient by helping to characterize the VDJ rearrangement in detail and by tracking minimal residual disease with high sensitivity and specificity.
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25
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Schmitz S, Schmitz EA, Crowe JE, Meiler J. The human antibody sequence space and structural design of the V, J regions, and CDRH3 with Rosetta. MAbs 2022; 14:2068212. [PMID: 35544469 PMCID: PMC9103704 DOI: 10.1080/19420862.2022.2068212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 04/05/2022] [Accepted: 04/14/2022] [Indexed: 12/14/2022] Open
Abstract
The human adaptive immune response enables the targeting of epitopes on pathogens with high specificity. Infection with a pathogen induces somatic hyper-mutation and B-cell selection processes that govern the shape and diversity of the antibody sequence landscape. To date, even the largest immunome repertoires of adaptive immune receptors acquired by next-generation sequencing cannot fully capture the vast antibody sequence space of a single individual, which is estimated to be at least 1012 potential sequences. Degeneracy of the genetic code means that the number of possible nucleotide triplets (64) is greater than the number of canonical amino acids (20), resulting in some amino acids being encoded by multiple triplets and different amino acids sharing the same nucleotide in 1 or 2 positions in the triplet. We hypothesize that the degeneracy of the genetic code can be used to statistically model an enlarged space of human antibody amino acid sequences, accommodating for the discrepancy between the observed and the hypothesized antibody sequence space. Facilitated by Bayesian statistics and immunome repertoire clustering, we calculated amino acid probabilities from single nucleotide frequencies to infer a human amino acid sequence space that is used to design human-like antibodies with Rosetta. We show that antibodies designed with our restraints are on average up to 16.6% more human-like in the V and J regions compared to the Rosetta designs produced without constraints. The human-likeness of the heavy-chain CDR3 region (CDRH3) could be increased for 8 of 27 antibodies compared to Rosetta designs with a similar number of mutations and could be successfully applied on Mus musculus antibodies to demonstrate humanization.
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Affiliation(s)
- Samuel Schmitz
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States
- Center of Structural Biology, Vanderbilt University, Nashville, Tennessee, United States
| | - Emily A. Schmitz
- Center of Structural Biology, Vanderbilt University, Nashville, Tennessee, United States
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, Tennessee, United States
| | - James E. Crowe
- Vanderbilt Vaccine Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States
- Departments of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States
- Center of Structural Biology, Vanderbilt University, Nashville, Tennessee, United States
- Institute for Drug Discovery, University Leipzig Medical School, Leipzig, Germany
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26
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Akbar R, Robert PA, Weber CR, Widrich M, Frank R, Pavlović M, Scheffer L, Chernigovskaya M, Snapkov I, Slabodkin A, Mehta BB, Miho E, Lund-Johansen F, Andersen JT, Hochreiter S, Hobæk Haff I, Klambauer G, Sandve GK, Greiff V. In silico proof of principle of machine learning-based antibody design at unconstrained scale. MAbs 2022; 14:2031482. [PMID: 35377271 PMCID: PMC8986205 DOI: 10.1080/19420862.2022.2031482] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Generative machine learning (ML) has been postulated to become a major driver in the computational design of antigen-specific monoclonal antibodies (mAb). However, efforts to confirm this hypothesis have been hindered by the infeasibility of testing arbitrarily large numbers of antibody sequences for their most critical design parameters: paratope, epitope, affinity, and developability. To address this challenge, we leveraged a lattice-based antibody-antigen binding simulation framework, which incorporates a wide range of physiological antibody-binding parameters. The simulation framework enables the computation of synthetic antibody-antigen 3D-structures, and it functions as an oracle for unrestricted prospective evaluation and benchmarking of antibody design parameters of ML-generated antibody sequences. We found that a deep generative model, trained exclusively on antibody sequence (one dimensional: 1D) data can be used to design conformational (three dimensional: 3D) epitope-specific antibodies, matching, or exceeding the training dataset in affinity and developability parameter value variety. Furthermore, we established a lower threshold of sequence diversity necessary for high-accuracy generative antibody ML and demonstrated that this lower threshold also holds on experimental real-world data. Finally, we show that transfer learning enables the generation of high-affinity antibody sequences from low-N training data. Our work establishes a priori feasibility and the theoretical foundation of high-throughput ML-based mAb design.
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Affiliation(s)
- Rahmad Akbar
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Norway
| | - Philippe A Robert
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Norway
| | - Cédric R Weber
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Michael Widrich
- Ellis Unit Linz and Lit Ai Lab, Institute for Machine Learning, Johannes Kepler University Linz, Linz, Austria
| | - Robert Frank
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Norway
| | | | | | - Maria Chernigovskaya
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Norway
| | - Igor Snapkov
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Norway
| | - Andrei Slabodkin
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Norway
| | - Brij Bhushan Mehta
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Norway
| | - Enkelejda Miho
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
| | - Fridtjof Lund-Johansen
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Norway
| | - Jan Terje Andersen
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Norway.,Institute of Clinical Medicine, Department of Pharmacology, University of Oslo, Oslo, Norway
| | - Sepp Hochreiter
- Ellis Unit Linz and Lit Ai Lab, Institute for Machine Learning, Johannes Kepler University Linz, Linz, Austria.,Institute of Advanced Research in Artificial Intelligence (IARAI), Austria
| | | | - Günter Klambauer
- Ellis Unit Linz and Lit Ai Lab, Institute for Machine Learning, Johannes Kepler University Linz, Linz, Austria
| | | | - Victor Greiff
- Department of Immunology, Oslo University Hospital Rikshospitalet and University of Oslo, Norway
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27
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Slabodkin A, Chernigovskaya M, Mikocziova I, Akbar R, Scheffer L, Pavlović M, Bashour H, Snapkov I, Mehta BB, Weber CR, Gutierrez-Marcos J, Sollid LM, Haff IH, Sandve GK, Robert PA, Greiff V. Individualized VDJ recombination predisposes the available Ig sequence space. Genome Res 2021; 31:2209-2224. [PMID: 34815307 PMCID: PMC8647828 DOI: 10.1101/gr.275373.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 10/20/2021] [Indexed: 11/25/2022]
Abstract
The process of recombination between variable (V), diversity (D), and joining (J) immunoglobulin (Ig) gene segments determines an individual's naive Ig repertoire and, consequently, (auto)antigen recognition. VDJ recombination follows probabilistic rules that can be modeled statistically. So far, it remains unknown whether VDJ recombination rules differ between individuals. If these rules differed, identical (auto)antigen-specific Ig sequences would be generated with individual-specific probabilities, signifying that the available Ig sequence space is individual specific. We devised a sensitivity-tested distance measure that enables inter-individual comparison of VDJ recombination models. We discovered, accounting for several sources of noise as well as allelic variation in Ig sequencing data, that not only unrelated individuals but also human monozygotic twins and even inbred mice possess statistically distinguishable immunoglobulin recombination models. This suggests that, in addition to genetic, there is also nongenetic modulation of VDJ recombination. We demonstrate that population-wide individualized VDJ recombination can result in orders of magnitude of difference in the probability to generate (auto)antigen-specific Ig sequences. Our findings have implications for immune receptor-based individualized medicine approaches relevant to vaccination, infection, and autoimmunity.
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Affiliation(s)
- Andrei Slabodkin
- Department of Immunology and Oslo University Hospital, University of Oslo, 0372 Oslo, Norway
| | - Maria Chernigovskaya
- Department of Immunology and Oslo University Hospital, University of Oslo, 0372 Oslo, Norway
| | - Ivana Mikocziova
- Department of Immunology and Oslo University Hospital, University of Oslo, 0372 Oslo, Norway
| | - Rahmad Akbar
- Department of Immunology and Oslo University Hospital, University of Oslo, 0372 Oslo, Norway
| | - Lonneke Scheffer
- Department of Informatics, University of Oslo, 0373 Oslo, Norway
| | - Milena Pavlović
- Department of Informatics, University of Oslo, 0373 Oslo, Norway
| | - Habib Bashour
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Igor Snapkov
- Department of Immunology and Oslo University Hospital, University of Oslo, 0372 Oslo, Norway
| | - Brij Bhushan Mehta
- Department of Immunology and Oslo University Hospital, University of Oslo, 0372 Oslo, Norway
| | - Cédric R Weber
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | | | - Ludvig M Sollid
- Department of Immunology and Oslo University Hospital, University of Oslo, 0372 Oslo, Norway
| | | | | | - Philippe A Robert
- Department of Immunology and Oslo University Hospital, University of Oslo, 0372 Oslo, Norway
| | - Victor Greiff
- Department of Immunology and Oslo University Hospital, University of Oslo, 0372 Oslo, Norway
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28
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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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29
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Biavati L, Huff CA, Ferguson A, Sidorski A, Stevens MA, Rudraraju L, Zucchinetti C, Ali SA, Imus P, Gocke CB, Gittelman RM, Johnson S, Sanders C, Vignali M, Gandhi A, Ye X, Noonan KA, Borrello I. An Allogeneic Multiple Myeloma GM-CSF-Secreting Vaccine with Lenalidomide Induces Long-term Immunity and Durable Clinical Responses in Patients in Near Complete Remission. Clin Cancer Res 2021; 27:6696-6708. [PMID: 34667029 DOI: 10.1158/1078-0432.ccr-21-1916] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/29/2021] [Accepted: 09/24/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE This proof-of-principle clinical trial evaluated whether an allogeneic multiple myeloma GM-CSF-secreting vaccine (MM-GVAX) in combination with lenalidomide could deepen the clinical response in patients with multiple myeloma in sustained near complete remission (nCR). PATIENTS AND METHODS Fifteen patients on lenalidomide were treated with MM-GVAX and pneumococcal conjugate vaccine (PCV; Prevnar) at 1, 2, 3, and 6 months. RESULTS Eight patients (53.3%) achieved a true CR. With a median follow-up of 5 years, the median progression-free survival had not been reached, and the median overall survival was 7.8 years from enrollment. MM-GVAX induced clonal T-cell expansion and measurable cytokine responses that persisted up to 7 years in all patients. At baseline, a higher minimal residual disease was predictive of early relapse. After vaccination, a lack of both CD27-DNAM1-CD8+ T cells and antigen-presenting cells was associated with disease progression. CONCLUSIONS MM-GVAX, along with lenalidomide, effectively primed durable immunity and resulted in long-term disease control, as suggested by the reappearance of a detectable, fluctuating M-spike without meeting the criteria for clinical relapse. For patients in a nCR, MM-GVAX administration was safe and resulted in prolonged clinical responses.
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Affiliation(s)
- Luca Biavati
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Carol Ann Huff
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Anna Ferguson
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Amy Sidorski
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - M Amanda Stevens
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Lakshmi Rudraraju
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Cristina Zucchinetti
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Syed Abbas Ali
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Philip Imus
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Christian B Gocke
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | | | | | | | | | | | - Xiaobu Ye
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Kimberly A Noonan
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland
| | - Ivan Borrello
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland.
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30
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Ghraichy M, von Niederhäusern V, Kovaltsuk A, Galson JD, Deane CM, Trück J. Different B cell subpopulations show distinct patterns in their IgH repertoire metrics. eLife 2021; 10:73111. [PMID: 34661527 PMCID: PMC8560093 DOI: 10.7554/elife.73111] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/17/2021] [Indexed: 12/11/2022] Open
Abstract
Several human B cell subpopulations are recognised in the peripheral blood, which play distinct roles in the humoral immune response. These cells undergo developmental and maturational changes involving VDJ recombination, somatic hypermutation and class switch recombination, altogether shaping their immunoglobulin heavy chain (IgH) repertoire. Here, we sequenced the IgH repertoire of naïve, marginal zone, switched and plasma cells from 10 healthy adults along with matched unsorted and in silico separated CD19+ bulk B cells. Using advanced bioinformatic analysis and machine learning, we show that sorted B cell subpopulations are characterised by distinct repertoire characteristics on both the individual sequence and the repertoire level. Sorted subpopulations shared similar repertoire characteristics with their corresponding in silico separated subsets. Furthermore, certain IgH repertoire characteristics correlated with the position of the constant region on the IgH locus. Overall, this study provides unprecedented insight over mechanisms of B cell repertoire control in peripherally circulating B cell subpopulations.
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Affiliation(s)
- Marie Ghraichy
- Division of Immunology, University Children's Hospital and Children's Research Center, University of Zurich (UZH), Zurich, Switzerland
| | - Valentin von Niederhäusern
- Division of Immunology, University Children's Hospital and Children's Research Center, University of Zurich (UZH), Zurich, Switzerland
| | | | - Jacob D Galson
- Division of Immunology, University Children's Hospital and Children's Research Center, University of Zurich (UZH), Zurich, Switzerland.,Alchemab Therapeutics Ltd, London, United Kingdom
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Johannes Trück
- Division of Immunology, University Children's Hospital and Children's Research Center, University of Zurich (UZH), Zurich, Switzerland
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31
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Japp AS, Meng W, Rosenfeld AM, Perry DJ, Thirawatananond P, Bacher RL, Liu C, Gardner JS, Atkinson MA, Kaestner KH, Brusko TM, Naji A, Luning Prak ET, Betts MR. TCR +/BCR + dual-expressing cells and their associated public BCR clonotype are not enriched in type 1 diabetes. Cell 2021; 184:827-839.e14. [PMID: 33545036 DOI: 10.1016/j.cell.2020.11.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 06/30/2020] [Accepted: 11/19/2020] [Indexed: 12/20/2022]
Abstract
Ahmed and colleagues recently described a novel hybrid lymphocyte expressing both a B and T cell receptor, termed double expresser (DE) cells. DE cells in blood of type 1 diabetes (T1D) subjects were present at increased numbers and enriched for a public B cell clonotype. Here, we attempted to reproduce these findings. While we could identify DE cells by flow cytometry, we found no association between DE cell frequency and T1D status. We were unable to identify the reported public B cell clone, or any similar clone, in bulk B cells or sorted DE cells from T1D subjects or controls. We also did not observe increased usage of the public clone VH or DH genes in B cells or in sorted DE cells. Taken together, our findings suggest that DE cells and their alleged public clonotype are not enriched in T1D. This Matters Arising paper is in response to Ahmed et al. (2019), published in Cell. See also the response by Ahmed et al. (2021), published in this issue.
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Affiliation(s)
- Alberto Sada Japp
- Department of Microbiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Wenzhao Meng
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Aaron M Rosenfeld
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Daniel J Perry
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, College of Medicine, Gainesville, FL 32610, USA
| | - Puchong Thirawatananond
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, College of Medicine, Gainesville, FL 32610, USA
| | - Rhonda L Bacher
- Department of Biostatistics, University of Florida, College of Medicine, Gainesville, FL 32610, USA
| | - Chengyang Liu
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Surgery, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jay S Gardner
- Department of Microbiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | -
- The Human Pancreas Analysis Program, Perelman School of Medicine, Philadelphia, PA 19104
| | - Mark A Atkinson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, College of Medicine, Gainesville, FL 32610, USA
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104
| | - Todd M Brusko
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida Diabetes Institute, College of Medicine, Gainesville, FL 32610, USA
| | - Ali Naji
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Surgery, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Eline T Luning Prak
- Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Michael R Betts
- Department of Microbiology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Immunology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA.
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32
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Foord E, Arruda LCM, Gaballa A, Klynning C, Uhlin M. Characterization of ascites- and tumor-infiltrating γδ T cells reveals distinct repertoires and a beneficial role in ovarian cancer. Sci Transl Med 2021; 13:13/577/eabb0192. [PMID: 33472952 DOI: 10.1126/scitranslmed.abb0192] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 09/15/2020] [Accepted: 12/16/2020] [Indexed: 12/18/2022]
Abstract
The role of γδ T cells in antitumor immunity has been under investigation for the past two decades, but little is known about their contribution to clinical outcomes in patients. Here, we set out to define the clonotypic, phenotypic, and functional features of γδ T cells in peripheral blood, ascites, and metastatic tumor tissue from patients with advanced epithelial ovarian cancer. T cell receptor (TCR) sequencing of the γ chain revealed that tumor-infiltrating γδ T cells have a unique and skewed repertoire with high TCR diversity and low clonality. In contrast, ascites-derived γδ T cells presented a lower TCR diversity and higher clonality, suggesting a TCR-dependent clonal focusing at this site. Further investigation showed that tumor samples had abundant γδ T cells with a tissue-resident, activation-associated phenotype, less usage of Vγ9 and an impaired response to adaptive-associated stimuli, implying an innate-like activation pathway, rather than an adaptive TCR-engaging pathway, at these tumor sites. Furthermore, high γδ T cell cytokine responsiveness upon stimulation was associated with a favorable outcome for patients in terms of both overall survival and reduced residual tumor burden after primary surgery. Last, the functionality of γδ T cells and patient survival were negatively affected by the proportions of CD39-expressing T cells, highlighting the potential of CD39 as a target to improve γδ T cell responses and unleash their antitumor capabilities.
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Affiliation(s)
- Emelie Foord
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 171 77 Stockholm, Sweden.
| | - Lucas C M Arruda
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Ahmed Gaballa
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 171 77 Stockholm, Sweden.,Department of Clinical Biochemistry, National Liver Institute, Menoufia University, 511 32 Shebin Elkom, Egypt
| | - Charlotte Klynning
- Department of Gynecological Oncology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Michael Uhlin
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 171 77 Stockholm, Sweden.,Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital, 141 86 Stockholm, Sweden.,Department of Applied Physics, Royal Institute of Technology, 100 44 Stockholm, Sweden
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33
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Andreano E, Paciello I, Bardelli M, Tavarini S, Sammicheli C, Frigimelica E, Guidotti S, Torricelli G, Biancucci M, D’Oro U, Chandramouli S, Bottomley MJ, Rappuoli R, Finco O, Buricchi F. The respiratory syncytial virus (RSV) prefusion F-protein functional antibody repertoire in adult healthy donors. EMBO Mol Med 2021; 13:e14035. [PMID: 33998144 PMCID: PMC8185550 DOI: 10.15252/emmm.202114035] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/10/2021] [Accepted: 04/13/2021] [Indexed: 12/27/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the leading cause of death from lower respiratory tract infection in infants and children, and is responsible for considerable morbidity and mortality in older adults. Vaccines for pregnant women and elderly which are in phase III clinical studies target people with pre-existing natural immunity against RSV. To investigate the background immunity which will be impacted by vaccination, we single cell-sorted human memory B cells and dissected functional and genetic features of neutralizing antibodies (nAbs) induced by natural infection. Most nAbs recognized both the prefusion and postfusion conformations of the RSV F-protein (cross-binders) while a smaller fraction bound exclusively to the prefusion conformation. Cross-binder nAbs used a wide array of gene rearrangements, while preF-binder nAbs derived mostly from the expansion of B-cell clonotypes from the IGHV1 germline. This latter class of nAbs recognizes an epitope located between Site Ø, Site II, and Site V on the F-protein, identifying an important site of pathogen vulnerability.
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Affiliation(s)
- Emanuele Andreano
- Department of Life SciencesUniversity of SienaSienaItaly
- GSK VaccinesSienaItaly
- Present address:
Monoclonal Antibody Discovery (MAD) LabFondazione Toscana Life SciencesSienaItaly
| | - Ida Paciello
- GSK VaccinesSienaItaly
- Present address:
Monoclonal Antibody Discovery (MAD) LabFondazione Toscana Life SciencesSienaItaly
| | | | | | | | | | | | | | | | | | - Sumana Chandramouli
- GSK VaccinesRockvilleMDUSA
- Present address:
Moderna Therapeutics IncCambridgeMAUSA
| | | | - Rino Rappuoli
- GSK VaccinesSienaItaly
- Faculty of MedicineImperial CollegeLondonUK
- Monoclonal Antibody Discovery (MAD) LabFondazione Toscana Life SciencesSienaItaly
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34
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Zhang Z, Jara CJ, Singh M, Xu H, Goodnow CC, Jackson KJ, Reed JH. Human transitional and IgM low mature naïve B cells preserve permissive B-cell receptors. Immunol Cell Biol 2021; 99:865-878. [PMID: 33988890 PMCID: PMC8453828 DOI: 10.1111/imcb.12478] [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: 04/07/2021] [Revised: 05/11/2021] [Accepted: 05/11/2021] [Indexed: 12/02/2022]
Abstract
The level of immunoglobulin M (IgM) displayed on the surface of peripheral blood B cells exhibits a broad dynamic range and has been associated with both development and selection. To determine whether IgM surface expression associates with distinct immunoglobulin heavy‐chain (IGH) repertoire properties, we performed deep IgM sequencing of peripheral blood transitional and mature naïve B cells in the upper and lower quartiles of surface IgM expression for 12 healthy donors. Mature naïve B cells within the lowest quartile for surface IgM expression displayed more diverse IGH features including increased complementarity‐determining region 3 length, IGHJ6 segment usage and aromatic amino acids compared with mature naïve B cells with high surface IgM. There were no differences between IGH repertoires for transitional B cells with high or low surface IgM. These findings suggest that a selection checkpoint during progression of transitional to mature naïve B cells reduces the breadth of the IGH repertoire among high surface IgM B cells but that diversity is preserved in B cells expressing low levels of surface IgM.
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Affiliation(s)
- Zhiguo Zhang
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Christopher J Jara
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Faculty of Medicine, St. Vincent's Clinical School, UNSW, Sydney, NSW, Australia
| | - Mandeep Singh
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Faculty of Medicine, St. Vincent's Clinical School, UNSW, Sydney, NSW, Australia
| | - Huji Xu
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Christopher C Goodnow
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,School of Medical Sciences and Cellular Genomics Futures Institute, UNSW, Sydney, NSW, Australia
| | | | - Joanne H Reed
- Garvan Institute of Medical Research, Sydney, NSW, Australia.,Faculty of Medicine, St. Vincent's Clinical School, UNSW, Sydney, NSW, Australia
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35
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Sangesland M, Yousif AS, Ronsard L, Kazer SW, Zhu AL, Gatter GJ, Hayward MR, Barnes RM, Quirindongo-Crespo M, Rohrer D, Lonberg N, Kwon D, Shalek AK, Lingwood D. A Single Human V H-gene Allows for a Broad-Spectrum Antibody Response Targeting Bacterial Lipopolysaccharides in the Blood. Cell Rep 2021; 32:108065. [PMID: 32846123 PMCID: PMC7446668 DOI: 10.1016/j.celrep.2020.108065] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/05/2020] [Accepted: 07/31/2020] [Indexed: 02/03/2023] Open
Abstract
B cell receptors (BCRs) display a combination of variable (V)-gene-encoded complementarity determining regions (CDRs) and adaptive/hypervariable CDR3 loops to engage antigens. It has long been proposed that the former tune for recognition of pathogens or groups of pathogens. To experimentally evaluate this within the human antibody repertoire, we perform immune challenges in transgenic mice that bear diverse human CDR3 and light chains but are constrained to different human VH-genes. We find that, of six commonly deployed VH sequences, only those CDRs encoded by IGHV1-2∗02 enable polyclonal antibody responses against bacterial lipopolysaccharide (LPS) when introduced to the bloodstream. The LPS is from diverse strains of gram-negative bacteria, and the VH-gene-dependent responses are directed against the non-variable and universal saccrolipid substructure of this antigen. This reveals a broad-spectrum anti-LPS response in which germline-encoded CDRs naturally hardwire the human antibody repertoire for recognition of a conserved microbial target.
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Affiliation(s)
- Maya Sangesland
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Ashraf S Yousif
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Larance Ronsard
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Samuel W Kazer
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science (IMES), Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St., Cambridge, MA 02142, USA
| | - Alex Lee Zhu
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - G James Gatter
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science (IMES), Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St., Cambridge, MA 02142, USA
| | - Matthew R Hayward
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Ralston M Barnes
- Bristol-Myers Squibb, 700 Bay Rd., Redwood City, CA 94063-2478, USA
| | | | - Daniel Rohrer
- Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St., Cambridge, MA 02142, USA
| | - Nils Lonberg
- Bristol-Myers Squibb, 700 Bay Rd., Redwood City, CA 94063-2478, USA
| | - Douglas Kwon
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Division of Infectious Diseases, Massachusetts General Hospital. 55 Fruit St., Boston, MA 02114, USA
| | - Alex K Shalek
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA; Institute for Medical Engineering and Science (IMES), Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; Broad Institute of Massachusetts Institute of Technology and Harvard, 415 Main St., Cambridge, MA 02142, USA
| | - Daniel Lingwood
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA.
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36
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Schmitz S, Soto C, Crowe JE, Meiler J. Human-likeness of antibody biologics determined by back-translation and comparison with large antibody variable gene repertoires. MAbs 2021; 12:1758291. [PMID: 32397786 PMCID: PMC8648325 DOI: 10.1080/19420862.2020.1758291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The antibody (Ab) germline gene rearrangement of variable (V), diversity (D), and joining (J) gene segments, as well as somatic hypermutation, give rise to the human Ab variable gene sequence repertoire. It is common to characterize single nucleotide frequencies of the variable region by alignment to species-specific wildtype germline genes. The increasing application of next-generation sequencing to immune repertoire studies has led to the compilation of increasing large adaptive immunome receptor repertoire datasets. We have developed a method that maps the sequence of a target Ab onto an immunome dataset of 326 million human Ab sequences. For this purpose, we created a position- and gene-specific scoring matrix (PGSSM) and its corresponding antibody similarity score. We characterized our PGSSM score and found that it strongly correlated with the phylogenetic distance of 181,355 Ab sequences from GenBank across 20 species. The most likely human nucleotide back-translation was obtained given only PGSSMs and the amino acid sequence of an Ab achieving a nucleotide sequence recovery of 95.9% and 97.2% for human heavy and light chains, respectively. In conclusion, the scoring of our back-translation is a valuable estimate for the similarity of an Ab sequence to the natural human repertoire. As expected, Ab therapeutic molecules developed from a human source showed a higher similarity to the repertoire than engineered Abs. Thus, the PGSSM metric introduced here can be used to engineer human-like Ab therapeutics.
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Affiliation(s)
- Samuel Schmitz
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Cinque Soto
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.,The Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James E Crowe
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA.,The Vaccine Center, Vanderbilt University Medical Center, Nashville, TN, USA.,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.,Institute for Drug Development, Leipzig University Medical School, Leipzig, SAC, Germany
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37
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Agudelo M, Palus M, Keeffe JR, Bianchini F, Svoboda P, Salát J, Peace A, Gazumyan A, Cipolla M, Kapoor T, Guidetti F, Yao KH, Elsterová J, Teislerová D, Chrdle A, Hönig V, Oliveira T, West AP, Lee YE, Rice CM, MacDonald MR, Bjorkman PJ, Růžek D, Robbiani DF, Nussenzweig MC. Broad and potent neutralizing human antibodies to tick-borne flaviviruses protect mice from disease. J Exp Med 2021; 218:e20210236. [PMID: 33831141 PMCID: PMC8040517 DOI: 10.1084/jem.20210236] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/30/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) is an emerging human pathogen that causes potentially fatal disease with no specific treatment. Mouse monoclonal antibodies are protective against TBEV, but little is known about the human antibody response to infection. Here, we report on the human neutralizing antibody response to TBEV in a cohort of infected and vaccinated individuals. Expanded clones of memory B cells expressed closely related anti-envelope domain III (EDIII) antibodies in both groups of volunteers. However, the most potent neutralizing antibodies, with IC50s below 1 ng/ml, were found only in individuals who recovered from natural infection. These antibodies also neutralized other tick-borne flaviviruses, including Langat, louping ill, Omsk hemorrhagic fever, Kyasanur forest disease, and Powassan viruses. Structural analysis revealed a conserved epitope near the lateral ridge of EDIII adjoining the EDI-EDIII hinge region. Prophylactic or early therapeutic antibody administration was effective at low doses in mice that were lethally infected with TBEV.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Monoclonal/administration & dosage
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/administration & dosage
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/administration & dosage
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Cells, Cultured
- Cohort Studies
- Cross Reactions/immunology
- Encephalitis Viruses, Tick-Borne/drug effects
- Encephalitis Viruses, Tick-Borne/immunology
- Encephalitis Viruses, Tick-Borne/physiology
- Encephalitis, Tick-Borne/immunology
- Encephalitis, Tick-Borne/prevention & control
- Encephalitis, Tick-Borne/virology
- Epitopes/immunology
- Female
- Humans
- Immunoglobulin G/administration & dosage
- Immunoglobulin G/immunology
- Mice, Inbred BALB C
- Sequence Homology, Amino Acid
- Survival Analysis
- Viral Envelope Proteins/genetics
- Viral Envelope Proteins/immunology
- Mice
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Affiliation(s)
- Marianna Agudelo
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Martin Palus
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Veterinary Research Institute, Brno, Czech Republic
| | - Jennifer R. Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Filippo Bianchini
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Pavel Svoboda
- Veterinary Research Institute, Brno, Czech Republic
- Department of Pharmacology and Pharmacy, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Jiří Salát
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Veterinary Research Institute, Brno, Czech Republic
| | - Avery Peace
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Tania Kapoor
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Francesca Guidetti
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Kai-Hui Yao
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Jana Elsterová
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Veterinary Research Institute, Brno, Czech Republic
| | | | - Aleš Chrdle
- Hospital České Budějovice, České Budějovice, Czech Republic
- Faculty of Social and Health Sciences, University of South Bohemia, České Budějovice, Czech Republic
- Royal Liverpool University Hospital, Liverpool, UK
| | - Václav Hönig
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Veterinary Research Institute, Brno, Czech Republic
| | - Thiago Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Yu E. Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Margaret R. MacDonald
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Daniel Růžek
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Veterinary Research Institute, Brno, Czech Republic
| | - Davide F. Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY
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38
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Prabakaran P, Chowdhury PS. Landscape of Non-canonical Cysteines in Human V H Repertoire Revealed by Immunogenetic Analysis. Cell Rep 2021; 31:107831. [PMID: 32610132 PMCID: PMC7326410 DOI: 10.1016/j.celrep.2020.107831] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/02/2020] [Accepted: 06/08/2020] [Indexed: 12/21/2022] Open
Abstract
Human antibody repertoire data captured through next-generation sequencing (NGS) has enabled deeper insights into B cell immunogenetics and paratope diversity. By analyzing large public NGS datasets, we map the landscape of non-canonical cysteines in human variable heavy-chain domains (VHs) at the repertoire level. We identify remarkable usage of non-canonical cysteines within the heavy-chain complementarity-determining region 3 (CDR-H3) and other CDRs and framework regions. Furthermore, our study reveals the diversity and location of non-canonical cysteines and their associated motifs in human VHs, which are reminiscent of and more complex than those found in other non-human species such as chicken, camel, llama, shark, and cow. These results explain how non-canonical cysteines strategically occur in the human antibodyome to expand its paratope space. This study will guide the design of human antibodies harboring disulfide-stabilized long CDR-H3s to access difficult-to-target epitopes and influence a paradigm shift in developability involving non-canonical cysteines. NGS-based non-canonical cysteine landscape in human VHs 1 to 8 non-canonical cysteines and up to 30% in long CDR-H3s An array of potential disulfide motifs adds paratope diversity Non-canonical cysteines in human VHs are reminiscent of lower animals
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Chen F, Tzarum N, Lin X, Giang E, Velázquez-Moctezuma R, Augestad EH, Nagy K, He L, Hernandez M, Fouch ME, Grinyó A, Chavez D, Doranz BJ, Prentoe J, Stanfield RL, Lanford R, Bukh J, Wilson IA, Zhu J, Law M. Functional convergence of a germline-encoded neutralizing antibody response in rhesus macaques immunized with HCV envelope glycoproteins. Immunity 2021; 54:781-796.e4. [PMID: 33675683 PMCID: PMC8046733 DOI: 10.1016/j.immuni.2021.02.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/14/2020] [Accepted: 02/10/2021] [Indexed: 12/14/2022]
Abstract
Human IGHV1-69-encoded broadly neutralizing antibodies (bnAbs) that target the hepatitis C virus (HCV) envelope glycoprotein (Env) E2 are important for protection against HCV infection. An IGHV1-69 ortholog gene, VH1.36, is preferentially used for bnAbs isolated from HCV Env-immunized rhesus macaques (RMs). Here, we studied the genetic, structural, and functional properties of VH1.36-encoded bnAbs generated by vaccination, in comparison to IGHV1-69-encoded bnAbs from HCV patients. Global B cell repertoire analysis confirmed the expansion of VH1.36-derived B cells in immunized animals. Most E2-specific, VH1.36-encoded antibodies cross-neutralized HCV. Crystal structures of two RM bnAbs with E2 revealed that the RM bnAbs engaged conserved E2 epitopes using similar molecular features as human bnAbs but with a different binding mode. Longitudinal analyses of the RM antibody repertoire responses during immunization indicated rapid lineage development of VH1.36-encoded bnAbs with limited somatic hypermutation. Our findings suggest functional convergence of a germline-encoded bnAb response to HCV Env with implications for vaccination in humans.
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Affiliation(s)
- Fang Chen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Netanel Tzarum
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Xiaohe Lin
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Erick Giang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Rodrigo Velázquez-Moctezuma
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Elias H Augestad
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Kenna Nagy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linling He
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | | | | | - Deborah Chavez
- Southwest National Primate Research Center at Texas Biomedical Research Institute, San Antonio, TX 788227, USA
| | | | - Jannick Prentoe
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Robyn L Stanfield
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Robert Lanford
- Southwest National Primate Research Center at Texas Biomedical Research Institute, San Antonio, TX 788227, USA
| | - Jens Bukh
- Copenhagen Hepatitis C Program (CO-HEP), Department of Infectious Diseases, Hvidovre Hospital, and Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Ian A Wilson
- 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 92037, USA.
| | - Jiang Zhu
- Department of Immunology and Microbiology, 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.
| | - Mansun Law
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Wang Z, Schmidt F, Weisblum Y, Muecksch F, Barnes CO, Finkin S, Schaefer-Babajew D, Cipolla M, Gaebler C, Lieberman JA, Oliveira TY, Yang Z, Abernathy ME, Huey-Tubman KE, Hurley A, Turroja M, West KA, Gordon K, Millard KG, Ramos V, Da Silva J, Xu J, Colbert RA, Patel R, Dizon J, Unson-O'Brien C, Shimeliovich I, Gazumyan A, Caskey M, Bjorkman PJ, Casellas R, Hatziioannou T, Bieniasz PD, Nussenzweig MC. mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants. Nature 2021; 592:616-622. [PMID: 33567448 PMCID: PMC8503938 DOI: 10.1038/s41586-021-03324-6] [Citation(s) in RCA: 981] [Impact Index Per Article: 327.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/03/2021] [Indexed: 12/16/2022]
Abstract
Here we report on the antibody and memory B cell responses of a cohort of 20 volunteers who received the Moderna (mRNA-1273) or Pfizer-BioNTech (BNT162b2) vaccine against SARS-CoV-21-4. Eight weeks after the second injection of vaccine, volunteers showed high levels of IgM and IgG anti-SARS-CoV-2 spike protein (S) and receptor-binding-domain (RBD) binding titre. Moreover, the plasma neutralizing activity and relative numbers of RBD-specific memory B cells of vaccinated volunteers were equivalent to those of individuals who had recovered from natural infection5,6. However, activity against SARS-CoV-2 variants that encode E484K-, N501Y- or K417N/E484K/N501-mutant S was reduced by a small-but significant-margin. The monoclonal antibodies elicited by the vaccines potently neutralize SARS-CoV-2, and target a number of different RBD epitopes in common with monoclonal antibodies isolated from infected donors5-8. However, neutralization by 14 of the 17 most-potent monoclonal antibodies that we tested was reduced or abolished by the K417N, E484K or N501Y mutation. Notably, these mutations were selected when we cultured recombinant vesicular stomatitis virus expressing SARS-CoV-2 S in the presence of the monoclonal antibodies elicited by the vaccines. Together, these results suggest that the monoclonal antibodies in clinical use should be tested against newly arising variants, and that mRNA vaccines may need to be updated periodically to avoid a potential loss of clinical efficacy.
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MESH Headings
- 2019-nCoV Vaccine mRNA-1273
- Adult
- Aged
- Antibodies, Monoclonal/blood
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- B-Lymphocytes/immunology
- BNT162 Vaccine
- COVID-19/immunology
- COVID-19/virology
- COVID-19 Vaccines/genetics
- COVID-19 Vaccines/immunology
- Cryoelectron Microscopy
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/immunology
- Epitopes, B-Lymphocyte/ultrastructure
- Female
- Humans
- Immunization, Secondary
- Immunoglobulin G/blood
- Immunoglobulin G/immunology
- Immunoglobulin M/blood
- Immunoglobulin M/immunology
- Immunologic Memory/immunology
- Male
- Middle Aged
- Models, Molecular
- Mutation
- Neutralization Tests
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
- mRNA Vaccines
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Affiliation(s)
- Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Shlomo Finkin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | | | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Jenna A Lieberman
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Morgan E Abernathy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Arlene Hurley
- Hospital Program Direction, The Rockefeller University, New York, NY, USA
| | - Martina Turroja
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Kamille A West
- Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Kristie Gordon
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Katrina G Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Justin Da Silva
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Jianliang Xu
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Robert A Colbert
- Pediatric Translational Research Branch and Office of the Clinical Director, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Roshni Patel
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Juan Dizon
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | | | - Irina Shimeliovich
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
- The NIH Regulome Project, National Institutes of Health, Bethesda, MD, USA.
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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A single donor is sufficient to produce a highly functional in vitro antibody library. Commun Biol 2021; 4:350. [PMID: 33742103 PMCID: PMC7979914 DOI: 10.1038/s42003-021-01881-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/19/2021] [Indexed: 01/31/2023] Open
Abstract
Antibody complementarity determining region diversity has been considered to be the most important metric for the production of a functional antibody library. Generally, the greater the antibody library diversity, the greater the probability of selecting a diverse array of high affinity leads. According to this paradigm, the primary means of elevating library diversity has been by increasing the number of donors. In the present study we explored the possibility of creating an in vitro antibody library from a single healthy individual, showing that the number of lymphocytes, rather than the number of donors, is the key criterion in the production of a diverse and functional antibody library. We describe the construction of a high-quality phage display library comprising 5 × 109 human antibodies by applying an efficient B cell extraction protocol from a single donor and a targeted V-gene amplification strategy favoring specific antibody families for their improved developability profiles. Each step of the library generation process was followed and validated by next generation sequencing to monitor the library quality and diversity. The functionality of the library was tested using several therapeutically relevant targets for which a vast number of different antibodies with desired biophysical properties were obtained.
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Abstract
Antibody responses in hepatitis C virus (HCV) have been a rather mysterious research topic for many investigators working in the field. Chronic HCV infection is often associated with dysregulation of immune functions particularly in B cells, leading to abnormal lymphoproliferation or the production of autoantibodies that exacerbate inflammation and extrahepatic diseases. When considering the antiviral function of antibody, it was difficult to endorse its role in HCV protection, whereas T-cell response has been shown unequivocally critical for natural recovery. Recent breakthroughs in the study of HCV and antigen-specific antibody responses provide important insights into viral vulnerability to antibodies and the immunogenetic and structural properties of the neutralizing antibodies. The new knowledge reinvigorates HCV vaccine research by illuminating a new path for the rational design of vaccine antigens to elicit broadly neutralizing antibodies for protection.
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Affiliation(s)
- Mansun Law
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California 92109, USA
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43
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Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected 78 million individuals and is responsible for over 1.7 million deaths to date. Infection is associated with the development of variable levels of antibodies with neutralizing activity, which can protect against infection in animal models1,2. Antibody levels decrease with time, but, to our knowledge, the nature and quality of the memory B cells that would be required to produce antibodies upon reinfection has not been examined. Here we report on the humoral memory response in a cohort of 87 individuals assessed at 1.3 and 6.2 months after infection with SARS-CoV-2. We find that titres of IgM and IgG antibodies against the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 decrease significantly over this time period, with IgA being less affected. Concurrently, neutralizing activity in plasma decreases by fivefold in pseudotype virus assays. By contrast, the number of RBD-specific memory B cells remains unchanged at 6.2 months after infection. Memory B cells display clonal turnover after 6.2 months, and the antibodies that they express have greater somatic hypermutation, resistance to RBD mutations and increased potency, indicative of continued evolution of the humoral response. Immunofluorescence and PCR analyses of intestinal biopsies obtained from asymptomatic individuals at 4 months after the onset of coronavirus disease 2019 (COVID-19) revealed the persistence of SARS-CoV-2 nucleic acids and immunoreactivity in the small bowel of 7 out of 14 individuals. We conclude that the memory B cell response to SARS-CoV-2 evolves between 1.3 and 6.2 months after infection in a manner that is consistent with antigen persistence.
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Ahmed R, Omidian Z, Giwa A, Donner T, Jie C, Hamad ARA. A reply to "TCR+/BCR+ dual-expressing cells and their associated public BCR clonotype are not enriched in type 1 diabetes". Cell 2021; 184:840-843. [PMID: 33545037 PMCID: PMC7935028 DOI: 10.1016/j.cell.2020.11.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/05/2020] [Accepted: 11/19/2020] [Indexed: 11/22/2022]
Abstract
We have recently identified a novel lymphocyte that is a dual expresser (DE) of TCRαβ and BCR. DEs in T1D patients are predominated by a public BCR clonotype (clone-x) that encodes a potent autoantigen that cross-activates insulin-reactive T cells. Betts and colleagues were able to detect DEs but alleged to not detect high DE frequency, clone-x, or similar clones in T1D patients. Unfortunately, the authors did not follow our methods and when they did, their flow cytometric data at two sites were conflicting. Moreover, contrary to their claim, we identified clones similar to clone-x in their data along with clones bearing the core motif (DTAMVYYFDYW). Additionally, their report of no increased usage of clone-x VH/DH genes by bulk B cells confirms rather than challenges our results. Finally, the authors failed to provide data verifying purity of their sorted DEs, making it difficult to draw reliable conclusion of their repertoire analysis. This Matters Arising Response paper addresses the Japp et al. (2021) Matters Arising paper, published concurrently in Cell.
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Affiliation(s)
- Rizwan Ahmed
- Department of Pathology, Johns Hopkins University School of Medicine, 720 Rutland Ave, Ross 664G, Baltimore, MD 21205, USA
| | - Zahra Omidian
- Department of Pathology, Johns Hopkins University School of Medicine, 720 Rutland Ave, Ross 664G, Baltimore, MD 21205, USA
| | - Adebola Giwa
- Department of Pathology, Johns Hopkins University School of Medicine, 720 Rutland Ave, Ross 664G, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University School of Medicine, 720 Rutland Ave, Ross 664G, Baltimore, MD 21205, USA
| | - Thomas Donner
- Department of Medicine, Johns Hopkins University School of Medicine, 720 Rutland Ave, Ross 664G, Baltimore, MD 21205, USA
| | - Chunfa Jie
- Department of Biochemistry and Nutrition, Des Moines University, 3200 Grand Ave, Ryan Hall 230, Des Moines, IA 50266, USA
| | - Abdel Rahim A Hamad
- Department of Pathology, Johns Hopkins University School of Medicine, 720 Rutland Ave, Ross 664G, Baltimore, MD 21205, USA; Department of Medicine, Johns Hopkins University School of Medicine, 720 Rutland Ave, Ross 664G, Baltimore, MD 21205, USA.
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45
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Wang Z, Schmidt F, Weisblum Y, Muecksch F, Barnes CO, Finkin S, Schaefer-Babajew D, Cipolla M, Gaebler C, Lieberman JA, Oliveira TY, Yang Z, Abernathy ME, Huey-Tubman KE, Hurley A, Turroja M, West KA, Gordon K, Millard KG, Ramos V, Da Silva J, Xu J, Colbert RA, Patel R, Dizon J, Unson-O'Brien C, Shimeliovich I, Gazumyan A, Caskey M, Bjorkman PJ, Casellas R, Hatziioannou T, Bieniasz PD, Nussenzweig MC. mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33501451 DOI: 10.1101/2021.01.15.426911] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
To date severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected over 100 million individuals resulting in over two million deaths. Many vaccines are being deployed to prevent coronavirus disease 2019 (COVID-19) including two novel mRNA-based vaccines 1,2 . These vaccines elicit neutralizing antibodies and appear to be safe and effective, but the precise nature of the elicited antibodies is not known 3-6 . Here we report on the antibody and memory B cell responses in a cohort of 20 volunteers who received either the Moderna (mRNA-1273) or Pfizer-BioNTech (BNT162b2) vaccines. Consistent with prior reports, 8 weeks after the second vaccine injection volunteers showed high levels of IgM, and IgG anti-SARS-CoV-2 spike protein (S) and receptor binding domain (RBD) binding titers 3,5,6 . Moreover, the plasma neutralizing activity, and the relative numbers of RBD-specific memory B cells were equivalent to individuals who recovered from natural infection 7,8 . However, activity against SARS-CoV-2 variants encoding E484K or N501Y or the K417N:E484K:N501Y combination was reduced by a small but significant margin. Consistent with these findings, vaccine-elicited monoclonal antibodies (mAbs) potently neutralize SARS-CoV-2, targeting a number of different RBD epitopes in common with mAbs isolated from infected donors. Structural analyses of mAbs complexed with S trimer suggest that vaccine- and virus-encoded S adopts similar conformations to induce equivalent anti-RBD antibodies. However, neutralization by 14 of the 17 most potent mAbs tested was reduced or abolished by either K417N, or E484K, or N501Y mutations. Notably, the same mutations were selected when recombinant vesicular stomatitis virus (rVSV)/SARS-CoV-2 S was cultured in the presence of the vaccine elicited mAbs. Taken together the results suggest that the monoclonal antibodies in clinical use should be tested against newly arising variants, and that mRNA vaccines may need to be updated periodically to avoid potential loss of clinical efficacy.
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46
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Ferrara F, Teixeira AA, Naranjo L, Erasmus MF, D'Angelo S, Bradbury ARM. Exploiting next-generation sequencing in antibody selections - a simple PCR method to recover binders. MAbs 2021; 12:1701792. [PMID: 31829073 PMCID: PMC7009332 DOI: 10.1080/19420862.2019.1701792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Antibody discovery using invitro display technologies such as phage and/or yeast display has become acornerstone in many research and development projects, including the creation of new drugs for clinical use. Traditionally, after the selection phase, random clones are isolated for binding validation and Sanger sequencing. More recently, next-generation sequencing (NGS) technology has allowed deeper insight into the antibody population after aselection campaign, enabling the identification of many more specific binders. However, this approach only provides the DNA sequences of potential binders, the properties of which need to be fully elucidated by obtaining corresponding clones and expressing them for further validation. Here we present arapid novel method to harvest potential clones identified by NGS that uses asimple PCR and yeast recombination approach. The protocol was tested in selections against three different targets and was able to recover clones at an abundance level that would be impractical to identify using traditional methods.
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Affiliation(s)
| | - Andre A Teixeira
- Specifica Inc., Santa Fe, NM, USA.,Bioscience Division, New Mexico Consortium, Los Alamos, NM, USA
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Gaebler C, Wang Z, Lorenzi JCC, Muecksch F, Finkin S, Tokuyama M, Cho A, Jankovic M, Schaefer-Babajew D, Oliveira TY, Cipolla M, Viant C, Barnes CO, Hurley A, Turroja M, Gordon K, Millard KG, Ramos V, Schmidt F, Weisblum Y, Jha D, Tankelevich M, Yee J, Shimeliovich I, Robbiani DF, Zhao Z, Gazumyan A, Hatziioannou T, Bjorkman PJ, Mehandru S, Bieniasz PD, Caskey M, Nussenzweig MC, Hagglof T, Schwartz RE, Bram Y, Martinez-Delgado G, Mendoza P, Breton G, Dizon J, Unson-O'Brien C, Patel R. Evolution of Antibody Immunity to SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33173867 DOI: 10.1101/2020.11.03.367391] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected 78 million individuals and is responsible for over 1.7 million deaths to date. Infection is associated with development of variable levels of antibodies with neutralizing activity that can protect against infection in animal models. Antibody levels decrease with time, but the nature and quality of the memory B cells that would be called upon to produce antibodies upon re-infection has not been examined. Here we report on the humoral memory response in a cohort of 87 individuals assessed at 1.3 and 6.2 months after infection. We find that IgM, and IgG anti-SARS-CoV-2 spike protein receptor binding domain (RBD) antibody titers decrease significantly with IgA being less affected. Concurrently, neutralizing activity in plasma decreases by five-fold in pseudotype virus assays. In contrast, the number of RBD-specific memory B cells is unchanged. Memory B cells display clonal turnover after 6.2 months, and the antibodies they express have greater somatic hypermutation, increased potency and resistance to RBD mutations, indicative of continued evolution of the humoral response. Analysis of intestinal biopsies obtained from asymptomatic individuals 4 months after coronavirus disease-2019 (COVID-19) onset, using immunofluorescence, or polymerase chain reaction, revealed persistence of SARS-CoV-2 nucleic acids and immunoreactivity in the small bowel of 7 out of 14 volunteers. We conclude that the memory B cell response to SARS-CoV-2 evolves between 1.3 and 6.2 months after infection in a manner that is consistent with antigen persistence.
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48
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Liu Q, Garg P, Hasdemir B, Wang L, Tuscano E, Sever E, Keane E, Hernandez AGL, Yuan TZ, Kwan E, Lai J, Szot G, Paruthiyil S, Axelrod F, K. Sato A. Functional GLP-1R antibodies identified from a synthetic GPCR-focused library demonstrate potent blood glucose control. MAbs 2021; 13:1893425. [PMID: 33706686 PMCID: PMC7971233 DOI: 10.1080/19420862.2021.1893425] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 02/04/2021] [Accepted: 02/17/2021] [Indexed: 11/15/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are a group of seven-transmembrane receptor proteins that have proven to be successful drug targets. Antibodies are becoming an increasingly promising modality to target these receptors due to their unique properties, such as exquisite specificity, long half-life, and fewer side effects, and their improved pharmacokinetic and pharmacodynamic profiles compared to peptides and small molecules, which results from their more favorable biodistribution. To date, there are only two US Food and Drug Administration-approved GPCR antibody drugs, namely erenumab and mogamulizumab, and this highlights the challenges encountered in identifying functional antibodies against GPCRs. Utilizing Twist's precision DNA writing technologies, we have created a GPCR-focused phage display library with 1 × 1010 diversity. Specifically, we mined endogenous GPCR binding ligand and peptide sequences and incorporated these binding motifs into the heavy chain complementarity-determining region 3 in a synthetic antibody library. Glucagon-like peptide-1 receptor (GLP-1 R) is a class B GPCR that acts as the receptor for the incretin GLP-1, which is released to regulate insulin levels in response to food intake. GLP-1 R agonists have been widely used to increase insulin secretion to lower blood glucose levels for the treatment of type 1 and type 2 diabetes, whereas GLP-1 R antagonists have applications in the treatment of severe hypoglycemia associated with bariatric surgery and hyperinsulinomic hypoglycemia. Here we present the discovery and creation of both antagonistic and agonistic GLP-1 R antibodies by panning this GPCR-focused phage display library on a GLP-1 R-overexpressing Chinese hamster ovary cell line and demonstrate their in vitro and in vivo functional activity.
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Affiliation(s)
- Qiang Liu
- Twist Biopharma, South San Francisco, CA, USA
| | - Pankaj Garg
- Twist Biopharma, South San Francisco, CA, USA
- Alamar Biosciences, Fremont, CA, USA
| | - Burcu Hasdemir
- Twist Biopharma, South San Francisco, CA, USA
- Catalyst Biosciences, South San Francisco, CA, USA
| | - Linya Wang
- Twist Biopharma, South San Francisco, CA, USA
| | | | - Emily Sever
- Twist Biopharma, South San Francisco, CA, USA
| | - Erica Keane
- Twist Biopharma, South San Francisco, CA, USA
| | | | - Tom Z. Yuan
- Twist Biopharma, South San Francisco, CA, USA
| | - Eric Kwan
- Twist Biopharma, South San Francisco, CA, USA
| | - Joyce Lai
- Twist Biopharma, South San Francisco, CA, USA
| | - Greg Szot
- Diabetes Center, University of California San Francisco, San Francisco, CA, USA
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49
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Giorgetti OB, Shingate P, O'Meara CP, Ravi V, Pillai NE, Tay BH, Prasad A, Iwanami N, Tan HH, Schorpp M, Venkatesh B, Boehm T. Antigen receptor repertoires of one of the smallest known vertebrates. SCIENCE ADVANCES 2021; 7:7/1/eabd8180. [PMID: 33523858 PMCID: PMC7775753 DOI: 10.1126/sciadv.abd8180] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/04/2020] [Indexed: 05/06/2023]
Abstract
The rules underlying the structure of antigen receptor repertoires are not yet fully defined, despite their enormous importance for the understanding of adaptive immunity. With current technology, the large antigen receptor repertoires of mice and humans cannot be comprehensively studied. To circumvent the problems associated with incomplete sampling, we have studied the immunogenetic features of one of the smallest known vertebrates, the cyprinid fish Paedocypris sp. "Singkep" ("minifish"). Despite its small size, minifish has the key genetic facilities characterizing the principal vertebrate lymphocyte lineages. As described for mammals, the frequency distributions of immunoglobulin and T cell receptor clonotypes exhibit the features of fractal systems, demonstrating that self-similarity is a fundamental property of antigen receptor repertoires of vertebrates, irrespective of body size. Hence, minifish achieve immunocompetence via a few thousand lymphocytes organized in robust scale-free networks, thereby ensuring immune reactivity even when cells are lost or clone sizes fluctuate during immune responses.
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Affiliation(s)
- Orlando B Giorgetti
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Prashant Shingate
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Connor P O'Meara
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Vydianathan Ravi
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Nisha E Pillai
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Boon-Hui Tay
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Aravind Prasad
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Norimasa Iwanami
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Heok Hui Tan
- Lee Kong Chian Natural History Museum, National University of Singapore, Singapore 117377, Singapore
| | - Michael Schorpp
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, A*STAR, Biopolis, Singapore 138673, Singapore.
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany.
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50
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Shi B, Dong X, Ma Q, Sun S, Ma L, Yu J, Wang X, Pan J, He X, Su D, Yao X. The Usage of Human IGHJ Genes Follows a Particular Non-random Selection: The Recombination Signal Sequence May Affect the Usage of Human IGHJ Genes. Front Genet 2020; 11:524413. [PMID: 33363565 PMCID: PMC7753069 DOI: 10.3389/fgene.2020.524413] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 11/06/2020] [Indexed: 12/02/2022] Open
Abstract
The formation of the B cell receptor (BCR) heavy chain variable region is derived from the germline V(D)J gene rearrangement according to the “12/23” rule and the “beyond 12/23” rule. The usage frequency of each V(D)J gene in the peripheral BCR repertoires is related to the initial recombination, self-tolerance selection, and the clonal proliferative response. However, their specific differences and possible mechanisms are still unknown. We analyzed in-frame and out-of-frame BCR-H repertoires from human samples with normal physiological and various pathological conditions by high-throughput sequencing. Our results showed that IGHJ gene frequency follows a similar pattern which is previously known, where IGHJ4 is used at high frequency (>40%), IGHJ6/IGHJ3/IGHJ5 is used at medium frequencies (10∼20%), and IGH2/IGHJ1 is used at low frequency (<4%) under whether normal physiological or various pathological conditions. However, our analysis of the recombination signal sequences suggested that the conserved non-amer and heptamer and certain 23 bp spacer length may affect the initial IGHD-IGHJ recombination, which results in different frequencies of IGHJ genes among the initial BCR-H repertoire. Based on this “initial repertoire,” we recommend that re-evaluation and further investigation are needed when analyzing the significance and mechanism of IGHJ gene frequency in self-tolerance selection and the clonal proliferative response.
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Affiliation(s)
- Bin Shi
- Department of Laboratory Medicine, Affiliated Hospital of Zunyi Medical University, Zunyi, China.,School of Laboratory Medicine, Zunyi Medical University, Zunyi, China
| | - Xiaoheng Dong
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Qingqing Ma
- 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, Affiliated Hospital of 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
| | - Jiang Yu
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Xiaomei Wang
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Juan Pan
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Xiaoyan He
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi, China
| | - Danhua Su
- Department of Immunology, Center of Immunomolecular Engineering, Innovation & Practice Base for Graduate Students Education, 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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