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Le Bihan T, Nunez de Villavicencio Diaz T, Reitzel C, Lange V, Park M, Beadle E, Wu L, Jovic M, Dubois RM, Couzens AL, Duan J, Han X, Liu Q, Ma B. De novo protein sequencing of antibodies for identification of neutralizing antibodies in human plasma post SARS-CoV-2 vaccination. Nat Commun 2024; 15:8790. [PMID: 39389968 PMCID: PMC11466954 DOI: 10.1038/s41467-024-53105-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 10/02/2024] [Indexed: 10/12/2024] Open
Abstract
The antibody response to vaccination and infection is a key component of the immune response to pathogens. Sequencing of peripheral B cells may not represent the complete B cell receptor repertoire. Here we present a method for sequencing human plasma-derived polyclonal IgG using a combination of mass spectrometry and B-cell sequencing. We investigate the IgG response to the Moderna Spikevax COVID-19 vaccine. From the sequencing data of the natural polyclonal response to vaccination, we generate 12 recombinant antibodies. Six derived recombinant antibodies, including four generated with de novo protein sequencing, exhibit similar or higher binding affinities than the original natural polyclonal antibody. Neutralization tests reveal that the six antibodies possess neutralizing capabilities against the target antigen. This research provides insights into sequencing polyclonal IgG antibodies and the potential of our approach in generating recombinant antibodies with robust binding affinity and neutralization capabilities. Directly examining the circulating IgG pool is crucial due to potential misrepresentations by B-cell analysis alone.
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Affiliation(s)
| | | | | | | | | | | | - Lin Wu
- Rapid Novor, Kitchener, ON, Canada
| | | | | | | | - Jin Duan
- Rapid Novor, Kitchener, ON, Canada
| | | | | | - Bin Ma
- Rapid Novor, Kitchener, ON, Canada.
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2
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Wang Q, Nag D, Baldwin SL, Coler RN, McNamara RP. Antibodies as key mediators of protection against Mycobacterium tuberculosis. Front Immunol 2024; 15:1430955. [PMID: 39286260 PMCID: PMC11402706 DOI: 10.3389/fimmu.2024.1430955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 08/13/2024] [Indexed: 09/19/2024] Open
Abstract
Tuberculosis (TB) is caused by infection with the bacterial pathogen Mycobacterium tuberculosis (M.tb) in the respiratory tract. There was an estimated 10.6 million people newly diagnosed with TB, and there were approximately 1.3 million deaths caused by TB in 2022. Although the global prevalence of TB has remained high for decades and is an annual leading cause of death attributed to infectious diseases, only one vaccine, Bacillus Calmette-Guérin (BCG), has been approved so far to prevent/attenuate TB disease. Correlates of protection or immunological mechanisms that are needed to control M.tb remain unknown. The protective role of antibodies after BCG vaccination has also remained largely unclear; however, recent studies have provided evidence for their involvement in protection against disease, as biomarkers for the state of infection, and as potential predictors of outcomes. Interestingly, the antibodies generated post-vaccination with BCG are linked to the activation of innate immune cascades, providing further evidence that antibody effector functions are critical for protection against respiratory pathogens such as M.tb. In this review, we aim to provide current knowledge of antibody application in TB diagnosis, prevention, and treatment. Particularly, this review will focus on 1) The role of antibodies in preventing M.tb infections through preventing Mtb adherence to epithelium, antibody-mediated phagocytosis, and antibody-mediated cellular cytotoxicity; 2) The M.tb-directed antibody response generated after vaccination and how humoral profiles with different glycosylation patterns of these antibodies are linked with protection against the disease state; and 3) How antibody-mediated immunity against M.tb can be further explored as early diagnosis biomarkers and different detection methods to combat the global M.tb burden. Broadening the paradigm of differentiated antibody profiling and antibody-based detection during TB disease progression offers new directions for diagnosis, treatment, and preventative strategies. This approach involves linking the aforementioned humoral responses with the disease state, progression, and clearance.
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Affiliation(s)
- Qixin Wang
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, United States
| | - Deepika Nag
- Seattle Children’s Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Susan L. Baldwin
- Seattle Children’s Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
| | - Rhea N. Coler
- Seattle Children’s Research Institute, Center for Global Infectious Disease Research, Seattle, WA, United States
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States
- Department of Global Health, University of Washington, Seattle, WA, United States
| | - Ryan P. McNamara
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, MA, United States
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3
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Gioacchino E, Vandelannoote K, Ruberto AA, Popovici J, Cantaert T. Unraveling the intricacies of host-pathogen interaction through single-cell genomics. Microbes Infect 2024; 26:105313. [PMID: 38369008 DOI: 10.1016/j.micinf.2024.105313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/23/2023] [Accepted: 02/13/2024] [Indexed: 02/20/2024]
Abstract
Single-cell genomics provide researchers with tools to assess host-pathogen interactions at a resolution previously inaccessible. Transcriptome analysis, epigenome analysis, and immune profiling techniques allow for a better comprehension of the heterogeneity underlying both the host response and infectious agents. Here, we highlight technological advancements and data analysis workflows that increase our understanding of host-pathogen interactions at the single-cell level. We review various studies that have used these tools to better understand host-pathogen dynamics in a variety of infectious disease contexts, including viral, bacterial, and parasitic diseases. We conclude by discussing how single-cell genomics can advance our understanding of host-pathogen interactions.
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Affiliation(s)
- Emanuele Gioacchino
- Immunology Unit, Institut Pasteur du Cambodge, The Pasteur Network, Phnom Penh, Cambodia
| | - Koen Vandelannoote
- Bacterial Phylogenomics Group, Institut Pasteur du Cambodge, The Pasteur Network, Phnom Penh, Cambodia
| | - Anthony A Ruberto
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA; Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Jean Popovici
- Malaria Research Unit, Institut Pasteur du Cambodge, The Pasteur Network, Phnom Penh, Cambodia; Infectious Disease Epidemiology and Analytics, Institut Pasteur, Paris, France
| | - Tineke Cantaert
- Immunology Unit, Institut Pasteur du Cambodge, The Pasteur Network, Phnom Penh, Cambodia.
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4
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Tuong ZK, van der Merwe R, Canete PF, Roco JA. Computational estimation of clonal diversity in autoimmunity. Immunol Cell Biol 2024; 102:692-701. [PMID: 39010261 DOI: 10.1111/imcb.12801] [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: 04/08/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/17/2024]
Abstract
Diversity is the cornerstone of the adaptive immune system, crucial for its effectiveness against constantly evolving pathogens that pose threats to higher vertebrates. Accurately measuring and interpreting this diversity presents challenges for immunologists, as changes in diversity and clonotype composition can tip the balance between protective immunity and autoimmunity. In this review, we present the current methods commonly used to measure diversity from single-cell T-cell receptor and B-cell receptor sequencing. We also discuss two case studies where single-cell sequencing and diversity estimations have led to breakthroughs in autoimmune disease discovery and therapeutic innovation, and reflect upon the necessity and importance of accurately defining and measuring lymphocyte diversity in these contexts.
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MESH Headings
- Humans
- Autoimmunity
- Animals
- Receptors, Antigen, T-Cell/metabolism
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/genetics
- Single-Cell Analysis
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/metabolism
- Autoimmune Diseases/immunology
- Computational Biology/methods
- Genetic Variation
- B-Lymphocytes/immunology
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Affiliation(s)
- Zewen Kelvin Tuong
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Rohan van der Merwe
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Pablo F Canete
- Ian Frazer Centre for Children's Immunotherapy Research, Child Health Research Centre, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Frazer Institute, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Jonathan A Roco
- Biological Data Science Institute, College of Science, The Australian National University, Canberra, ACT, Australia
- Clinical Hub for Interventional Research, College of Health & Medicine, The Australian National University, Canberra, ACT, Australia
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5
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Bardwell B, Bay J, Colburn Z. The clinical applications of immunosequencing. Curr Res Transl Med 2024; 72:103439. [PMID: 38447267 DOI: 10.1016/j.retram.2024.103439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/20/2023] [Accepted: 01/11/2024] [Indexed: 03/08/2024]
Abstract
Technological advances in high-throughput sequencing have opened the door for the interrogation of adaptive immune responses at unprecedented scale. It is now possible to determine the sequences of antibodies or T-cell receptors produced by individual B and T cells in a sample. This capability, termed immunosequencing, has transformed the study of both infectious and non-infectious diseases by allowing the tracking of dynamic changes in B and T cell clonal populations over time. This has improved our understanding of the pathology of cancers, autoimmune diseases, and infectious diseases. However, to date there has been only limited clinical adoption of the technology. Advances over the last decade and on the horizon that reduce costs and improve interpretability could enable widespread clinical use. Many clinical applications have been proposed and, while most are still undergoing research and development, some methods relying on immunosequencing data have been implemented, the most widespread of which is the detection of measurable residual disease. Here, we review the diagnostic, prognostic, and therapeutic applications of immunosequencing for both infectious and non-infectious diseases.
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Affiliation(s)
- B Bardwell
- Department of Clinical Investigation, Madigan Army Medical Center, 9040 Jackson Ave, Tacoma, WA 98431, USA
| | - J Bay
- Department of Medicine, Madigan Army Medical Center, 9040 Jackson Ave, Tacoma, WA 98431, USA
| | - Z Colburn
- Department of Clinical Investigation, Madigan Army Medical Center, 9040 Jackson Ave, Tacoma, WA 98431, USA.
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6
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David AF, Heinzel A, Kammer M, Aschauer C, Reindl-Schwaighofer R, Hu K, Chen HS, Muckenhuber M, Kubetz A, Weijler AM, Worel N, Edinger M, Berlakovich G, Lion T, Sykes M, Wekerle T, Oberbauer R. Combination cell therapy leads to clonal deletion of donor-specific T cells in kidney transplant recipients. EBioMedicine 2024; 106:105239. [PMID: 38996766 PMCID: PMC11284950 DOI: 10.1016/j.ebiom.2024.105239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/25/2024] [Accepted: 06/27/2024] [Indexed: 07/14/2024] Open
Abstract
BACKGROUND Induction of donor-specific tolerance is a promising approach to achieve long-term graft patency in transplantation with little to no maintenance immunosuppression. Changes to the recipient's T cell receptor (TCR) repertoire are understood to play a pivotal role in the establishment of a robust state of tolerance in chimerism-based transplantation protocols. METHODS We investigated changes to the TCR repertoires of patients participating in an ongoing prospective, controlled, phase I/IIa trial designed to evaluate the safety and efficacy of combination cell therapy in living donor kidney transplantation. Using high-throughput sequencing, we characterized the repertoires of six kidney recipients who also received bone marrow from the same donor (CKBMT), together with an infusion of polyclonal autologous Treg cells instead of myelosuppression. FINDINGS Patients undergoing combination cell therapy exhibited partial clonal deletion of donor-reactive CD4+ T cells at one, three, and six months post-transplant, compared to control patients receiving the same immunosuppression regimen but no cell therapy (p = 0.024). The clonality, R20 and turnover rates of the CD4+ and CD8+ TCR repertoires were comparable in both groups, showing our protocol caused no excessive repertoire shift or loss of diversity. Treg clonality was lower in the case group than in control (p = 0.033), suggesting combination cell therapy helps to preserve Treg diversity. INTERPRETATION Overall, our data indicate that combining Treg cell therapy with CKBMT dampens the alloimmune response to transplanted kidneys in humans in the absence of myelosuppression. FUNDING This study was funded by the Vienna Science and Technology Fund (WWTF).
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Affiliation(s)
- Ana F David
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Andreas Heinzel
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Michael Kammer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria; Center for Medical Data Science, Institute for Clinical Biometrics, Medical University of Vienna, Vienna, Austria
| | - Constantin Aschauer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Roman Reindl-Schwaighofer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Karin Hu
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Hao-Shan Chen
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Moritz Muckenhuber
- Division of Transplantation, Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Anna Kubetz
- Division of Transplantation, Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Anna Marianne Weijler
- Division of Transplantation, Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Nina Worel
- Department of Transfusion Medicine and Cell Therapy, Medical University of Vienna, Vienna, Austria
| | - Matthias Edinger
- University Hospital Regensburg, Department of Internal Medicine III & Regensburg Center for Interventional Immunology (RCI), Regensburg, Germany
| | - Gabriela Berlakovich
- Division of Transplantation, Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Thomas Lion
- St. Anna Children's Cancer, Research Institute and Labdia Labordiagnostik, Vienna, Austria
| | - Megan Sykes
- Columbian Center for Translational Immunology, Department of Medicine, Columbia University, New York City, NY, United States
| | - Thomas Wekerle
- Division of Transplantation, Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Rainer Oberbauer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria.
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7
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Fiala J, Schuster D, Ollivier S, Pengelley S, Lubeck M, Busch F, Jankevics A, Raether O, Greisch JF, Heck AJR. Protein-Centric Analysis of Personalized Antibody Repertoires Using LC-MS-Based Fab-Profiling on a timsTOF. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1292-1300. [PMID: 38662593 PMCID: PMC11157643 DOI: 10.1021/jasms.4c00076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 06/06/2024]
Abstract
Endogenous antibodies, or immunoglobulins (Igs), abundantly present in body fluids, represent some of the most challenging samples to analyze, largely due to the immense variability in their sequences and concentrations. It has been estimated that our body can produce billions of different Ig proteins with different isotypes, making their individual analysis seemingly impossible. However, recent advances in protein-centric proteomics using LC-MS coupled to Orbitrap mass analyzers to profile intact Fab fragments formed by selective cleavage at the IgG-hinge revealed that IgG repertoires may be less diverse, albeit unique for each donor. Serum repertoires seem to be dominated by a few hundred clones that cumulatively make up 50-95% of the total IgG content. Enabling such analyses required careful optimization of the chromatography and mass analysis, as all Fab analytes are highly alike in mass (46-51 kDa) and sequence. To extend the opportunities of this mass-spectrometry-based profiling of antibody repertoires, we here report the optimization and evaluation of an alternative MS platform, namely, the timsTOF, for antibody repertoire profiling. The timsTOF mass analyzer has gained traction in recent years for peptide-centric proteomics and found wide applicability in plasma proteomics, affinity proteomics, and HLA peptidomics, to name a few. However, for protein-centric analysis, this platform has been less explored. Here, we demonstrate that the timsTOF platform can be adapted to perform protein-centric LC-MS-based profiling of antibody repertoires. In a side-by-side comparison of the timsTOF and the Orbitrap we demonstrate that the extracted serum antibody repertoires are alike qualitatively and quantitatively, whereby in particular the sensitivity of the timsTOF platform excels. Future incorporation of advanced top-down capabilities on the timsTOF may make this platform a very valuable alternative for protein-centric proteomics and top-down proteomics and thus also for personalized antibody repertoire profiling.
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Affiliation(s)
- Jan Fiala
- Biomolecular
Mass Spectrometry & Proteomics, Bijvoet Center for Biomolecular
Research & Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The
Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Dina Schuster
- Biomolecular
Mass Spectrometry & Proteomics, Bijvoet Center for Biomolecular
Research & Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The
Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Simon Ollivier
- Biomolecular
Mass Spectrometry & Proteomics, Bijvoet Center for Biomolecular
Research & Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The
Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Stuart Pengelley
- Bruker
Daltonics GmbH & Co. KG, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Markus Lubeck
- Bruker
Daltonics GmbH & Co. KG, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Florian Busch
- Bruker
Switzerland AG, 8117 Fällanden, Zurich Switzerland
| | - Andris Jankevics
- Biomolecular
Mass Spectrometry & Proteomics, Bijvoet Center for Biomolecular
Research & Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The
Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Oliver Raether
- Bruker
Daltonics GmbH & Co. KG, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | | | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry & Proteomics, Bijvoet Center for Biomolecular
Research & Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The
Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
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8
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Lee S, Ko Y, Lee HW, Oh WJ, Hong HG, Ariyaratne D, Im SJ, Kim TJ. Two distinct subpopulations of marginal zone B cells exhibit differential antibody-producing capacities and radioresistance. Cell Mol Immunol 2024; 21:393-408. [PMID: 38424169 PMCID: PMC10978899 DOI: 10.1038/s41423-024-01126-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 12/27/2023] [Indexed: 03/02/2024] Open
Abstract
Marginal zone (MZ) B cells, which are splenic innate-like B cells that rapidly secrete antibodies (Abs) against blood-borne pathogens, are composed of heterogeneous subpopulations. Here, we showed that MZ B cells can be divided into two distinct subpopulations according to their CD80 expression levels. CD80high MZ B cells exhibited greater Ab-producing, proliferative, and IL-10-secreting capacities than did CD80low MZ B cells. Notably, CD80high MZ B cells survived 2-Gy whole-body irradiation, whereas CD80low MZ B cells were depleted by irradiation and then repleted with one month after irradiation. Depletion of CD80low MZ B cells led to accelerated development of type II collagen (CII)-induced arthritis upon immunization with bovine CII. CD80high MZ B cells exhibited higher expression of genes involved in proliferation, plasma cell differentiation, and the antioxidant response. CD80high MZ B cells expressed more autoreactive B cell receptors (BCRs) that recognized double-stranded DNA or CII, expressed more immunoglobulin heavy chain sequences with shorter complementarity-determining region 3 sequences, and included more clonotypes with no N-nucleotides or with B-1a BCR sequences than CD80low MZ B cells. Adoptive transfer experiments showed that CD21+CD23+ transitional 2 MZ precursors preferentially generated CD80low MZ B cells and that a proportion of CD80low MZ B cells were converted into CD80high MZ B cells; in contrast, CD80high MZ B cells stably remained CD80high MZ B cells. In summary, MZ B cells can be divided into two subpopulations according to their CD80 expression levels, Ab-producing capacity, radioresistance, and autoreactivity, and these findings may suggest a hierarchical composition of MZ B cells with differential stability and BCR specificity.
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Affiliation(s)
- Sujin Lee
- Department of Immunology, Graduate School of Basic Medical Science, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
| | - Yeunjung Ko
- Department of Immunology, Graduate School of Basic Medical Science, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
- Immunology and Microbiology Graduate Program, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hyun Woo Lee
- Department of Immunology, Graduate School of Basic Medical Science, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
| | - Won Joon Oh
- Department of Immunology, Graduate School of Basic Medical Science, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
| | - Hun Gi Hong
- Department of Immunology, Graduate School of Basic Medical Science, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea
| | - Dinuka Ariyaratne
- Department of Immunology and Molecular Medicine, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Se Jin Im
- Department of Immunology, Graduate School of Basic Medical Science, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea.
| | - Tae Jin Kim
- Department of Immunology, Graduate School of Basic Medical Science, Sungkyunkwan University School of Medicine, Suwon, 16419, Republic of Korea.
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9
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Barton J, Gaspariunas A, Galson JD, Leem J. Building Representation Learning Models for Antibody Comprehension. Cold Spring Harb Perspect Biol 2024; 16:a041462. [PMID: 38012013 PMCID: PMC10910360 DOI: 10.1101/cshperspect.a041462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Antibodies are versatile proteins with both the capacity to bind a broad range of targets and a proven track record as some of the most successful therapeutics. However, the development of novel antibody therapeutics is a lengthy and costly process. It is challenging to predict the functional and biophysical properties of antibodies from their amino acid sequence alone, requiring numerous experiments for full characterization. Machine learning, specifically deep representation learning, has emerged as a family of methods that can complement wet lab approaches and accelerate the overall discovery and engineering process. Here, we review advances in antibody sequence representation learning, and how this has improved antibody structure prediction and facilitated antibody optimization. We discuss challenges in the development and implementation of such models, such as the lack of publicly available, well-curated antibody function data and highlight opportunities for improvement. These and future advances in machine learning for antibody sequences have the potential to increase the success rate in developing new therapeutics, resulting in broader access to transformative medicines and improved patient outcomes.
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Affiliation(s)
- Justin Barton
- Alchemab Therapeutics Ltd, London N1C 4AX, United Kingdom
| | | | - Jacob D Galson
- Alchemab Therapeutics Ltd, London N1C 4AX, United Kingdom
| | - Jinwoo Leem
- Alchemab Therapeutics Ltd, London N1C 4AX, United Kingdom
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10
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Shimizu T, Sun L, Ohnishi K. Influence of pre-B cell receptor deficiency on the immunoglobulin repertoires in peripheral blood B cells before and after immunization. Mol Immunol 2024; 166:87-100. [PMID: 38271880 DOI: 10.1016/j.molimm.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/17/2023] [Accepted: 01/03/2024] [Indexed: 01/27/2024]
Abstract
During B cell development, pre-B cell receptor (pre-BCR), comprising the immunoglobulin heavy chain (HC) and surrogate light chain (SLC), plays a crucial role. The expression of pre-BCR serves as a certification of HC quality, confirming its ability to associate with the SLC and light chain (LC). In mice lacking SLC, the absence of this quality control mechanism leads to a distorted repertoire of HCs in the spleen and bone marrow. In this study, we conducted a comparative analysis of the immunoglobulin gene repertoire in peripheral blood cells of both wild-type mice and pre-BCR-deficient mice. Our findings reveal differences not only in the μ HC repertoire but also in the α HC and κ LC repertoires of the pre-BCR-deficient mice. These results suggest that the pre-BCR-mediated quality check of HC influences the selection of class-switched HC and LC repertoires. To further explore the impact of pre-BCR deficiency, we immunized these mice with thymus-dependent antigens and compared the antigen-responding repertoires. Our observations indicate that the affinity maturation pathways remain consistent between wild-type mice and pre-BCR-deficient mice, albeit with variations in the degree of maturation.
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Affiliation(s)
- Takeyuki Shimizu
- Department of Immunology, Kochi Medical School, Kochi University, Nankoku, Kochi 783-8505, Japan.
| | - Lin Sun
- Department of Immunology, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
| | - Kazuo Ohnishi
- Department of Immunology, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
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11
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Huang T, Pi C, Xu X, Feng Y, Zhang J, Gu H, Fang J. Effect of BAFF blockade on the B cell receptor repertoire and transcriptome in a mouse model of systemic lupus erythematosus. Front Immunol 2024; 14:1307392. [PMID: 38264661 PMCID: PMC10803406 DOI: 10.3389/fimmu.2023.1307392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024] Open
Abstract
Introduction Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease. Anti-B-cell-activating factor (BAFF) therapy effectively depletes B cells and reduces SLE disease activity. This research aimed to evaluate the effect of BAFF blockade on B cell receptor (BCR) repertoire and gene expression. Methods Through next-generation sequencing, we analyzed gene expression and BCR repertoire in MRL/lpr mice that received long-term anti-BAFF therapy. Based on gene expression profiles, we predicted the relative proportion of immune cells using ImmuCellAI-mouse, validating our predictions via flow cytometry and FluoroSpot. Results The loss of BCR repertoire diversity and richness, along with increased clonality and differential frequency distribution of the immunoglobulin heavy chain variable (IGHV) segment gene usage, were observed in BAFF-blockade mice. Meanwhile, the distribution of complementarity-determining region 3 (CDR3) length and CDR3 amino acid usage remained unaffected. BAFF blockade resulted in extensive changes in gene expression, particularly that of genes related to B cells and immunoglobulins. Besides, the tumor necrosis factor (TNF)-α responses and interferon (IFN)-α/γ were downregulated, consistent with the decrease in IFN-γ and TNF-α serum levels following anti-BAFF therapy. In addition, BAFF blockade significantly reduced B cell subpopulations and plasmacytoid dendritic cells, and caused the depletion of antibody-secreting cells. Discussion Our comparative BCR repertoire and transcriptome analyses of MRL/lpr mice subjected to BAFF blockade provide innovative insights into the molecular pathophysiology of SLE.
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Affiliation(s)
- Tao Huang
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Chenyu Pi
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xiaoqing Xu
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yan Feng
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jingming Zhang
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Hua Gu
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jianmin Fang
- School of Life Sciences and Technology, Tongji University, Shanghai, China
- Biomedical Research Center, Tongji University Suzhou Institute, Suzhou, Jiangsu, China
- Department of Neurology, Tongji Hospital, Tongji University, Shanghai, China
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12
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Vitallé J, Zenarruzabeitia O, Merino-Pérez A, Terrén I, Orrantia A, Pacho de Lucas A, Iribarren JA, García-Fraile LJ, Balsalobre L, Amo L, de Andrés B, Borrego F. Human IgM hiCD300a + B Cells Are Circulating Marginal Zone Memory B Cells That Respond to Pneumococcal Polysaccharides and Their Frequency Is Decreased in People Living with HIV. Int J Mol Sci 2023; 24:13754. [PMID: 37762055 PMCID: PMC10530418 DOI: 10.3390/ijms241813754] [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: 07/27/2023] [Revised: 08/18/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
CD300a is differentially expressed among B cell subsets, although its expression in immunoglobulin (Ig)M+ B cells is not well known. We identified a B cell subset expressing CD300a and high levels of IgM (IgMhiCD300a+). The results showed that IgMhiCD300a+ B cells were CD10-CD27+CD25+IgDloCD21hiCD23-CD38loCD1chi, suggesting that they are circulating marginal zone (MZ) IgM memory B cells. Regarding the immunoglobulin repertoire, IgMhiCD300a+ B cells exhibited a higher mutation rate and usage of the IgH-VDJ genes than the IgM+CD300a- counterpart. Moreover, the shorter complementarity-determining region 3 (CDR3) amino acid (AA) length from IgMhiCD300a+ B cells together with the predicted antigen experience repertoire indicates that this B cell subset has a memory phenotype. IgM memory B cells are important in T cell-independent responses. Accordingly, we demonstrate that this particular subset secretes higher amounts of IgM after stimulation with pneumococcal polysaccharides or a toll-like receptor 9 (TLR9) agonist than IgM+CD300a- cells. Finally, the frequency of IgMhiCD300a+ B cells was lower in people living with HIV-1 (PLWH) and it was inversely correlated with the years with HIV infection. Altogether, these data help to identify a memory B cell subset that contributes to T cell-independent responses to pneumococcal infections and may explain the increase in severe pneumococcal infections and the impaired responses to pneumococcal vaccination in PLWH.
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Affiliation(s)
- Joana Vitallé
- Immunopathology Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (O.Z.); (A.M.-P.); (I.T.); (A.O.); (L.A.)
- Instituto de Biomedicina de Sevilla (IBiS), Virgen del Rocío University Hospital, CSIC, University of Seville, 41013 Seville, Spain
| | - Olatz Zenarruzabeitia
- Immunopathology Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (O.Z.); (A.M.-P.); (I.T.); (A.O.); (L.A.)
| | - Aitana Merino-Pérez
- Immunopathology Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (O.Z.); (A.M.-P.); (I.T.); (A.O.); (L.A.)
| | - Iñigo Terrén
- Immunopathology Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (O.Z.); (A.M.-P.); (I.T.); (A.O.); (L.A.)
| | - Ane Orrantia
- Immunopathology Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (O.Z.); (A.M.-P.); (I.T.); (A.O.); (L.A.)
| | - Arantza Pacho de Lucas
- Regulation of the Immune System Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Immunology Service, Cruces University Hospital, 48903 Barakaldo, Spain
| | - José A. Iribarren
- Department of Infectious Diseases, Donostia University Hospital, Biodonostia Health Research Institute, 20014 Donostia-San Sebastián, Spain;
| | - Lucio J. García-Fraile
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, 28029 Madrid, Spain;
- Department of Internal Medicine, La Princesa University Hospital, 28006 Madrid, Spain
| | - Luz Balsalobre
- Laboratory of Microbiology, UR Salud, Infanta Sofía University Hospital, 28702 Madrid, Spain;
| | - Laura Amo
- Immunopathology Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (O.Z.); (A.M.-P.); (I.T.); (A.O.); (L.A.)
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Belén de Andrés
- Immunobiology Department, Carlos III Health Institute, 28220 Madrid, Spain;
| | - Francisco Borrego
- Immunopathology Group, Biocruces Bizkaia Health Research Institute, 48903 Barakaldo, Spain; (O.Z.); (A.M.-P.); (I.T.); (A.O.); (L.A.)
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
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13
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Calonga-Solís V, Olbrich M, Ott F, Adelman Cipolla G, Malheiros D, Künstner A, Farias TD, Camargo CM, Petzl-Erler ML, Busch H, Fähnrich A, Augusto DG. The landscape of the immunoglobulin repertoire in endemic pemphigus foliaceus. Front Immunol 2023; 14:1189251. [PMID: 37575223 PMCID: PMC10421657 DOI: 10.3389/fimmu.2023.1189251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 07/05/2023] [Indexed: 08/15/2023] Open
Abstract
Introduction Primarily driven by autoreactive B cells, pemphigus foliaceus (PF) is an uncommon autoimmune blistering skin disease of sporadic occurrence worldwide. However, PF reaches a prevalence of 3% in the endemic areas of Brazil, the highest ever registered for any autoimmune disease, which indicates environmental factors influencing the immune response in susceptible individuals. We aimed to provide insights into the immune repertoire of patients with PF living in the endemic region of the disease, compared to healthy individuals from the endemic region and a non-endemic area. Methods We characterized the B-cell repertoire in i) nontreated patients (n=5); ii) patients under immunosuppressive treatment (n=5); iii) patients in remission without treatment (n=6); and two control groups iv) from the endemic (n=6) and v) non-endemic areas in Brazil (n=4). We used total RNA extracted from peripheral blood mononuclear cells and performed a comprehensive characterization of the variable region of immunoglobulin heavy chain (IGH) in IgG and IgM using next-generation sequencing. Results Compared to individuals from a different area, we observed remarkably lower clonotype diversity in the B-cell immune repertoire of patients and controls from the endemic area (p < 0.02), suggesting that the immune repertoire in the endemic area is under geographically specific and intense environmental pressure. Moreover, we observed longer CDR3 sequences in patients, and we identified differential disease-specific usage of IGHV segments, including increased IGHV3-30 and decreased IGHV3-23 in patients with active disease (p < 0.04). Finally, our robust network analysis discovered clusters of CDR3 sequences uniquely observed in patients with PF. Discussion Our results indicate that environmental factors, in addition to disease state, impact the characteristics of the repertoire. Our findings can be applied to further investigation of the environmental factors that trigger pemphigus and expand the knowledge for identifying new targeted and more effective therapies.
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Affiliation(s)
- Verónica Calonga-Solís
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Michael Olbrich
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Fabian Ott
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | | | - Danielle Malheiros
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Axel Künstner
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Ticiana D.J. Farias
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Carolina M. Camargo
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | | | - Hauke Busch
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Anke Fähnrich
- Medical Systems Biology Group, Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Danillo G. Augusto
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, United States
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14
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Kim JW, Kim S, Yang SY, Joung JG, Hwang S. T-Cell Receptor Repertoire Characteristics Associated with Prognostic Significance in High-Grade Serous Ovarian Carcinoma. Genes (Basel) 2023; 14:genes14040785. [PMID: 37107543 PMCID: PMC10137910 DOI: 10.3390/genes14040785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
High-grade serous ovarian carcinoma (HGSOC) is a fatal gynecological malignancy. Somatic recombination occurring during T-cell receptor (TCR) development results in TCR diversity, and the TCR repertoire, thus produced, is associated with immune response. This study analyzed the difference in the TCR repertoire and their prognostic significance in 51 patients with HGSOC. The patient's clinical characteristics, gene expression pattern, TCR clonotypes, and degree of tumor-infiltrating leukocytes (TILs) were analyzed, and the patients were divided into groups depending on their recurrence pattern, tumor-infiltrating leukocyte (TIL) score, and homologous recombinant repair pathway deficiency (HRD)-associated mutations. The TCR repertoire was low in patients with recurrence and showed the expansion of eight TCR segments. Interestingly, a few genes correlated with the TCRs also showed a difference in expression according to the prognosis. Among them, seven genes were related to immune responses and KIAA1199 was up-regulated in ovarian cancer. Our study shows that the differences in the TCR repertoire in patients with ovarian cancer and their associated immune pathways could affect the prognosis of HGSOC.
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Affiliation(s)
- Ju-Won Kim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
| | - Sewha Kim
- Department of Pathology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam 13496, Republic of Korea
- Department of Pathology, Korea Medical Institute, Seoul 03173, Republic of Korea
| | - So-Yun Yang
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
| | - Je-Gun Joung
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
- Institute for Biomedical Informatics, CHA University School of Medicine, Seongnam 13488, Republic of Korea
- CHA Future Medicine Research Institute, CHA Bundang Medical Center, Seongnam 13488, Republic of Korea
| | - Sohyun Hwang
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Republic of Korea
- Department of Pathology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam 13496, Republic of Korea
- CHA Future Medicine Research Institute, CHA Bundang Medical Center, Seongnam 13488, Republic of Korea
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15
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Qu M, Liang Z, Chen Y, Wang Y, Wang H, Liu Z, Liu Y, Dong Y, Ge X, Li H, Zhou X. Antibodies Targeting the Cell Wall Induce Protection against Virulent Mycobacterium bovis Infection. Microbiol Spectr 2023; 11:e0343122. [PMID: 36847491 PMCID: PMC10100962 DOI: 10.1128/spectrum.03431-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/11/2022] [Indexed: 03/01/2023] Open
Abstract
Accumulating evidence indicates that antibodies can protect against some intracellular pathogens. Mycobacterium bovis is an intracellular bacterium, and its cell wall (CW) is essential for its virulence and survival. However, the questions of whether antibodies play a protective role in immunity against M. bovis infection and what effects antibodies specific to the CW of M. bovis have still remain unclear. Here, we report that antibodies targeting the CW of an isolated pathogenic M. bovis strain and that of an attenuated bacillus Calmette-Guérin (BCG) strain could induce protection against virulent M. bovis infection in vitro and in vivo. Further research found that the antibody-induced protection was mainly achieved by promoting Fc gamma receptor (FcγR)-mediated phagocytosis, inhibiting bacterial intracellular growth, and enhancing the fusion of phagosomes and lysosomes, and it also depended on T cells for its efficacy. Additionally, we analyzed and characterized the B-cell receptor (BCR) repertoires of CW-immunized mice via next-generation sequencing. CW immunization stimulated BCR changes in the complementarity determining region 3 (CDR3) isotype distribution, gene usage, and somatic hypermutation. Overall, our study validates the idea that antibodies targeting the CW induce protection against virulent M. bovis infection. This study highlights the importance of antibodies targeting the CW in the defense against tuberculosis. IMPORTANCE M. bovis is the causative agent of animal tuberculosis (TB) and human TB. Research on M. bovis is of great public health significance. Currently, TB vaccines are mainly aimed at eliciting protection by enhancement of cell-mediated immunity, and there are few studies on protective antibodies. This is the first report of protective antibodies against M. bovis infection, and the antibodies had both preventive and even therapeutic effects in an M. bovis infection mouse model. Additionally, we reveal the relationship between CDR3 gene diversity and the immune characteristics of the antibodies. These results will provide valuable advice for the rational development of TB vaccines.
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Affiliation(s)
- Mengjin Qu
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhengmin Liang
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yulan Chen
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yuanzhi Wang
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Haoran Wang
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Ziyi Liu
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yiduo Liu
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yuhui Dong
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xin Ge
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Hao Li
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xiangmei Zhou
- College of Veterinary Medicine, China Agricultural University, Beijing, China
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16
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Henze L, Braun J, Meyer-Arndt L, Jürchott K, Schlotz M, Michel J, Grossegesse M, Mangold M, Dingeldey M, Kruse B, Holenya P, Mages N, Reimer U, Eckey M, Schnatbaum K, Wenschuh H, Timmermann B, Klein F, Nitsche A, Giesecke-Thiel C, Loyal L, Thiel A. Primary ChAdOx1 vaccination does not reactivate pre-existing, cross-reactive immunity. Front Immunol 2023; 14:1056525. [PMID: 36798117 PMCID: PMC9927399 DOI: 10.3389/fimmu.2023.1056525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/10/2023] [Indexed: 02/04/2023] Open
Abstract
Currently available COVID-19 vaccines include inactivated virus, live attenuated virus, mRNA-based, viral vectored and adjuvanted protein-subunit-based vaccines. All of them contain the spike glycoprotein as the main immunogen and result in reduced disease severity upon SARS-CoV-2 infection. While we and others have shown that mRNA-based vaccination reactivates pre-existing, cross-reactive immunity, the effect of vector vaccines in this regard is unknown. Here, we studied cellular and humoral responses in heterologous adenovirus-vector-based ChAdOx1 nCOV-19 (AZ; Vaxzeria, AstraZeneca) and mRNA-based BNT162b2 (BNT; Comirnaty, BioNTech/Pfizer) vaccination and compared it to a homologous BNT vaccination regimen. AZ primary vaccination did not lead to measurable reactivation of cross-reactive cellular and humoral immunity compared to BNT primary vaccination. Moreover, humoral immunity induced by primary vaccination with AZ displayed differences in linear spike peptide epitope coverage and a lack of anti-S2 IgG antibodies. Contrary to primary AZ vaccination, secondary vaccination with BNT reactivated pre-existing, cross-reactive immunity, comparable to homologous primary and secondary mRNA vaccination. While induced anti-S1 IgG antibody titers were higher after heterologous vaccination, induced CD4+ T cell responses were highest in homologous vaccinated. However, the overall TCR repertoire breadth was comparable between heterologous AZ-BNT-vaccinated and homologous BNT-BNT-vaccinated individuals, matching TCR repertoire breadths after SARS-CoV-2 infection, too. The reasons why AZ and BNT primary vaccination elicits different immune response patterns to essentially the same antigen, and the associated benefits and risks, need further investigation to inform vaccine and vaccination schedule development.
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Affiliation(s)
- Larissa Henze
- Si-M/"Der Simulierte Mensch" a science framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Regenerative Immunology and Aging, BIH Immunomics, Berlin Institute of Health, Berlin, Germany
| | - Julian Braun
- Si-M/"Der Simulierte Mensch" a science framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Regenerative Immunology and Aging, BIH Immunomics, Berlin Institute of Health, Berlin, Germany
| | - Lil Meyer-Arndt
- Si-M/"Der Simulierte Mensch" a science framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Regenerative Immunology and Aging, BIH Immunomics, Berlin Institute of Health, Berlin, Germany.,NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Department of Neurology with Experimental Neurology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Karsten Jürchott
- Si-M/"Der Simulierte Mensch" a science framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Regenerative Immunology and Aging, BIH Immunomics, Berlin Institute of Health, Berlin, Germany
| | - Maike Schlotz
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Janine Michel
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Marica Grossegesse
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Maike Mangold
- Si-M/"Der Simulierte Mensch" a science framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Regenerative Immunology and Aging, BIH Immunomics, Berlin Institute of Health, Berlin, Germany
| | - Manuela Dingeldey
- Si-M/"Der Simulierte Mensch" a science framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Regenerative Immunology and Aging, BIH Immunomics, Berlin Institute of Health, Berlin, Germany
| | - Beate Kruse
- Si-M/"Der Simulierte Mensch" a science framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Regenerative Immunology and Aging, BIH Immunomics, Berlin Institute of Health, Berlin, Germany
| | | | - Norbert Mages
- Si-M/"Der Simulierte Mensch" a science framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Regenerative Immunology and Aging, BIH Immunomics, Berlin Institute of Health, Berlin, Germany.,Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ulf Reimer
- JPT Peptide Technologies GmbH, Berlin, Germany
| | - Maren Eckey
- JPT Peptide Technologies GmbH, Berlin, Germany
| | | | | | | | - Florian Klein
- Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany.,German Center for Infection Research (DZIF), Partner site Bonn-Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Andreas Nitsche
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | | | - Lucie Loyal
- Si-M/"Der Simulierte Mensch" a science framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Regenerative Immunology and Aging, BIH Immunomics, Berlin Institute of Health, Berlin, Germany
| | - Andreas Thiel
- Si-M/"Der Simulierte Mensch" a science framework of Technische Universität Berlin and Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Regenerative Immunology and Aging, BIH Immunomics, Berlin Institute of Health, Berlin, Germany
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17
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Blazso P, Csomos K, Tipton CM, Ujhazi B, Walter JE. Lineage Reconstruction of In Vitro Identified Antigen-Specific Autoreactive B Cells from Adaptive Immune Receptor Repertoires. Int J Mol Sci 2022; 24:ijms24010225. [PMID: 36613668 PMCID: PMC9820449 DOI: 10.3390/ijms24010225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
The emergence, survival, growth and maintenance of autoreactive (AR) B-cell clones, the hallmark of humoral autoimmunity, leave their footprints in B-cell receptor repertoires. Collecting IgH sequences related to polyreactive (PR) ones from adaptive immune receptor repertoire (AIRR) datasets make the reconstruction and analysis of PR/AR B-cell lineages possible. We developed a computational approach, named ImmChainTracer, to extract members and to visualize clonal relationships of such B-cell lineages. Our approach was successfully applied on the IgH repertoires of patients suffering from monogenic hypomorphic RAG1 and 2 deficiency (pRD) or polygenic systemic lupus erythematosus (SLE) autoimmune diseases to identify relatives of AR IgH sequences and to track their fate in AIRRs. Signs of clonal expansion, affinity maturation and class-switching events in PR/AR and non-PR/AR B-cell lineages were revealed. An extension of our method towards B-cell expansion caused by any trigger (e.g., infection, vaccination or antibody development) may provide deeper insight into antigen specific B-lymphogenesis.
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Affiliation(s)
- Peter Blazso
- Department of Pediatrics, University of Szeged, 6720 Szeged, Hungary
- Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
- Correspondence: (P.B.); (J.E.W.)
| | - Krisztian Csomos
- Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
| | - Christopher M. Tipton
- Department of Medicine, Division of Rheumatology, Emory University, Atlanta, GA 30322, USA
| | - Boglarka Ujhazi
- Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
| | - Jolan E. Walter
- Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children’s Hospital, St. Petersburg, FL 33701, USA
- Division of Allergy and Immunology, Massachusetts General Hospital for Children, Boston, MA 02114, USA
- Correspondence: (P.B.); (J.E.W.)
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18
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Shevyrev DV, Tereshchenko VP, Sennikov SV. The Enigmatic Nature of the TCR-pMHC Interaction: Implications for CAR-T and TCR-T Engineering. Int J Mol Sci 2022; 23:ijms232314728. [PMID: 36499057 PMCID: PMC9740949 DOI: 10.3390/ijms232314728] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/11/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
The interaction of the T-cell receptor (TCR) with a peptide in the major histocompatibility complex (pMHC) plays a central role in the adaptive immunity of higher chordates. Due to the high specificity and sensitivity of this process, the immune system quickly recognizes and efficiently responds to the appearance of foreign and altered self-antigens. This is important for ensuring anti-infectious and antitumor immunity, in addition to maintaining self-tolerance. The most common parameter used for assessing the specificity of TCR-pMHC interaction is affinity. This thermodynamic characteristic is widely used not only in various theoretical aspects, but also in practice, for example, in the engineering of various T-cell products with a chimeric (CAR-T) or artificial (TCR-engineered T-cell) antigen receptor. However, increasing data reveal the fact that, in addition to the thermodynamic component, the specificity of antigen recognition is based on the kinetics and mechanics of the process, having even greater influence on the selectivity of the process and T lymphocyte activation than affinity. Therefore, the kinetic and mechanical aspects of antigen recognition should be taken into account when designing artificial antigen receptors, especially those that recognize antigens in the MHC complex. This review describes the current understanding of the nature of the TCR-pMHC interaction, in addition to the thermodynamic, kinetic, and mechanical principles underlying the specificity and high sensitivity of this interaction.
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Affiliation(s)
- D. V. Shevyrev
- Laboratory of molecular Immunology, Research Institute for Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia
- Center for Cell Technology and Immunology, Sirius University of Science and Technology, 354340 Sochi, Russia
- Correspondence: ; Tel.: +7-9231345505
| | - V. P. Tereshchenko
- Laboratory of molecular Immunology, Research Institute for Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia
- Center for Cell Technology and Immunology, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - S. V. Sennikov
- Laboratory of molecular Immunology, Research Institute for Fundamental and Clinical Immunology, 630099 Novosibirsk, Russia
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19
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Michaeli M, Carlotti E, Hazanov H, Gribben JG, Mehr R. Mutational patterns along different evolution paths of follicular lymphoma. Front Oncol 2022; 12:1029995. [DOI: 10.3389/fonc.2022.1029995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022] Open
Abstract
Follicular lymphoma (FL) is an indolent disease, characterized by a median life expectancy of 18-20 years and by intermittent periods of relapse and remission. FL frequently transforms into the more aggressive diffuse large B cell lymphoma (t-FL). In previous studies, the analysis of immunoglobulin heavy chain variable region (IgHV) genes in sequential biopsies from the same patient revealed two different patterns of tumor clonal evolution: direct evolution, through acquisition of additional IgHV mutations over time, or divergent evolution, in which lymphoma clones from serial biopsies independently develop from a less-mutated common progenitor cell (CPC). Our goal in this study was to characterize the somatic hypermutation (SHM) patterns of IgHV genes in sequential FL samples from the same patients, and address the question of whether the mutation mechanisms (SHM targeting, DNA repair or both), or selection forces acting on the tumor clones, were different in FL samples compared to healthy control samples, or in late relapsed/transformed FL samples compared to earlier ones. Our analysis revealed differences in the distribution of mutations from each of the nucleotides when tumor and non-tumor clones were compared, while FL and transformed FL (t-FL) tumor clones displayed similar mutation distributions. Lineage tree measurements suggested that either initial clone affinity or selection thresholds were lower in FL samples compared to controls, but similar between FL and t-FL samples. Finally, we observed that both FL and t-FL tumor clones tend to accumulate larger numbers of potential N-glycosylation sites due to the introduction of new SHM. Taken together, these results suggest that transformation into t-FL, in contrast to initial FL development, is not associated with any major changes in DNA targeting or repair, or the selection threshold of the tumor clone.
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20
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Etter MM, Martins TA, Kulsvehagen L, Pössnecker E, Duchemin W, Hogan S, Sanabria-Diaz G, Müller J, Chiappini A, Rychen J, Eberhard N, Guzman R, Mariani L, Melie-Garcia L, Keller E, Jelcic I, Pargger H, Siegemund M, Kuhle J, Oechtering J, Eich C, Tzankov A, Matter MS, Uzun S, Yaldizli Ö, Lieb JM, Psychogios MN, Leuzinger K, Hirsch HH, Granziera C, Pröbstel AK, Hutter G. Severe Neuro-COVID is associated with peripheral immune signatures, autoimmunity and neurodegeneration: a prospective cross-sectional study. Nat Commun 2022; 13:6777. [DOI: 10.1038/s41467-022-34068-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractGrowing evidence links COVID-19 with acute and long-term neurological dysfunction. However, the pathophysiological mechanisms resulting in central nervous system involvement remain unclear, posing both diagnostic and therapeutic challenges. Here we show outcomes of a cross-sectional clinical study (NCT04472013) including clinical and imaging data and corresponding multidimensional characterization of immune mediators in the cerebrospinal fluid (CSF) and plasma of patients belonging to different Neuro-COVID severity classes. The most prominent signs of severe Neuro-COVID are blood-brain barrier (BBB) impairment, elevated microglia activation markers and a polyclonal B cell response targeting self-antigens and non-self-antigens. COVID-19 patients show decreased regional brain volumes associating with specific CSF parameters, however, COVID-19 patients characterized by plasma cytokine storm are presenting with a non-inflammatory CSF profile. Post-acute COVID-19 syndrome strongly associates with a distinctive set of CSF and plasma mediators. Collectively, we identify several potentially actionable targets to prevent or intervene with the neurological consequences of SARS-CoV-2 infection.
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21
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Lee S, Yang JI, Lee JH, Lee HW, Kim TJ. Low-Level Expression of CD138 Marks Naturally Arising Anergic B Cells. Immune Netw 2022; 22:e50. [PMID: 36627940 PMCID: PMC9807963 DOI: 10.4110/in.2022.22.e50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 12/30/2022] Open
Abstract
Autoreactive B cells are not entirely deleted, but some remain as immunocompetent or anergic B cells. Although the persistence of autoreactive B cells as anergic cells has been shown in transgenic mouse models with the expression of B cell receptor (BCR) reactive to engineered self-antigen, the characterization of naturally occurring anergic B cells is important to identify them and understand their contribution to immune regulation or autoimmune diseases. We report here that a low-level expression of CD138 in the splenic B cells marks naturally arising anergic B cells, not plasma cells. The CD138int B cells consisted of IgMlowIgDhigh follicular (FO) B cells and transitional 3 B cells in homeostatic conditions. The CD138int FO B cells showed an anergic gene expression profile shared with that of monoclonal anergic B cells expressing engineered BCRs and the gene expression profile was different from those of plasma cells, age-associated B cells, or germinal center B cells. The anergic state of the CD138int FO B cells was confirmed by attenuated Ca2+ response and failure to upregulate CD69 upon BCR engagement with anti-IgM, anti-IgD, anti-Igκ, or anti-IgG. The BCR repertoire of the CD138int FO B cells was distinct from that of the CD138- FO B cells and included some class-switched B cells with low-level somatic mutations. These findings demonstrate the presence of polyclonal anergic B cells in the normal mice that are characterized by low-level expression of CD138, IgM downregulation, reduced Ca2+ and CD69 responses upon BCR engagement, and distinct BCR repertoire.
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Affiliation(s)
| | | | - Joo Hee Lee
- Department of Immunology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Hyun Woo Lee
- Department of Immunology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Tae Jin Kim
- Department of Immunology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
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22
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Xu Z, Ismanto HS, Zhou H, Saputri DS, Sugihara F, Standley DM. Advances in antibody discovery from human BCR repertoires. FRONTIERS IN BIOINFORMATICS 2022; 2:1044975. [PMID: 36338807 PMCID: PMC9631452 DOI: 10.3389/fbinf.2022.1044975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Antibodies make up an important and growing class of compounds used for the diagnosis or treatment of disease. While traditional antibody discovery utilized immunization of animals to generate lead compounds, technological innovations have made it possible to search for antibodies targeting a given antigen within the repertoires of B cells in humans. Here we group these innovations into four broad categories: cell sorting allows the collection of cells enriched in specificity to one or more antigens; BCR sequencing can be performed on bulk mRNA, genomic DNA or on paired (heavy-light) mRNA; BCR repertoire analysis generally involves clustering BCRs into specificity groups or more in-depth modeling of antibody-antigen interactions, such as antibody-specific epitope predictions; validation of antibody-antigen interactions requires expression of antibodies, followed by antigen binding assays or epitope mapping. Together with innovations in Deep learning these technologies will contribute to the future discovery of diagnostic and therapeutic antibodies directly from humans.
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Affiliation(s)
- Zichang Xu
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hendra S. Ismanto
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hao Zhou
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Dianita S. Saputri
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Fuminori Sugihara
- Core Instrumentation Facility, Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Daron M. Standley
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Department Systems Immunology, Immunology Frontier Research Center, Osaka University, Suita, Japan
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23
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Aysola V, Abd C, Kuo AH, Gupta N. Ezrin Promotes Antigen Receptor Diversity during B Cell Development by Supporting Ig H Chain Variable Gene Recombination. Immunohorizons 2022; 6:722-729. [DOI: 10.4049/immunohorizons.2100103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023] Open
Abstract
Abstract
Genome-level rearrangements of Ig genes during B cell development are critical for generation of a diverse repertoire of BCRs that bind to a multitude of foreign Ags and some self Ags. Bone marrow B cell development involves a variety of cell–cell interactions, cell migration, and receptor signaling that likely benefit from the activity of membrane-cytoskeletal reorganizing proteins. However, the specific contribution of such proteins toward BCR repertoire diversification is poorly understood. Ezrin is a membrane-cytoskeletal linker protein that regulates mature B cell activation through spatial organization of the BCR. We employed next-generation sequencing to investigate whether Ezrin plays a role in IgH rearrangements and generation of BCR diversity in developing bone marrow B cells. BCR repertoire development occurred stochastically in B cell progenitors from both control and B cell conditional Ezrin-deficient mice. However, the loss of Ezrin resulted in fewer unique CDRs (CDR3s) in the BCRs and reduced Shannon entropy. Ezrin-deficient pre-B cells revealed similar utilization of joining (J) genes but significantly fewer variable (V) genes, thereby decreasing V-J combinatorial diversity. V-J junctional diversity, measured by CDR3 length and nucleotide additions and deletions, was not altered in Ezrin-deficient pre-B cells. Mechanistically, Ezrin-deficient cells showed a marked decrease in RAG1 gene expression, indicating a less efficient DNA recombination machinery. Overall, our results demonstrate that Ezrin shapes the BCR repertoire through combinatorial diversification.
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Affiliation(s)
- Varun Aysola
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH
| | - Christina Abd
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH
| | - Alexander H. Kuo
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH
| | - Neetu Gupta
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH
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24
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The major role of junctional diversity in the horse antibody repertoire. Mol Immunol 2022; 151:231-241. [PMID: 36179605 DOI: 10.1016/j.molimm.2022.09.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/20/2022]
Abstract
The antibody repertoire (Rep-seq) sequencing revolutionized the diversity of antigen B cell receptor studies, allowing deep and quantitative analysis to decipher the role of adaptive immunity in health and disease. Particularly, horse (Equus caballus) polyclonal antibodies have been produced and used since the century XIX to treat and prophylaxis diphtheria, tuberculosis, tetanus, pneumonia, and, more recently, COVID-19. However, our knowledge about the horse B cell receptors repertories is minimal. We present a deep horse antibody heavy chain repertoire (IGH) characterization of non-infected horses using NGS (Next generation sequencing). This study obtained a mean of 248,169 unique IgM clones and 66,141 unique IgG clones from four domestic adult horses. Rarefaction analysis showed sequence coverage was between 52 % and 82 % in IgM and IgG isotypes. We observed that besides horses antibody can use all functional IGHV genes, around 80 % of their antibodies use only three IGHV gene segments, and around 55 % use only one IGHJ gene segment. This limited VJ diversity seems to be compensated by the junctional diversity of these antibodies. We observed that the junctional diversity in horse antibodies is widespread, present in more than 90 % of horse antibodies. Besides this, the length of this region seems to be higher in horse antibodies than in other species. N1 and N2 nucleotides addition range from 0 to 111 nucleotides. In addition, around 45 % of the antibody clones have more than ten nucleotides in both the N1 and N2 junction regions. This diversity mechanism may be one of the most important in providing variability to the equine antibody repertoire. This study provides new insights regarding horse antibody composition, diversity generation, and particularities compared to other species, such as the frequency and length of N nucleotide addition. This study also points out the urgent need to better characterize TdT in horses and other species to better understand antibody repertoire characteristics.
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25
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Waltari E, Nafees S, McCutcheon KM, Wong J, Pak JE. AIRRscape: An interactive tool for exploring B-cell receptor repertoires and antibody responses. PLoS Comput Biol 2022; 18:e1010052. [PMID: 36126074 PMCID: PMC9524643 DOI: 10.1371/journal.pcbi.1010052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 09/30/2022] [Accepted: 09/04/2022] [Indexed: 11/18/2022] Open
Abstract
The sequencing of antibody repertoires of B-cells at increasing coverage and depth has led to the identification of vast numbers of immunoglobulin heavy and light chains. However, the size and complexity of these Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) datasets makes it difficult to perform exploratory analyses. To aid in data exploration, we have developed AIRRscape, an R Shiny-based interactive web browser application that enables B-cell receptor (BCR) and antibody feature discovery through comparisons among multiple repertoires. Using AIRR-seq data as input, AIRRscape starts by aggregating and sorting repertoires into interactive and explorable bins of germline V-gene, germline J-gene, and CDR3 length, providing a high-level view of the entire repertoire. Interesting subsets of repertoires can be quickly identified and selected, and then network topologies of CDR3 motifs can be generated for further exploration. Here we demonstrate AIRRscape using patient BCR repertoires and sequences of published monoclonal antibodies to investigate patterns of humoral immunity to three viral pathogens: SARS-CoV-2, HIV-1, and DENV (dengue virus). AIRRscape reveals convergent antibody sequences among datasets for all three pathogens, although HIV-1 antibody datasets display limited convergence and idiosyncratic responses. We have made AIRRscape available as a web-based Shiny application, along with code on GitHub to encourage its open development and use by immuno-informaticians, virologists, immunologists, vaccine developers, and other scientists that are interested in exploring and comparing multiple immune receptor repertoires.
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Affiliation(s)
- Eric Waltari
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- * E-mail: (EW); (JEP)
| | - Saba Nafees
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | | | - Joan Wong
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
| | - John E. Pak
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- * E-mail: (EW); (JEP)
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26
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Mikelov AI, Alekseeva EI, Komech EA, Staroverov DB, Turchaninova MA, Shugay M, Chudakov DM, Bazykin GA, Zvyagin IV. Memory persistence and differentiation into antibody-secreting cells accompanied by positive selection in longitudinal BCR repertoires. eLife 2022; 11:79254. [PMID: 36107479 PMCID: PMC9525062 DOI: 10.7554/elife.79254] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 09/11/2022] [Indexed: 11/18/2022] Open
Abstract
The stability and plasticity of B cell-mediated immune memory ensures the ability to respond to the repeated challenges. We have analyzed the longitudinal dynamics of immunoglobulin heavy chain repertoires from memory B cells, plasmablasts, and plasma cells from the peripheral blood of generally healthy volunteers. We reveal a high degree of clonal persistence in individual memory B cell subsets, with inter-individual convergence in memory and antibody-secreting cells (ASCs). ASC clonotypes demonstrate clonal relatedness to memory B cells, and are transient in peripheral blood. We identify two clusters of expanded clonal lineages with differing prevalence of memory B cells, isotypes, and persistence. Phylogenetic analysis revealed signs of reactivation of persisting memory B cell-enriched clonal lineages, accompanied by new rounds of affinity maturation during proliferation and differentiation into ASCs. Negative selection contributes to both persisting and reactivated lineages, preserving the functionality and specificity of B cell receptors (BCRs) to protect against current and future pathogens.
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Affiliation(s)
| | | | | | | | | | | | | | - Georgii A Bazykin
- Institute of Translational Medicine, Pirogov Russian National Research Medical University
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27
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Zhuo Y, Yang X, Shuai P, Yang L, Wen X, Zhong X, Yang S, Xu S, Liu Y, Zhang Z. Evaluation and comparison of adaptive immunity through analyzing the diversities and clonalities of T-cell receptor repertoires in the peripheral blood. Front Immunol 2022; 13:916430. [PMID: 36159829 PMCID: PMC9493076 DOI: 10.3389/fimmu.2022.916430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022] Open
Abstract
The adaptive immune system plays an important role in defending against different kinds of diseases, including infection and cancer. There has been a longtime need for a simple method to quantitatively evaluate the potency of adaptive immunity in our bodies. The tremendously diversified T-cell receptor (TCR) repertoires are the foundation of the adaptive immune system. In this study, we analyzed the expressed TCRβ repertoires in the peripheral blood of 582 healthy donors and 60 cancer patients. The TCR repertoire in each individual is different, with different usages of TCR Vβ and Jβ genes. Importantly, the TCR diversity and clonality change along with age and disease situation. Most elder individuals and cancer patients have elevated numbers of large TCRβ clones and reduced numbers of shared common clones, and thus, they have very low TCR diversity index (D50) values. These results reveal the alteration of the expressed TCRβ repertoire with aging and oncogenesis, and thus, we hypothesize that the TCR diversity and clonality in the peripheral blood might be used to evaluate and compare the adaptive immunities among different individuals in clinical practice.
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Affiliation(s)
- Yue Zhuo
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xin Yang
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Ping Shuai
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Liangliang Yang
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xueping Wen
- Department of Technology, Chengdu ExAb Biotechnology, LTD, Chengdu, China
| | - Xuemei Zhong
- Department of Technology, Chengdu ExAb Biotechnology, LTD, Chengdu, China
| | - Shihan Yang
- Department of Technology, Chengdu ExAb Biotechnology, LTD, Chengdu, China
| | - Shaoxian Xu
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Yuping Liu
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Zhixin Zhang, ; Yuping Liu,
| | - Zhixin Zhang
- Department of Health Management & Institute of Health Management, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Zhixin Zhang, ; Yuping Liu,
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28
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Fraley ER, Khanal S, Pierce SH, LeMaster CA, McLennan R, Pastinen T, Bradley T. Effects of Prior Infection with SARS-CoV-2 on B Cell Receptor Repertoire Response during Vaccination. Vaccines (Basel) 2022; 10:1477. [PMID: 36146555 PMCID: PMC9506540 DOI: 10.3390/vaccines10091477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/29/2022] [Indexed: 11/24/2022] Open
Abstract
Understanding the B cell response to SARS-CoV-2 vaccines is a high priority. High-throughput sequencing of the B cell receptor (BCR) repertoire allows for dynamic characterization of B cell response. Here, we sequenced the BCR repertoire of individuals vaccinated by the Pfizer SARS-CoV-2 mRNA vaccine. We compared BCR repertoires of individuals with previous COVID-19 infection (seropositive) to individuals without previous infection (seronegative). We discovered that vaccine-induced expanded IgG clonotypes had shorter heavy-chain complementarity determining region 3 (HCDR3), and for seropositive individuals, these expanded clonotypes had higher somatic hypermutation (SHM) than seronegative individuals. We uncovered shared clonotypes present in multiple individuals, including 28 clonotypes present across all individuals. These 28 shared clonotypes had higher SHM and shorter HCDR3 lengths compared to the rest of the BCR repertoire. Shared clonotypes were present across both serotypes, indicating convergent evolution due to SARS-CoV-2 vaccination independent of prior viral exposure.
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Affiliation(s)
- Elizabeth R. Fraley
- Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
| | - Santosh Khanal
- Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
| | - Stephen H. Pierce
- Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Cas A. LeMaster
- Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
| | - Rebecca McLennan
- Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
| | - Tomi Pastinen
- Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
| | - Todd Bradley
- Genomic Medicine Center, Children’s Mercy Research Institute, Children’s Mercy Kansas City, Kansas City, MO 64108, USA
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Pediatrics, University of Missouri-Kansas City School of Medicine, Kansas City, MO 64108, USA
- Department of Pediatrics, University of Kansas Medical Center, Kansas City, KS 66160, USA
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29
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The splenic T cell receptor repertoire during an immune response against a complex antigen: Expanding private clones accumulate in the high and low copy number region. PLoS One 2022; 17:e0273264. [PMID: 36001559 PMCID: PMC9401120 DOI: 10.1371/journal.pone.0273264] [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: 04/22/2022] [Accepted: 08/04/2022] [Indexed: 11/19/2022] Open
Abstract
Large cellular antigens comprise a variety of different epitopes leading to a T cell response of extreme diversity. Therefore, tracking such a response by next generation sequencing of the T cell receptor (TCR) in order to identify common TCR properties among the expanding T cells represents an enormous challenge. In the present study we adapted a set of established indices to elucidate alterations in the TCR repertoire regarding sequence similarities between TCRs including VJ segment usage and diversity of nucleotide coding of a single TCR. We combined the usage of these indices with a new systematic splitting strategy regarding the copy number of the extracted clones to divide the repertoire into multiple fractions for separate analysis. We implemented this new analytic approach using the splenic TCR repertoire following immunization with sheep red blood cells (SRBC) in mice. As expected, early after immunization presumably antigen-specific clones accumulated in high copy number fractions, but at later time points similar accumulation of specific clones occurred within the repertoire fractions of lowest copy number. For both repertoire regions immunized animals could reliably be distinguished from control in a classification approach, demonstrating the robustness of the two effects at the individual level. The direction in which the indices shifted after immunization revealed that for both the early and the late effect alterations in repertoire parameters were caused by antigen-specific private clones displacing non-specific public clones. Taken together, tracking antigen-specific clones by their displacement of average TCR repertoire characteristics in standardized repertoire fractions ensures that our analytical approach is fairly independent from the antigen in question and thus allows the in-depth characterization of a variety of immune responses.
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30
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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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31
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Lomakin YA, Zvyagin IV, Ovchinnikova LA, Kabilov MR, Staroverov DB, Mikelov A, Tupikin AE, Zakharova MY, Bykova NA, Mukhina VS, Favorov AV, Ivanova M, Simaniv T, Rubtsov YP, Chudakov DM, Zakharova MN, Illarioshkin SN, Belogurov AA, Gabibov AG. Deconvolution of B cell receptor repertoire in multiple sclerosis patients revealed a delay in tBreg maturation. Front Immunol 2022; 13:803229. [PMID: 36052064 PMCID: PMC9425031 DOI: 10.3389/fimmu.2022.803229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundB lymphocytes play a pivotal regulatory role in the development of the immune response. It was previously shown that deficiency in B regulatory cells (Bregs) or a decrease in their anti-inflammatory activity can lead to immunological dysfunctions. However, the exact mechanisms of Bregs development and functioning are only partially resolved. For instance, only a little is known about the structure of their B cell receptor (BCR) repertoires in autoimmune disorders, including multiple sclerosis (MS), a severe neuroinflammatory disease with a yet unknown etiology. Here, we elucidate specific properties of B regulatory cells in MS.MethodsWe performed a prospective study of the transitional Breg (tBreg) subpopulations with the CD19+CD24highCD38high phenotype from MS patients and healthy donors by (i) measuring their content during two diverging courses of relapsing-remitting MS: benign multiple sclerosis (BMS) and highly active multiple sclerosis (HAMS); (ii) analyzing BCR repertoires of circulating B cells by high-throughput sequencing; and (iii) measuring the percentage of CD27+ cells in tBregs.ResultsThe tBregs from HAMS patients carry the heavy chain with a lower amount of hypermutations than tBregs from healthy donors. The percentage of transitional CD24highCD38high B cells is elevated, whereas the frequency of differentiated CD27+ cells in this transitional B cell subset was decreased in the MS patients as compared with healthy donors.ConclusionsImpaired maturation of regulatory B cells is associated with MS progression.
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Affiliation(s)
- Yakov A. Lomakin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Ivan V. Zvyagin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Leyla A. Ovchinnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Marsel R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch Russian Academy of Sciences (RAS), Novosibirsk, Russia
| | - Dmitriy B. Staroverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Artem Mikelov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexey E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch Russian Academy of Sciences (RAS), Novosibirsk, Russia
| | - Maria Y. Zakharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nadezda A. Bykova
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences (RAS), Moscow, Russia
| | - Vera S. Mukhina
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences (RAS), Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences (RAS), Moscow, Russia
| | - Alexander V. Favorov
- Vavilov Institute of General Genetics, Russian Academy of Sciences (RAS), Moscow, Russia
- Quantitative Sciences Division, Department of Oncology, Johns Hopkins University, Baltimore, MD, United States
| | - Maria Ivanova
- Neuroinfection Department of the Research Center of Neurology, Moscow, Russia
| | - Taras Simaniv
- Neuroinfection Department of the Research Center of Neurology, Moscow, Russia
| | - Yury P. Rubtsov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
| | - Dmitriy M. Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
- Department of Molecular Technologies, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Maria N. Zakharova
- Neuroinfection Department of the Research Center of Neurology, Moscow, Russia
| | | | - Alexey A. Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
- Department of Biological Chemistry, Evdokimov Moscow State University of Medicine and Dentistry, Moscow, Russia
- *Correspondence: Alexey A. Belogurov Jr., ; Alexander G. Gabibov,
| | - Alexander G. Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia
- Department of Life Sciences, Higher School of Economics, Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
- *Correspondence: Alexey A. Belogurov Jr., ; Alexander G. Gabibov,
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Shiohara M, Suzuki S, Shichinohe S, Ishigaki H, Nakayama M, Nomura N, Shingai M, Sekiya T, Ohno M, Iida S, Kawai N, Kawahara M, Yamagishi J, Ito K, Mitsumata R, Ikeda T, Motokawa K, Sobue T, Kida H, Ogasawara K, Itoh Y. Inactivated whole influenza virus particle vaccines induce neutralizing antibodies with an increase in immunoglobulin gene subclones of B-lymphocytes in cynomolgus macaques. Vaccine 2022; 40:4026-4037. [PMID: 35641357 DOI: 10.1016/j.vaccine.2022.05.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 03/03/2022] [Accepted: 05/17/2022] [Indexed: 10/18/2022]
Abstract
The All-Japan Influenza Vaccine Study Group has been developing a more effective vaccine than the current split vaccines for seasonal influenza virus infection. In the present study, the efficacy of formalin- and/or β-propiolactone-inactivated whole virus particle vaccines for seasonal influenza was compared to that of the current ether-treated split vaccines in a nonhuman primate model. The monovalent whole virus particle vaccines or split vaccines of influenza A virus (H1N1) and influenza B virus (Victoria lineage) were injected subcutaneously into naïve cynomolgus macaques twice. The whole virus particle vaccines induced higher titers of neutralizing antibodies against H1N1 influenza A virus and influenza B virus in the plasma of macaques than did the split vaccines. At challenge with H1N1 influenza A virus or influenza B virus, the virus titers in nasal swabs and the increases in body temperatures were lower in the macaques immunized with the whole virus particle vaccine than in those immunized with the split vaccine. Repertoire analyses of immunoglobulin heavy chain genes demonstrated that the number of B-lymphocyte subclones was increased in macaques after the 1st vaccination with the whole virus particle vaccine, but not with the split vaccine, indicating that the whole virus particle vaccine induced the activation of vaccine antigen-specific B-lymphocytes more vigorously than did the split vaccine at priming. Thus, the present findings suggest that the superior antibody induction ability of the whole virus particle vaccine as compared to the split vaccine is attributable to its stimulatory properties on the subclonal differentiation of antigen-specific B-lymphocytes.
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Affiliation(s)
- Masanori Shiohara
- Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Saori Suzuki
- Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Shintaro Shichinohe
- Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Hirohito Ishigaki
- Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Misako Nakayama
- Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan
| | - Naoki Nomura
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Masashi Shingai
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Toshiki Sekiya
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan
| | - Marumi Ohno
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Sayaka Iida
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naoko Kawai
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Mamiko Kawahara
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Junya Yamagishi
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kimihito Ito
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | | | | | - Kenji Motokawa
- Business Planning & Management Department, Daiichi Sankyo Biotech Co. Ltd., Saitama, Japan
| | - Tomoyoshi Sobue
- Group III, Modality Research Laboratories, Daiichi Sankyo Co. Ltd., Tokyo, Japan
| | - Hiroshi Kida
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan; Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Sapporo, Japan; Collaborating Research Center for the Control of Infectious Diseases, Nagasaki University, Nagasaki, Japan
| | - Kazumasa Ogasawara
- Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan; International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasushi Itoh
- Division of Pathogenesis and Disease Regulation, Department of Pathology, Shiga University of Medical Science, Otsu, Japan.
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Olsen TH, Moal IH, Deane CM. AbLang: an antibody language model for completing antibody sequences. BIOINFORMATICS ADVANCES 2022; 2:vbac046. [PMID: 36699403 PMCID: PMC9710568 DOI: 10.1093/bioadv/vbac046] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/14/2022] [Indexed: 01/28/2023]
Abstract
Motivation General protein language models have been shown to summarize the semantics of protein sequences into representations that are useful for state-of-the-art predictive methods. However, for antibody specific problems, such as restoring residues lost due to sequencing errors, a model trained solely on antibodies may be more powerful. Antibodies are one of the few protein types where the volume of sequence data needed for such language models is available, e.g. in the Observed Antibody Space (OAS) database. Results Here, we introduce AbLang, a language model trained on the antibody sequences in the OAS database. We demonstrate the power of AbLang by using it to restore missing residues in antibody sequence data, a key issue with B-cell receptor repertoire sequencing, e.g. over 40% of OAS sequences are missing the first 15 amino acids. AbLang restores the missing residues of antibody sequences better than using IMGT germlines or the general protein language model ESM-1b. Further, AbLang does not require knowledge of the germline of the antibody and is seven times faster than ESM-1b. Availability and implementation AbLang is a python package available at https://github.com/oxpig/AbLang. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Tobias H Olsen
- Department of Statistics, University of Oxford, Oxford OX1 3LB, UK
| | - Iain H Moal
- GSK Medicines Research Centre, GlaxoSmithKline, Stevenage SG1 2NY, UK
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Chen Y, Ye Z, Zhang Y, Xie W, Chen Q, Lan C, Yang X, Zeng H, Zhu Y, Ma C, Tang H, Wang Q, Guan J, Chen S, Li F, Yang W, Yan H, Yu X, Zhang Z. A Deep Learning Model for Accurate Diagnosis of Infection Using Antibody Repertoires. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 208:2675-2685. [PMID: 35606050 DOI: 10.4049/jimmunol.2200063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
The adaptive immune receptor repertoire consists of the entire set of an individual's BCRs and TCRs and is believed to contain a record of prior immune responses and the potential for future immunity. Analyses of TCR repertoires via deep learning (DL) methods have successfully diagnosed cancers and infectious diseases, including coronavirus disease 2019. However, few studies have used DL to analyze BCR repertoires. In this study, we collected IgG H chain Ab repertoires from 276 healthy control subjects and 326 patients with various infections. We then extracted a comprehensive feature set consisting of 10 subsets of repertoire-level features and 160 sequence-level features and tested whether these features can distinguish between infected individuals and healthy control subjects. Finally, we developed an ensemble DL model, namely, DL method for infection diagnosis (https://github.com/chenyuan0510/DeepID), and used this model to differentiate between the infected and healthy individuals. Four subsets of repertoire-level features and four sequence-level features were selected because of their excellent predictive performance. The DL method for infection diagnosis outperformed traditional machine learning methods in distinguishing between healthy and infected samples (area under the curve = 0.9883) and achieved a multiclassification accuracy of 0.9104. We also observed differences between the healthy and infected groups in V genes usage, clonal expansion, the complexity of reads within clone, the physical properties in the α region, and the local flexibility of the CDR3 amino acid sequence. Our results suggest that the Ab repertoire is a promising biomarker for the diagnosis of various infections.
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Affiliation(s)
- Yuan Chen
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhiming Ye
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Division of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yanfang Zhang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wenxi Xie
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Qingyun Chen
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Chunhong Lan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xiujia Yang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Huikun Zeng
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yan Zhu
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Cuiyu Ma
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Haipei Tang
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Qilong Wang
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Junjie Guan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Sen Chen
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Fenxiang Li
- Department of Infectious Disease Control and Prevention, Center for Disease Control and Prevention of Southern Theatre Command, Guangzhou, China
| | - Wei Yang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Huacheng Yan
- Department of Infectious Disease Control and Prevention, Center for Disease Control and Prevention of Southern Theatre Command, Guangzhou, China
| | - Xueqing Yu
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China;
- Division of Nephrology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhenhai Zhang
- Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China;
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- State Key Laboratory of Organ Failure Research, Division of Nephrology, Southern Medical University, Guangzhou, China; and
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China
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Langlois de Septenville A, Boudjoghra M, Bravetti C, Armand M, Salson M, Giraud M, Davi F. Immunoglobulin Gene Mutational Status Assessment by Next Generation Sequencing in Chronic Lymphocytic Leukemia. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2453:153-167. [PMID: 35622326 DOI: 10.1007/978-1-0716-2115-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
B cell receptor (BcR) immunoglobulins (IG) display a tremendous diversity due to complex DNA rearrangements, the V(D)J recombination, further enhanced by the somatic hypermutation process. In chronic lymphocytic leukemia (CLL), the mutational load of the clonal BcR IG expressed by the leukemic cells constitutes an important prognostic and predictive biomarker. Here, we provide a reliable methodology capable of determining the mutational status of IG genes in CLL using high-throughput sequencing, starting from leukemic cell DNA or RNA.
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Affiliation(s)
| | - Myriam Boudjoghra
- AP-HP, Pitié-Salpêtrière Hospital, Laboratory of Hematology, Paris, France
| | - Clotilde Bravetti
- AP-HP, Pitié-Salpêtrière Hospital, Laboratory of Hematology, Paris, France
- Sorbonne Université, Paris, France
| | - Marine Armand
- AP-HP, Pitié-Salpêtrière Hospital, Laboratory of Hematology, Paris, France
- Sorbonne Université, Paris, France
| | - Mikaël Salson
- Université de Lille, CNRS, UMR 9189-CRIStAL, Inria, Lille, France
| | - Mathieu Giraud
- Université de Lille, CNRS, UMR 9189-CRIStAL, Inria, Lille, France
| | - Frederic Davi
- AP-HP, Pitié-Salpêtrière Hospital, Laboratory of Hematology, Paris, France.
- Sorbonne Université, Paris, France.
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Mahita J, Kim DG, Son S, Choi Y, Kim HS, Bailey-Kellogg C. Computational epitope binning reveals functional equivalence of sequence-divergent paratopes. Comput Struct Biotechnol J 2022; 20:2169-2180. [PMID: 35615020 PMCID: PMC9118127 DOI: 10.1016/j.csbj.2022.04.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 11/26/2022] Open
Abstract
Epitope binning groups target-specific protein binders recognizing the same binding region. The “Epibin” method utilizes docking models to computationally predict competition and identify bins. Epibin recapitulated binding competition of repebody variants as determined by immunoassays. In addition, Epibin enabled identification of ‘paratope-equivalent’ residues in sequence-dissimilar variants. Computational epitope binning can scale to allow characterization of entire antigen-specific antibody repertoires.
The therapeutic efficacy of a protein binder largely depends on two factors: its binding site and its binding affinity. Advances in in vitro library display screening and next-generation sequencing have enabled accelerated development of strong binders, yet identifying their binding sites still remains a major challenge. The differentiation, or “binning”, of binders into different groups that recognize distinct binding sites on their target is a promising approach that facilitates high-throughput screening of binders that may show different biological activity. Here we study the extent to which the information contained in the amino acid sequences comprising a set of target-specific binders can be leveraged to bin them, inferring functional equivalence of their binding regions, or paratopes, based directly on comparison of the sequences, their modeled structures, or their modeled interactions. Using a leucine-rich repeat binding scaffold known as a “repebody” as the source of diversity in recognition against interleukin-6 (IL-6), we show that the “Epibin” approach introduced here effectively utilized structural modelling and docking to extract specificity information encoded in the repebody amino acid sequences and thereby successfully recapitulate IL-6 binding competition observed in immunoassays. Furthermore, our computational binning provided a basis for designing in vitro mutagenesis experiments to pinpoint specificity-determining residues. Finally, we demonstrate that the Epibin approach can extend to antibodies, retrospectively comparing its predictions to results from antigen-specific antibody competition studies. The study thus demonstrates the utility of modeling structure and binding from the amino acid sequences of different binders against the same target, and paves the way for larger-scale binning and analysis of entire repertoires.
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Aschauer C, Jelencsics K, Hu K, Gregorich M, Reindl-Schwaighofer R, Wenda S, Wekerle T, Heinzel A, Oberbauer R. Effects of Reduced-Dose Anti-Human T-Lymphocyte Globulin on Overall and Donor-Specific T-Cell Repertoire Reconstitution in Sensitized Kidney Transplant Recipients. Front Immunol 2022; 13:843452. [PMID: 35281040 PMCID: PMC8913717 DOI: 10.3389/fimmu.2022.843452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundPre-sensitized kidney transplant recipients have a higher risk for rejection following kidney transplantation and therefore receive lymphodepletional induction therapy with anti-human T-lymphocyte globulin (ATLG) whereas non-sensitized patients are induced in many centers with basiliximab. The time course of lymphocyte reconstitution with regard to the overall and donor-reactive T-cell receptor (TCR) specificity remains elusive.Methods/DesignFive kidney transplant recipients receiving a 1.5-mg/kg ATLG induction therapy over 7 days and five patients with 2 × 20 mg basiliximab induction therapy were longitudinally monitored. Peripheral mononuclear cells were sampled pre-transplant and within 1, 3, and 12 months after transplantation, and their overall and donor-reactive TCRs were determined by next-generation sequencing of the TCR beta CDR3 region. Overall TCR repertoire diversity, turnover, and donor specificity were assessed at all timepoints.ResultsWe observed an increase in the donor-reactive TCR repertoire after transplantation in patients, independent of lymphocyte counts or induction therapy. Donor-reactive CD4 T-cell frequency in the ATLG group increased from 1.14% + -0.63 to 2.03% + -1.09 and from 0.93% + -0.63 to 1.82% + -1.17 in the basiliximab group in the first month. Diversity measurements of the entire T-cell repertoire and repertoire turnover showed no statistical difference between the two induction therapies. The difference in mean clonality between groups was 0.03 and 0.07 pre-transplant in the CD4 and CD8 fractions, respectively, and was not different over time (CD4: F(1.45, 11.6) = 0.64 p = 0.496; CD8: F(3, 24) = 0.60 p = 0.620). The mean difference in R20, a metric for immune dominance, between groups was -0.006 in CD4 and 0.001 in CD8 T-cells and not statistically different between the groups and subsequent timepoints (CD4: F(3, 24) = 0.85 p = 0.479; CD8: F(1.19, 9.52) = 0.79 p = 0.418).ConclusionReduced-dose ATLG induction therapy led to an initial lymphodepletion followed by an increase in the percentage of donor-reactive T-cells after transplantation similar to basiliximab induction therapy. Furthermore, reduced-dose ATLG did not change the overall TCR repertoire in terms of a narrowed or skewed TCR repertoire after immune reconstitution, comparable to non-depletional induction therapy.
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Affiliation(s)
- Constantin Aschauer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Kira Jelencsics
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Karin Hu
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Mariella Gregorich
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
- Section for Clinical Biometrics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Roman Reindl-Schwaighofer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Sabine Wenda
- Department of Blood Group Serology and Transfusion Medicine, Medical University Vienna, Vienna, Austria
| | - Thomas Wekerle
- Division of Transplantation, Department of General Surgery, Medical University of Vienna, Vienna, Austria
| | - Andreas Heinzel
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
- *Correspondence: Andreas Heinzel, ; Rainer Oberbauer,
| | - Rainer Oberbauer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
- *Correspondence: Andreas Heinzel, ; Rainer Oberbauer,
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Tan M, Ma J, Yang X, You Q, Guo X, Li Y, Wang R, Han G, Chen Y, Qiu X, Wang X, Zhang L. Quantitative proteomics reveals differential immunoglobulin-associated proteome (IgAP) in patients of acute myocardial infarction and chronic coronary syndromes. J Proteomics 2022; 252:104449. [PMID: 34890869 DOI: 10.1016/j.jprot.2021.104449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/15/2022]
Abstract
B cells and immunoglobulins are implicated in the pathogenesis of chronic diseases, including coronary artery disease (CAD). However, it remains elusive how the humoral immunity is incriminated in the disease progression of CAD. Using serum samples of chronic coronary syndrome (CCS) and acute myocardial infarction (AMI), we conducted a quantitative profiling of the proteomic landscape recognized by immunoglobulins, which we term immunoglobulin-associated proteome (IgAP). Intriguingly, CCS and AMI patients displayed distinctive IgAP profiles that enriched proteins in the pathways of blood coagulation regulation and lipoprotein transport, suggesting that CCS-AMI transition involves changes of these pathways that are associated with immunoglobulins. Furthermore, we identified immunoglobulin-bound coagulation factor X (F10) as a potential biomarker and validated it with an independent cohort of CCS, AMI and healthy individuals. Our study indicates that IgAP proteins may serve as novel diagnostic biomarkers for CCS and AMI. SIGNIFICANCE: Our work it demonstrates a clear implication of immunoglobulin-associated proteome (IgAP), the proteomic landscape recognized by immunoglobulins, in the pathogenesis of CAD. In addition, it reports for the first time that immunoglobulin-bound F10 is implicated in CAD.
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Affiliation(s)
- Miaomiao Tan
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China; Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Jing Ma
- Department of Cardiology First Medical Center of Chinese PLA General Hospital, Beijing 18 100853, China
| | - Xi Yang
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
| | - Qi You
- Department of Cardiology First Medical Center of Chinese PLA General Hospital, Beijing 18 100853, China
| | - Xiaoxin Guo
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Yiuhei Li
- Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Rui Wang
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China; Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Guiyuan Han
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China; Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Yundai Chen
- Department of Cardiology First Medical Center of Chinese PLA General Hospital, Beijing 18 100853, China
| | - Xiaoyan Qiu
- Department of Immunology, School of Basic Medical Sciences, Peking University, Beijing 100191, China; Peking University Center for Human Disease Genomics, Beijing 100191, China
| | - Xin Wang
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China; Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Liang Zhang
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China; Department of Biomedical Sciences, College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China.
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Mack EKM, Hartmann S, Ross P, Wollmer E, Mann C, Neubauer A, Brendel C, Hoffmann J. Monitoring multiple myeloma in the peripheral blood based on cell-free DNA and circulating plasma cells. Ann Hematol 2022; 101:811-824. [PMID: 35106639 PMCID: PMC8913458 DOI: 10.1007/s00277-022-04771-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/16/2022] [Indexed: 11/25/2022]
Abstract
With the advent of novel, highly effective therapies for multiple myeloma (MM), classical serologic monitoring appears insufficient for response assessment and prediction of relapse. Moreover, serologic studies in MM are hampered by interference of therapeutic antibodies. The detection of malignant plasma cell clones by next generation sequencing (NGS) or multiparameter flow cytometry (MFC) circumvents these difficulties and can be performed in the peripheral blood (pB) by targeting circulating cell-free DNA (cfDNA) or circulating plasma cells (CPCs), thus also avoiding an invasive sampling procedure. Here, we applied NGS of VJ light chain (LC) rearrangements in cfDNA and MFC of magnetically-enriched CD138-positive CPCs (me-MFC) to investigate disease burden in unselected MM patients. Sequencing was successful for 114/130 (87.7%) cfDNA samples and me-MFC results were analyzable for 196/205 (95.6%) samples. MM clones were detectable in 38.9% of samples taken at initial diagnosis or relapse (ID/RD), but only in 11.8% of samples taken during complete remission (CR). Circulating MM plasma cells were present in 83.3% of ID/RD samples and 9.9% of CR samples. Residual disease assessment by NGS or me-MFC in samples taken during very good partial remission or CR was 80% concordant. Notably, 4/4 (NGS) and 5/8 (me-MFC) positive CR samples were from patients with oligo- or non-secretory myeloma. The time to progression was shorter if there was evidence of residual myeloma in the pB. Together, our findings indicate that our two novel analytical approaches accurately indicate the course of MM and may be particularly valuable for monitoring patients with serologically non-trackable disease.
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Affiliation(s)
- Elisabeth K M Mack
- Department of Hematology, Oncology and Immunology, Philipps-University Marburg and University Hospital Gießen and Marburg, 35032, Baldingerstraße, Marburg, Germany.
| | - Sören Hartmann
- Department of Hematology, Oncology and Immunology, Philipps-University Marburg and University Hospital Gießen and Marburg, 35032, Baldingerstraße, Marburg, Germany
| | - Petra Ross
- Department of Hematology, Oncology and Immunology, Philipps-University Marburg and University Hospital Gießen and Marburg, 35032, Baldingerstraße, Marburg, Germany
| | - Ellen Wollmer
- Department of Hematology, Oncology and Immunology, Philipps-University Marburg and University Hospital Gießen and Marburg, 35032, Baldingerstraße, Marburg, Germany
| | - Christoph Mann
- Department of Hematology, Oncology and Immunology, Philipps-University Marburg and University Hospital Gießen and Marburg, 35032, Baldingerstraße, Marburg, Germany
| | - Andreas Neubauer
- Department of Hematology, Oncology and Immunology, Philipps-University Marburg and University Hospital Gießen and Marburg, 35032, Baldingerstraße, Marburg, Germany
| | - Cornelia Brendel
- Department of Hematology, Oncology and Immunology, Philipps-University Marburg and University Hospital Gießen and Marburg, 35032, Baldingerstraße, Marburg, Germany
| | - Jörg Hoffmann
- Department of Hematology, Oncology and Immunology, Philipps-University Marburg and University Hospital Gießen and Marburg, 35032, Baldingerstraße, Marburg, Germany.
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Aschauer C, Jelencsics K, Hu K, Heinzel A, Gregorich MG, Vetter J, Schaller S, Winkler SM, Weinberger J, Pimenov L, Gualdoni GA, Eder M, Kainz A, Troescher AR, Regele H, Reindl-Schwaighofer R, Wekerle T, Huppa JB, Sykes M, Oberbauer R. Prospective Tracking of Donor-Reactive T-Cell Clones in the Circulation and Rejecting Human Kidney Allografts. Front Immunol 2021; 12:750005. [PMID: 34721420 PMCID: PMC8552542 DOI: 10.3389/fimmu.2021.750005] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Background Antigen recognition of allo-peptides and HLA molecules leads to the activation of donor-reactive T-cells following transplantation, potentially causing T-cell-mediated rejection (TCMR). Sequencing of the T-cell receptor (TCR) repertoire can be used to track the donor-reactive repertoire in blood and tissue of patients after kidney transplantation. Methods/Design In this prospective cohort study, 117 non-sensitized kidney transplant recipients with anti-CD25 induction were included. Peripheral mononuclear cells (PBMCs) were sampled pre-transplant and at the time of protocol or indication biopsies together with graft tissue. Next-generation sequencing (NGS) of the CDR3 region of the TCRbeta chain was performed after donor stimulation in mixed lymphocyte reactions to define the donor-reactive TCR repertoire. Blood and tissue of six patients experiencing a TCMR and six patients without rejection on protocol biopsies were interrogated for these TCRs. To elucidate common features of T-cell clonotypes, a network analysis of the TCR repertoires was performed. Results After transplantation, the frequency of circulating donor-reactive CD4 T-cells increased significantly from 0.86 ± 0.40% to 2.06 ± 0.40% of all CD4 cells (p < 0.001, mean dif.: -1.197, CI: -1.802, -0.593). The number of circulating donor-reactive CD4 clonotypes increased from 0.72 ± 0.33% to 1.89 ± 0.33% (p < 0.001, mean dif.: -1.168, CI: -1.724, -0.612). No difference in the percentage of donor-reactive T-cells in the circulation at transplant biopsy was found between subjects experiencing a TCMR and the control group [p = 0.64 (CD4+), p = 0.52 (CD8+)]. Graft-infiltrating T-cells showed an up to six-fold increase of donor-reactive T-cell clonotypes compared to the blood at the same time (3.7 vs. 0.6% and 2.4 vs. 1.5%), but the infiltrating TCR repertoire was not reflected by the composition of the circulating TCR repertoire despite some overlap. Network analysis showed a distinct segregation of the donor-reactive repertoire with higher modularity than the overall TCR repertoire in the blood. These findings indicate an unchoreographed process of diverse T-cell clones directed against numerous non-self antigens found in the allograft. Conclusion Donor-reactive T-cells are enriched in the kidney allograft during a TCMR episode, and dominant tissue clones are also found in the blood. Trial Registration Clinicaltrials.gov: NCT: 03422224 (https://clinicaltrials.gov/ct2/show/NCT03422224).
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Affiliation(s)
- Constantin Aschauer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Kira Jelencsics
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Karin Hu
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Andreas Heinzel
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Mariella Gloria Gregorich
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria.,Section for Clinical Biometrics, Center for Medical Statistics, Informatics and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Julia Vetter
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg im Muehlkreis, Austria
| | - Susanne Schaller
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg im Muehlkreis, Austria
| | - Stephan M Winkler
- Bioinformatics Research Group, University of Applied Sciences Upper Austria, Hagenberg im Muehlkreis, Austria
| | - Johannes Weinberger
- Research Laboratory of Infection Biology, Department of Medicine, Medical University of Vienna, Vienna, Austria
| | - Lisabeth Pimenov
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Guido A Gualdoni
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Michael Eder
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Alexander Kainz
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | | | - Heinz Regele
- Department of Pathology, Medical University of Vienna, Vienna, Austria
| | - Roman Reindl-Schwaighofer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Thomas Wekerle
- Department of General Surgery, Division of Transplantation, Section of Transplantation Immunology, Medical University of Vienna, Vienna, Austria
| | - Johannes Bernhard Huppa
- Center for Pathophysiology, Infectiology and Immunology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Megan Sykes
- Columbian Center for Translational Immunology, Department of Medicine, Columbia University, New York City, NY, United States
| | - Rainer Oberbauer
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
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Halper-Stromberg E, McCall CM, Haley LM, Lin MT, Vogt S, Gocke CD, Eshleman JR, Stevens W, Martinson NA, Epeldegui M, Holdhoff M, Bettegowda C, Glantz MJ, Ambinder RF, Xian RR. CloneRetriever: An Automated Algorithm to Identify Clonal B and T Cell Gene Rearrangements by Next-Generation Sequencing for the Diagnosis of Lymphoid Malignancies. Clin Chem 2021; 67:1524-1533. [PMID: 34491318 PMCID: PMC8965457 DOI: 10.1093/clinchem/hvab141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/10/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Clonal immunoglobulin and T-cell receptor rearrangements serve as tumor-specific markers that have become mainstays of the diagnosis and monitoring of lymphoid malignancy. Next-generation sequencing (NGS) techniques targeting these loci have been successfully applied to lymphoblastic leukemia and multiple myeloma for minimal residual disease detection. However, adoption of NGS for primary diagnosis remains limited. METHODS We addressed the bioinformatics challenges associated with immune cell sequencing and clone detection by designing a novel web tool, CloneRetriever (CR), which uses machine-learning principles to generate clone classification schemes that are customizable, and can be applied to large datasets. CR has 2 applications-a "validation" mode to derive a clonality classifier, and a "live" mode to screen for clones by applying a validated and/or customized classifier. In this study, CR-generated multiple classifiers using 2 datasets comprising 106 annotated patient samples. A custom classifier was then applied to 36 unannotated samples. RESULTS The optimal classifier for clonality required clonal dominance ≥4.5× above background, read representation ≥8% of all reads, and technical replicate agreement. Depending on the dataset and analysis step, the optimal algorithm yielded sensitivities of 81%-90%, specificities of 97%-100%, areas under the curve of 91%-94%, positive predictive values of 92-100%, and negative predictive values of 88%-98%. Customization of the algorithms yielded 95%-100% concordance with gold-standard clonality determination, including rescue of indeterminate samples. Application to a set of unknowns showed concordance rates of 83%-96%. CONCLUSIONS CR is an out-of-the-box ready and user-friendly software designed to identify clonal rearrangements in large NGS datasets for the diagnosis of lymphoid malignancies.
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Affiliation(s)
| | - Chad M McCall
- Department of Pathology, Duke University School of Medicine, Durham, NC
| | - Lisa M Haley
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Ming-Tseh Lin
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Samantha Vogt
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD
| | - Christopher D Gocke
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - James R Eshleman
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Wendy Stevens
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
| | - Neil A Martinson
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD
- Perinatal HIV Research Unit (PHRU), University of the Witwatersrand, Johannesburg, South Africa
| | - Marta Epeldegui
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Matthias Holdhoff
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Chetan Bettegowda
- Department of Neurosurgery, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins School of Medicine, Baltimore, MD
| | - Michael J Glantz
- Department of Neurosurgery, Medicine, and Neurology, Penn State Milton S. Hershey Medical Center, Hershey, PA
| | - Richard F Ambinder
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
| | - Rena R Xian
- Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD
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Olsen TH, Boyles F, Deane CM. Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences. Protein Sci 2021; 31:141-146. [PMID: 34655133 PMCID: PMC8740823 DOI: 10.1002/pro.4205] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 11/17/2022]
Abstract
The antibody repertoires of individuals and groups have been used to explore disease states, understand vaccine responses, and drive therapeutic development. The arrival of B‐cell receptor repertoire sequencing has enabled researchers to get a snapshot of these antibody repertoires, and as more data are generated, increasingly in‐depth studies are possible. However, most publicly available data only exist as raw FASTQ files, making the data hard to access, process, and compare. The Observed Antibody Space (OAS) database was created in 2018 to offer clean, annotated, and translated repertoire data. In this paper, we describe an update to OAS that has been driven by the increasing volume of data and the appearance of paired (VH/VL) sequence data. OAS is now accessible via a new web server, with standardized search parameters and a new sequence‐based search option. The new database provides both nucleotides and amino acids for every sequence, with additional sequence annotations to make the data Minimal Information about Adaptive Immune Receptor Repertoire compliant, and comments on potential problems with the sequence. OAS now contains 25 new studies, including severe acute respiratory syndrome coronavirus 2 data and paired sequencing data. The new database is accessible at http://opig.stats.ox.ac.uk/webapps/oas/, and all data are freely available for download.
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Affiliation(s)
- Tobias H Olsen
- Department of Statistics, University of Oxford, Oxford, UK
| | - Fergus Boyles
- Department of Statistics, University of Oxford, Oxford, UK
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Ye H, Cheng L, Ju B, Xu G, Liu Y, Zhang S, Wang L, Zhang Z. SCIGA: Software for large-scale, single-cell immunoglobulin repertoire analysis. Gigascience 2021; 10:giab050. [PMID: 34585238 PMCID: PMC8478610 DOI: 10.1093/gigascience/giab050] [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: 12/08/2020] [Revised: 03/19/2021] [Accepted: 06/28/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND B-cell immunoglobulin repertoires with paired heavy and light chain can be determined by means of 10X single-cell V(D)J sequencing. Precise and quick analysis of 10X single-cell immunoglobulin repertoires remains a challenge owing to the high diversity of immunoglobulin repertoires and a lack of specialized software that can analyze such diverse data. FINDINGS In this study, specialized software for 10X single-cell immunoglobulin repertoire analysis was developed. SCIGA (Single-Cell Immunoglobulin Repertoire Analysis) is an easy-to-use pipeline that performs read trimming, immunoglobulin sequence assembly and annotation, heavy and light chain pairing, statistical analysis, visualization, and multiple sample integration analysis, which is all achieved by using a 1-line command. Then SCIGA was used to profile the single-cell immunoglobulin repertoires of 9 patients with coronavirus disease 2019 (COVID-19). Four neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified from these repertoires. CONCLUSIONS SCIGA provides a complete and quick analysis for 10X single-cell V(D)J sequencing datasets. It can help researchers to interpret B-cell immunoglobulin repertoires with paired heavy and light chain.
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Affiliation(s)
- Haocheng Ye
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518112, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
| | - Lin Cheng
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518112, China
| | - Bin Ju
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518112, China
| | - Gang Xu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518112, China
| | - Yang Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518112, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, 201508, China
| | - Lifei Wang
- Department of Radiology, National Clinical Research Center for Infectious Disease, Shenzhen, Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518112, China
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518112, China
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Liu H, Pan W, Tang C, Tang Y, Wu H, Yoshimura A, Deng Y, He N, Li S. The methods and advances of adaptive immune receptors repertoire sequencing. Theranostics 2021; 11:8945-8963. [PMID: 34522220 PMCID: PMC8419057 DOI: 10.7150/thno.61390] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/09/2021] [Indexed: 12/13/2022] Open
Abstract
The adaptive immune response is a powerful tool, capable of recognizing, binding to, and neutralizing a vast number of internal and external threats via T or B lymphatic receptors with widespread sets of antigen specificities. The emergence of high-throughput sequencing technology and bioinformatics provides opportunities for research in the fields of life sciences and medicine. The analysis and annotation for immune repertoire data can reveal biologically meaningful information, including immune prediction, target antigens, and effective evaluation. Continuous improvements of the immunological repertoire sequencing methods and analysis tools will help to minimize the experimental and calculation errors and realize the immunological information to meet the clinical requirements. That said, the clinical application of adaptive immune repertoire sequencing requires appropriate experimental methods and standard analytical tools. At the population cell level, we can acquire the overview of cell groups, but the information about a single cell is not obtained accurately. The information that is ignored may be crucial for understanding the heterogeneity of each cell, gene expression and drug response. The combination of high-throughput sequencing and single-cell technology allows us to obtain single-cell information with low-cost and high-throughput. In this review, we summarized the current methods and progress in this area.
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Affiliation(s)
- Hongmei Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Wenjing Pan
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Congli Tang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Yujie Tang
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Haijing Wu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hu-nan Key Laboratory of Medical Epigenomics, Changsha, Hunan, China
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Nongyue He
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
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Massive surge of mRNA expression of clonal B-cell receptor in patients with COVID-19. Heliyon 2021; 7:e07748. [PMID: 34395931 PMCID: PMC8352648 DOI: 10.1016/j.heliyon.2021.e07748] [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] [Received: 04/02/2021] [Revised: 07/19/2021] [Accepted: 08/06/2021] [Indexed: 12/03/2022] Open
Abstract
Background Antibody production is one of the primary mechanisms for recovery from coronavirus disease 2019 (COVID-19). It is speculated that massive clonal expansion of B cells, which can produce clinically meaningful neutralizing antibodies, occurs in patients who recover on the timing of acquiring adaptive immunity. Methods To evaluate fluctuations in clonal B cells and the size of the clones, we chronologically assessed the B-cell receptor (BCR) repertoire in three patients with COVID-19 who recovered around 10 days after symptom onset. Results We focused on the three dominant clonotypes (top 3) in each individual. The percentage frequencies of the top 3 clonotypes increased rapidly and accounted for 27.8 % on day 9 in patient 1, 10.4 % on day 12 in patient 2, and 10.8 % on day 11 in patient 3, respectively. The frequencies of these top 3 clonotypes rapidly decreased as the patients’ clinical symptoms improved. Furthermore, BCR network analysis revealed that accumulation of clusters composed of similar complementarity-determining region 3 (CDR3) sequences were rapidly formed, grew, and reached their maximum size around 10 days after symptom onset. Conclusions BCR repertoire analysis revealed that a massive surge of some unique BCRs occurs during the acquisition of adaptive immunity and recovery. The peaks were more prominent than expected. These results provide insight into the important role of BCRs in the recovery from COVID-19 and raise the possibility of developing neutralizing antibodies as COVID-19 immunotherapy.
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Patel RB, Hernandez R, Carlson P, Grudzinski J, Bates AM, Jagodinsky JC, Erbe A, Marsh IR, Arthur I, Aluicio-Sarduy E, Sriramaneni RN, Jin WJ, Massey C, Rakhmilevich AL, Vail D, Engle JW, Le T, Kim K, Bednarz B, Sondel PM, Weichert J, Morris ZS. Low-dose targeted radionuclide therapy renders immunologically cold tumors responsive to immune checkpoint blockade. Sci Transl Med 2021; 13:13/602/eabb3631. [PMID: 34261797 DOI: 10.1126/scitranslmed.abb3631] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 02/10/2021] [Accepted: 06/24/2021] [Indexed: 12/12/2022]
Abstract
Molecular and cellular effects of radiotherapy on tumor microenvironment (TME) can help prime and propagate antitumor immunity. We hypothesized that delivering radiation to all tumor sites could augment response to immunotherapies. We tested an approach to enhance response to immune checkpoint inhibitors (ICIs) by using targeted radionuclide therapy (TRT) to deliver radiation semiselectively to tumors. NM600, an alkylphosphocholine analog that preferentially accumulates in most tumor types, chelates a radioisotope and semiselectively delivers it to the TME for therapeutic or diagnostic applications. Using serial 86Y-NM600 positron emission tomography (PET) imaging, we estimated the dosimetry of 90Y-NM600 in immunologically cold syngeneic murine models that do not respond to ICIs alone. We observed strong therapeutic efficacy and reported optimal dose (2.5 to 5 gray) and sequence for 90Y-NM600 in combination with ICIs. After combined treatment, 45 to 66% of mice exhibited complete response and tumor-specific T cell memory, compared to 0% with 90Y-NM600 or ICI alone. This required expression of STING in tumor cells. Combined TRT and ICI activated production of proinflammatory cytokines in the TME, promoted tumor infiltration by and clonal expansion of CD8+ T cells, and reduced metastases. In mice bearing multiple tumors, combining TRT with moderate-dose (12 gray) external beam radiotherapy (EBRT) targeting a single tumor augmented response to ICIs compared to combination of ICIs with either TRT or EBRT alone. The safety of TRT was confirmed in a companion canine study. Low-dose TRT represents a translatable approach to promote response to ICIs for many tumor types, regardless of location.
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Affiliation(s)
- Ravi B Patel
- Department of Radiation Oncology, University of Pittsburgh Hillman Cancer Center, Pittsburgh, PA 15213, USA.
| | - Reinier Hernandez
- Department of Radiology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Peter Carlson
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Joseph Grudzinski
- Department of Radiology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Amber M Bates
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Justin C Jagodinsky
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Amy Erbe
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Ian R Marsh
- Department of Medical Physics, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Ian Arthur
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | | | - Raghava N Sriramaneni
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Won Jong Jin
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Christopher Massey
- Department of Radiology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | | | - David Vail
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53792, USA.,Barbara A. Suran Comparative Oncology Institute, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Johnathan W Engle
- Department of Radiology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Trang Le
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - KyungMann Kim
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Bryan Bednarz
- Department of Radiology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Paul M Sondel
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI 53792, USA.,Department of Pediatrics, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Jamey Weichert
- Department of Radiology, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Zachary S Morris
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI 53792, USA.
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Shevyrev D, Tereshchenko V, Kozlov V. Immune Equilibrium Depends on the Interaction Between Recognition and Presentation Landscapes. Front Immunol 2021; 12:706136. [PMID: 34394106 PMCID: PMC8362327 DOI: 10.3389/fimmu.2021.706136] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/12/2021] [Indexed: 12/15/2022] Open
Abstract
In this review, we described the structure and organization of antigen-recognizing repertoires of B and T cells from the standpoint of modern immunology. We summarized the latest advances in bioinformatics analysis of sequencing data from T and B cell repertoires and also presented contemporary ideas about the mechanisms of clonal diversity formation at different stages of organism development. At the same time, we focused on the importance of the allelic variants of the HLA genes and spectra of presented antigens for the formation of T-cell receptors (TCR) landscapes. The main idea of this review is that immune equilibrium and proper functioning of immunity are highly dependent on the interaction between the recognition and the presentation landscapes of antigens. Certain changes in these landscapes can occur during life, which can affect the protective function of adaptive immunity. We described some mechanisms associated with these changes, for example, the conversion of effector cells into regulatory cells and vice versa due to the trans-differentiation or bystander effect, changes in the clonal organization of the general TCR repertoire due to homeostatic proliferation or aging, and the background for the altered presentation of some antigens due to SNP mutations of MHC, or the alteration of the presenting antigens due to post-translational modifications. The authors suggest that such alterations can lead to an increase in the risk of the development of oncological and autoimmune diseases and influence the sensitivity of the organism to different infectious agents.
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Affiliation(s)
- Daniil Shevyrev
- Laboratory of Clinical Immunopathology, Research Institute for Fundamental and Clinical Immunology, Novosibirsk, Russia
| | - Valeriy Tereshchenko
- Laboratory of Molecular Immunology, Research Institute for Fundamental and Clinical Immunology, Novosibirsk, Russia
| | - Vladimir Kozlov
- Laboratory of Clinical Immunopathology, Research Institute for Fundamental and Clinical Immunology, Novosibirsk, Russia
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Aizik L, Dror Y, Taussig D, Barzel A, Carmi Y, Wine Y. Antibody Repertoire Analysis of Tumor-Infiltrating B Cells Reveals Distinct Signatures and Distributions Across Tissues. Front Immunol 2021; 12:705381. [PMID: 34349765 PMCID: PMC8327180 DOI: 10.3389/fimmu.2021.705381] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/29/2021] [Indexed: 12/12/2022] Open
Abstract
The role of B cells in the tumor microenvironment (TME) has largely been under investigated, and data regarding the antibody repertoire encoded by B cells in the TME and the adjacent lymphoid organs are scarce. Here, we utilized B cell receptor high-throughput sequencing (BCR-Seq) to profile the antibody repertoire signature of tumor-infiltrating lymphocyte B cells (TIL−Bs) in comparison to B cells from three anatomic compartments in a mouse model of triple-negative breast cancer. We found that TIL-Bs exhibit distinct antibody repertoire measures, including high clonal polarization and elevated somatic hypermutation rates, suggesting a local antigen-driven B-cell response. Importantly, TIL-Bs were highly mutated but non-class switched, suggesting that class-switch recombination may be inhibited in the TME. Tracing the distribution of TIL-B clones across various compartments indicated that they migrate to and from the TME. The data thus suggests that antibody repertoire signatures can serve as indicators for identifying tumor-reactive B cells.
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Affiliation(s)
- Ligal Aizik
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yael Dror
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - David Taussig
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Adi Barzel
- The School of Neurobiology, Biochemistry and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yaron Carmi
- Department of Pathology, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yariv Wine
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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Trück J, Eugster A, Barennes P, Tipton CM, Luning Prak ET, Bagnara D, Soto C, Sherkow JS, Payne AS, Lefranc MP, Farmer A, Bostick M, Mariotti-Ferrandiz E. Biological controls for standardization and interpretation of adaptive immune receptor repertoire profiling. eLife 2021; 10:e66274. [PMID: 34037521 PMCID: PMC8154019 DOI: 10.7554/elife.66274] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/15/2021] [Indexed: 12/15/2022] Open
Abstract
Use of adaptive immune receptor repertoire sequencing (AIRR-seq) has become widespread, providing new insights into the immune system with potential broad clinical and diagnostic applications. However, like many high-throughput technologies, it comes with several problems, and the AIRR Community was established to understand and help solve them. We, the AIRR Community's Biological Resources Working Group, have surveyed scientists about the need for standards and controls in generating and annotating AIRR-seq data. Here, we review the current status of AIRR-seq, provide the results of our survey, and based on them, offer recommendations for developing AIRR-seq standards and controls, including future work.
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Affiliation(s)
- Johannes Trück
- University Children’s Hospital and the Children’s Research Center, University of ZurichZurichSwitzerland
| | - Anne Eugster
- CRTD Center for Regenerative Therapies Dresden, Faculty of Medicine, Technische Universität DresdenDresdenGermany
| | - Pierre Barennes
- Sorbonne Université U959, Immunology-Immunopathology-Immunotherapy (i3)ParisFrance
- AP-HP Hôpital Pitié-Salpêtrière, Biotherapy (CIC-BTi)ParisFrance
| | - Christopher M Tipton
- Lowance Center for Human Immunology, Emory University School of MedicineAtlantaUnited States
| | - Eline T Luning Prak
- Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Davide Bagnara
- University of Genoa, Department of Experimental MedicineGenoaItaly
| | - Cinque Soto
- The Vanderbilt Vaccine Center, Vanderbilt University Medical CenterNashvilleUnited States
- Department of Pediatrics, Vanderbilt University Medical CenterNashvilleUnited States
| | - Jacob S Sherkow
- College of Law, University of IllinoisChampaignUnited States
- Center for Advanced Studies in Biomedical Innovation Law, University of Copenhagen Faculty of LawCopenhagenDenmark
- Carl R. Woese Institute for Genomic Biology, University of IllinoisUrbana, IllinoisUnited States
| | - Aimee S Payne
- Perelman School of Medicine, University of PennsylvaniaPhiladelphiaUnited States
| | - Marie-Paule Lefranc
- IMGT, The International ImMunoGeneTics Information System (IMGT), Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), CNRS, University of MontpellierMontpellierFrance
- Laboratoire d'ImmunoGénétique Moléculaire (LIGM) CNRS, University of MontpellierMontpellierFrance
- Institut de Génétique Humaine (IGH), CNRS, University of MontpellierMontpellierFrance
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50
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Large-scale analysis of 2,152 Ig-seq datasets reveals key features of B cell biology and the antibody repertoire. Cell Rep 2021; 35:109110. [PMID: 33979623 DOI: 10.1016/j.celrep.2021.109110] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/09/2021] [Accepted: 04/20/2021] [Indexed: 12/20/2022] Open
Abstract
Antibody repertoire sequencing enables researchers to acquire millions of B cell receptors and investigate these molecules at the single-nucleotide level. This power and resolution in studying humoral responses have led to its wide applications. However, most of these studies were conducted with a limited number of samples. Given the extraordinary diversity, assessment of these key features with a large sample set is demanded. Thus, we collect and systematically analyze 2,152 high-quality heavy-chain antibody repertoires. Our study reveals that 52 core variable genes universally contribute to more than 99% of each individual's repertoire; a distal interspersed preferences characterize V gene recombination; the number of public clones between two repertoires follows a linear model, and the positive selection dominates at RGYW motif in somatic hypermutations. Thus, this population-level analysis resolves some critical features of the antibody repertoire and may have significant value to the large cadre of scientists.
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