1
|
McIntire KM, Meng H, Lin TH, Kim W, Moore NE, Han J, McMahon M, Wang M, Malladi SK, Mohammed BM, Zhou JQ, Schmitz AJ, Hoehn KB, Carreño JM, Yellin T, Suessen T, Middleton WD, Teefey SA, Presti RM, Krammer F, Turner JS, Ward AB, Wilson IA, Kleinstein SH, Ellebedy AH. Maturation of germinal center B cells after influenza virus vaccination in humans. J Exp Med 2024; 221:e20240668. [PMID: 38935072 PMCID: PMC11211068 DOI: 10.1084/jem.20240668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Germinal centers (GC) are microanatomical lymphoid structures where affinity-matured memory B cells and long-lived bone marrow plasma cells are primarily generated. It is unclear how the maturation of B cells within the GC impacts the breadth and durability of B cell responses to influenza vaccination in humans. We used fine needle aspiration of draining lymph nodes to longitudinally track antigen-specific GC B cell responses to seasonal influenza vaccination. Antigen-specific GC B cells persisted for at least 13 wk after vaccination in two out of seven individuals. Monoclonal antibodies (mAbs) derived from persisting GC B cell clones exhibit enhanced binding affinity and breadth to influenza hemagglutinin (HA) antigens compared with related GC clonotypes isolated earlier in the response. Structural studies of early and late GC-derived mAbs from one clonal lineage in complex with H1 and H5 HAs revealed an altered binding footprint. Our study shows that inducing sustained GC reactions after influenza vaccination in humans supports the maturation of responding B cells.
Collapse
Affiliation(s)
- Katherine M. McIntire
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Hailong Meng
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Ting-Hui Lin
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Wooseob Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Department of Microbiology, Korea University College of Medicine, Seoul, Korea
| | - Nina E. Moore
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Meagan McMahon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Meng Wang
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Sameer Kumar Malladi
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Bassem M. Mohammed
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Julian Q. Zhou
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Aaron J. Schmitz
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Kenneth B. Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Temima Yellin
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Teresa Suessen
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - William D. Middleton
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - Sharlene A. Teefey
- Mallinckrodt Institute of Radiology, Washington University School of Medicine, St Louis, MO, USA
| | - Rachel M. Presti
- Department of Internal Medicine-Infectious Diseases, Washington University School of Medicine, St Louis, MO, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jackson S. Turner
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Andrew B. Ward
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Steven H. Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Ali H. Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St. Louis, MO, USA
- The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| |
Collapse
|
2
|
Ramirez SI, Faraji F, Hills LB, Lopez PG, Goodwin B, Stacey HD, Sutton HJ, Hastie KM, Saphire EO, Kim HJ, Mashoof S, Yan CH, DeConde AS, Levi G, Crotty S. Immunological memory diversity in the human upper airway. Nature 2024:10.1038/s41586-024-07748-8. [PMID: 39085605 DOI: 10.1038/s41586-024-07748-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 06/24/2024] [Indexed: 08/02/2024]
Abstract
The upper airway is an important site of infection, but immune memory in the human upper airway is poorly understood, with implications for COVID-19 and many other human diseases1-4. Here we demonstrate that nasal and nasopharyngeal swabs can be used to obtain insights into these challenging problems, and define distinct immune cell populations, including antigen-specific memory B cells and T cells, in two adjacent anatomical sites in the upper airway. Upper airway immune cell populations seemed stable over time in healthy adults undergoing monthly swabs for more than 1 year, and prominent tissue resident memory T (TRM) cell and B (BRM) cell populations were defined. Unexpectedly, germinal centre cells were identified consistently in many nasopharyngeal swabs. In subjects with SARS-CoV-2 breakthrough infections, local virus-specific BRM cells, plasma cells and germinal centre B cells were identified, with evidence of local priming and an enrichment of IgA+ memory B cells in upper airway compartments compared with blood. Local plasma cell populations were identified with transcriptional profiles of longevity. Local virus-specific memory CD4+ TRM cells and CD8+ TRM cells were identified, with diverse additional virus-specific T cells. Age-dependent upper airway immunological shifts were observed. These findings provide new understanding of immune memory at a principal mucosal barrier tissue in humans.
Collapse
Affiliation(s)
- Sydney I Ramirez
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Farhoud Faraji
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, CA, USA
| | - L Benjamin Hills
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Paul G Lopez
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Benjamin Goodwin
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Hannah D Stacey
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Henry J Sutton
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kathryn M Hastie
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Erica Ollmann Saphire
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Hyun Jik Kim
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Otorhinolaryngology, College of Medicine, Seoul National University, Seoul, Korea
| | - Sara Mashoof
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Carol H Yan
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, CA, USA
| | - Adam S DeConde
- Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, CA, USA
| | - Gina Levi
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Shane Crotty
- Center for Vaccine Innovation, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
3
|
Gabernet G, Marquez S, Bjornson R, Peltzer A, Meng H, Aron E, Lee NY, Jensen CG, Ladd D, Polster M, Hanssen F, Heumos S, Yaari G, Kowarik MC, Nahnsen S, Kleinstein SH. nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework. PLoS Comput Biol 2024; 20:e1012265. [PMID: 39058741 PMCID: PMC11305553 DOI: 10.1371/journal.pcbi.1012265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 08/07/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools have been developed to reconstruct B cell and T cell receptor sequences from AIRR-seq data and infer B and T cell clonal relationships. However, currently available tools offer limited parallelization across samples, scalability or portability to high-performance computing infrastructures. To address this need, we developed nf-core/airrflow, an end-to-end bulk and single-cell AIRR-seq processing workflow which integrates the Immcantation Framework following BCR and TCR sequencing data analysis best practices. The Immcantation Framework is a comprehensive toolset, which allows the processing of bulk and single-cell AIRR-seq data from raw read processing to clonal inference. nf-core/airrflow is written in Nextflow and is part of the nf-core project, which collects community contributed and curated Nextflow workflows for a wide variety of analysis tasks. We assessed the performance of nf-core/airrflow on simulated sequencing data with sequencing errors and show example results with real datasets. To demonstrate the applicability of nf-core/airrflow to the high-throughput processing of large AIRR-seq datasets, we validated and extended previously reported findings of convergent antibody responses to SARS-CoV-2 by analyzing 97 COVID-19 infected individuals and 99 healthy controls, including a mixture of bulk and single-cell sequencing datasets. Using this dataset, we extended the convergence findings to 20 additional subjects, highlighting the applicability of nf-core/airrflow to validate findings in small in-house cohorts with reanalysis of large publicly available AIRR datasets.
Collapse
Affiliation(s)
- Gisela Gabernet
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Susanna Marquez
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Robert Bjornson
- Yale Center for Research Computing, New Haven, Connecticut, United States of America
| | | | - Hailong Meng
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Edel Aron
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - Noah Y. Lee
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - Cole G. Jensen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
| | - David Ladd
- oNKo-Innate Pty Ltd, Melbourne, Victoria, Australia
| | - Mark Polster
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, Tübingen, Germany
- M3 Research Center, University Hospital, Tübingen, Germany
| | - Friederike Hanssen
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, Tübingen, Germany
- M3 Research Center, University Hospital, Tübingen, Germany
| | - Simon Heumos
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, Tübingen, Germany
- M3 Research Center, University Hospital, Tübingen, Germany
| | | | - Gur Yaari
- Faculty of Engineering, Bar Ilan University, Ramat Gan, Israel
| | - Markus C. Kowarik
- Department of Neurology and Stroke, Center for Neurology, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Hertie Institute for Clinical Brain Research, Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Sven Nahnsen
- Quantitative Biology Center, Eberhard-Karls University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard-Karls University of Tübingen, Tübingen, Germany
- M3 Research Center, University Hospital, Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard-Karls University of Tübingen, Tübingen, Germany
| | - Steven H. Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| |
Collapse
|
4
|
Jensen CG, Sumner JA, Kleinstein SH, Hoehn KB. Inferring B Cell Phylogenies from Paired H and L Chain BCR Sequences with Dowser. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 212:1579-1588. [PMID: 38557795 PMCID: PMC11073909 DOI: 10.4049/jimmunol.2300851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024]
Abstract
Abs are vital to human immune responses and are composed of genetically variable H and L chains. These structures are initially expressed as BCRs. BCR diversity is shaped through somatic hypermutation and selection during immune responses. This evolutionary process produces B cell clones, cells that descend from a common ancestor but differ by mutations. Phylogenetic trees inferred from BCR sequences can reconstruct the history of mutations within a clone. Until recently, BCR sequencing technologies separated H and L chains, but advancements in single-cell sequencing now pair H and L chains from individual cells. However, it is unclear how these separate genes should be combined to infer B cell phylogenies. In this study, we investigated strategies for using paired H and L chain sequences to build phylogenetic trees. We found that incorporating L chains significantly improved tree accuracy and reproducibility across all methods tested. This improvement was greater than the difference between tree-building methods and persisted even when mixing bulk and single-cell sequencing data. However, we also found that many phylogenetic methods estimated significantly biased branch lengths when some L chains were missing, such as when mixing single-cell and bulk BCR data. This bias was eliminated using maximum likelihood methods with separate branch lengths for H and L chain gene partitions. Thus, we recommend using maximum likelihood methods with separate H and L chain partitions, especially when mixing data types. We implemented these methods in the R package Dowser: https://dowser.readthedocs.io.
Collapse
Affiliation(s)
- Cole G. Jensen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Jacob A. Sumner
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, 06520, USA
| | - Steven H. Kleinstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Kenneth B. Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Current address: Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| |
Collapse
|
5
|
Cornejo A, Franco C, Rodriguez-Nuñez M, García A, Belisario I, Mayora S, Garzaro DJ, Zambrano JL, Jaspe RC, Hidalgo M, Parra-Giménez N, Claro FE, Liprandi F, de Waard JH, Rangel HR, Pujol FH. Humoral Immunity across the SARS-CoV-2 Spike after Sputnik V (Gam-COVID-Vac) Vaccination. Antibodies (Basel) 2024; 13:41. [PMID: 38804309 PMCID: PMC11130906 DOI: 10.3390/antib13020041] [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: 03/20/2024] [Revised: 04/21/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024] Open
Abstract
SARS-CoV-2 vaccines have contributed to attenuating the burden of the COVID-19 pandemic by promoting the development of effective immune responses, thus reducing the spread and severity of the pandemic. A clinical trial with the Sputnik-V vaccine was conducted in Venezuela from December 2020 to July 2021. The aim of this study was to explore the antibody reactivity of vaccinated individuals towards different regions of the spike protein (S). Neutralizing antibody (NAb) activity was assessed using a commercial surrogate assay, detecting NAbs against the receptor-binding domain (RBD), and a plaque reduction neutralization test. NAb levels were correlated with the reactivity of the antibodies to the spike regions over time. The presence of Abs against nucleoprotein was also determined to rule out the effect of exposure to the virus during the clinical trial in the serological response. A high serological reactivity was observed to S and specifically to S1 and the RBD. S2, although recognized with lower intensity by vaccinated individuals, was the subunit exhibiting the highest cross-reactivity in prepandemic sera. This study is in agreement with the high efficacy reported for the Sputnik V vaccine and shows that this vaccine is able to induce an immunity lasting for at least 180 days. The dissection of the Ab reactivity to different regions of S allowed us to identify the relevance of epitopes outside the RBD that are able to induce NAbs. This research may contribute to the understanding of vaccine immunity against SARS-CoV-2, which could contribute to the design of future vaccine strategies.
Collapse
Affiliation(s)
- Alejandro Cornejo
- Laboratorio de Bioquímica Celular, Centro de Microbiología y Biología Celular, Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas 1020A, Venezuela;
| | - Christopher Franco
- Laboratorio de Virología Celular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (C.F.); (J.L.Z.)
| | - Mariajose Rodriguez-Nuñez
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (M.R.-N.); (D.J.G.); (R.C.J.); (H.R.R.)
| | - Alexis García
- Instituto de Inmunología, Universidad Central de Venezuela (UCV), Caracas 1040A, Venezuela; (A.G.); (I.B.); (S.M.)
| | - Inirida Belisario
- Instituto de Inmunología, Universidad Central de Venezuela (UCV), Caracas 1040A, Venezuela; (A.G.); (I.B.); (S.M.)
| | - Soriuska Mayora
- Instituto de Inmunología, Universidad Central de Venezuela (UCV), Caracas 1040A, Venezuela; (A.G.); (I.B.); (S.M.)
| | - Domingo José Garzaro
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (M.R.-N.); (D.J.G.); (R.C.J.); (H.R.R.)
| | - José Luis Zambrano
- Laboratorio de Virología Celular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (C.F.); (J.L.Z.)
| | - Rossana Celeste Jaspe
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (M.R.-N.); (D.J.G.); (R.C.J.); (H.R.R.)
| | - Mariana Hidalgo
- Laboratorio de Inmunoparasitología, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela;
| | - Nereida Parra-Giménez
- Laboratorio de Fisiología de Parásitos, Centro Biofísica y Bioquímica, IVIC, Caracas 1020A, Venezuela;
| | - Franklin Ennodio Claro
- Departamento de Tuberculosis, Servicio Autónomo Instituto de Biomedicina “Dr. Jacinto Convit”, UCV, Caracas 1010A, Venezuela; (F.E.C.); (J.H.d.W.)
| | - Ferdinando Liprandi
- Laboratorio de Biología de Virus, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela;
| | - Jacobus Henri de Waard
- Departamento de Tuberculosis, Servicio Autónomo Instituto de Biomedicina “Dr. Jacinto Convit”, UCV, Caracas 1010A, Venezuela; (F.E.C.); (J.H.d.W.)
- Laboratorios de Investigación, Facultad de Ciencias de Salud, Universidad de Las Américas (UDLA), Quito 170125, Ecuador
| | - Héctor Rafael Rangel
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (M.R.-N.); (D.J.G.); (R.C.J.); (H.R.R.)
| | - Flor Helene Pujol
- Laboratorio de Virología Molecular, Centro de Microbiología y Biología Celular, IVIC, Caracas 1020A, Venezuela; (M.R.-N.); (D.J.G.); (R.C.J.); (H.R.R.)
| |
Collapse
|
6
|
Lee H, Shin K, Lee Y, Lee S, Lee S, Lee E, Kim SW, Shin HY, Kim JH, Chung J, Kwon S. Identification of B cell subsets based on antigen receptor sequences using deep learning. Front Immunol 2024; 15:1342285. [PMID: 38576618 PMCID: PMC10991714 DOI: 10.3389/fimmu.2024.1342285] [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: 11/21/2023] [Accepted: 03/07/2024] [Indexed: 04/06/2024] Open
Abstract
B cell receptors (BCRs) denote antigen specificity, while corresponding cell subsets indicate B cell functionality. Since each B cell uniquely encodes this combination, physical isolation and subsequent processing of individual B cells become indispensable to identify both attributes. However, this approach accompanies high costs and inevitable information loss, hindering high-throughput investigation of B cell populations. Here, we present BCR-SORT, a deep learning model that predicts cell subsets from their corresponding BCR sequences by leveraging B cell activation and maturation signatures encoded within BCR sequences. Subsequently, BCR-SORT is demonstrated to improve reconstruction of BCR phylogenetic trees, and reproduce results consistent with those verified using physical isolation-based methods or prior knowledge. Notably, when applied to BCR sequences from COVID-19 vaccine recipients, it revealed inter-individual heterogeneity of evolutionary trajectories towards Omicron-binding memory B cells. Overall, BCR-SORT offers great potential to improve our understanding of B cell responses.
Collapse
Affiliation(s)
- Hyunho Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Kyoungseob Shin
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Yongju Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Soobin Lee
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Seungyoun Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eunjae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Seung Woo Kim
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ha Young Shin
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Hoon Kim
- Department of Dermatology and Cutaneous Biology Research Institute, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Junho Chung
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Biomedical Science, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
- Inter-University Semiconductor Research Center, Seoul National University, Seoul, Republic of Korea
| |
Collapse
|
7
|
Gabernet G, Marquez S, Bjornson R, Peltzer A, Meng H, Aron E, Lee NY, Jensen C, Ladd D, Hanssen F, Heumos S, Yaari G, Kowarik MC, Nahnsen S, Kleinstein SH. nf-core/airrflow: an adaptive immune receptor repertoire analysis workflow employing the Immcantation framework. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576147. [PMID: 38293151 PMCID: PMC10827190 DOI: 10.1101/2024.01.18.576147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) is a valuable experimental tool to study the immune state in health and following immune challenges such as infectious diseases, (auto)immune diseases, and cancer. Several tools have been developed to reconstruct B cell and T cell receptor sequences from AIRR-seq data and infer B and T cell clonal relationships. However, currently available tools offer limited parallelization across samples, scalability or portability to high-performance computing infrastructures. To address this need, we developed nf-core/airrflow, an end-to-end bulk and single-cell AIRR-seq processing workflow which integrates the Immcantation Framework following BCR and TCR sequencing data analysis best practices. The Immcantation Framework is a comprehensive toolset, which allows the processing of bulk and single-cell AIRR-seq data from raw read processing to clonal inference. nf-core/airrflow is written in Nextflow and is part of the nf-core project, which collects community contributed and curated Nextflow workflows for a wide variety of analysis tasks. We assessed the performance of nf-core/airrflow on simulated sequencing data with sequencing errors and show example results with real datasets. To demonstrate the applicability of nf-core/airrflow to the high-throughput processing of large AIRR-seq datasets, we validated and extended previously reported findings of convergent antibody responses to SARS-CoV-2 by analyzing 97 COVID-19 infected individuals and 99 healthy controls, including a mixture of bulk and single-cell sequencing datasets. Using this dataset, we extended the convergence findings to 20 additional subjects, highlighting the applicability of nf-core/airrflow to validate findings in small in-house cohorts with reanalysis of large publicly available AIRR datasets. nf-core/airrflow is available free of charge, under the MIT license on GitHub (https://github.com/nf-core/airrflow). Detailed documentation and example results are available on the nf-core website at (https://nf-co.re/airrflow).
Collapse
|
8
|
Hoehn KB, Kleinstein SH. B cell phylogenetics in the single cell era. Trends Immunol 2024; 45:62-74. [PMID: 38151443 PMCID: PMC10872299 DOI: 10.1016/j.it.2023.11.004] [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: 10/26/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/29/2023]
Abstract
The widespread availability of single-cell RNA sequencing (scRNA-seq) has led to the development of new methods for understanding immune responses. Single-cell transcriptome data can now be paired with B cell receptor (BCR) sequences. However, RNA from BCRs cannot be analyzed like most other genes because BCRs are genetically diverse within individuals. In humans, BCRs are shaped through recombination followed by mutation and selection for antigen binding. As these processes co-occur with cell division, B cells can be studied using phylogenetic trees representing the mutations within a clone. B cell trees can link experimental timepoints, tissues, or cellular subtypes. Here, we review the current state and potential of how B cell phylogenetics can be combined with single-cell data to understand immune responses.
Collapse
Affiliation(s)
- Kenneth B Hoehn
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.
| | - Steven H Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| |
Collapse
|
9
|
Han AX, de Jong SPJ, Russell CA. Co-evolution of immunity and seasonal influenza viruses. Nat Rev Microbiol 2023; 21:805-817. [PMID: 37532870 DOI: 10.1038/s41579-023-00945-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2023] [Indexed: 08/04/2023]
Abstract
Seasonal influenza viruses cause recurring global epidemics by continually evolving to escape host immunity. The viral constraints and host immune responses that limit and drive the evolution of these viruses are increasingly well understood. However, it remains unclear how most of these advances improve the capacity to reduce the impact of seasonal influenza viruses on human health. In this Review, we synthesize recent progress made in understanding the interplay between the evolution of immunity induced by previous infections or vaccination and the evolution of seasonal influenza viruses driven by the heterogeneous accumulation of antibody-mediated immunity in humans. We discuss the functional constraints that limit the evolution of the viruses, the within-host evolutionary processes that drive the emergence of new virus variants, as well as current and prospective options for influenza virus control, including the viral and immunological barriers that must be overcome to improve the effectiveness of vaccines and antiviral drugs.
Collapse
Affiliation(s)
- Alvin X Han
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Simon P J de Jong
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Colin A Russell
- Department of Medical Microbiology & Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
- Department of Global Health, School of Public Health, Boston University, Boston, MA, USA.
| |
Collapse
|
10
|
Jensen CG, Sumner JA, Kleinstein SH, Hoehn KB. Inferring B cell phylogenies from paired heavy and light chain BCR sequences with Dowser. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560187. [PMID: 37873135 PMCID: PMC10592837 DOI: 10.1101/2023.09.29.560187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Antibodies are vital to human immune responses and are composed of genetically variable heavy and light chains. These structures are initially expressed as B cell receptors (BCRs). BCR diversity is shaped through somatic hypermutation and selection during immune responses. This evolutionary process produces B cell clones, cells that descend from a common ancestor but differ by mutations. Phylogenetic trees inferred from BCR sequences can reconstruct the history of mutations within a clone. Until recently, BCR sequencing technologies separated heavy and light chains, but advancements in single cell sequencing now pair heavy and light chains from individual cells. However, it is unclear how these separate genes should be combined to infer B cell phylogenies. In this study, we investigated strategies for using paired heavy and light chain sequences to build phylogenetic trees. We found incorporating light chains significantly improved tree accuracy and reproducibility across all methods tested. This improvement was greater than the difference between tree building methods and persisted even when mixing bulk and single cell sequencing data. However, we also found that many phylogenetic methods estimated significantly biased branch lengths when some light chains were missing, such as when mixing single cell and bulk BCR data. This bias was eliminated using maximum likelihood methods with separate branch lengths for heavy and light chain gene partitions. Thus, we recommend using maximum likelihood methods with separate heavy and light chain partitions, especially when mixing data types. We implemented these methods in the R package Dowser: https://dowser.readthedocs.io.
Collapse
Affiliation(s)
- Cole G. Jensen
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
| | - Jacob A. Sumner
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, 06520, USA
| | - Steven H. Kleinstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Kenneth B. Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Current address: Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| |
Collapse
|
11
|
Mopuri R, Welbourn S, Charles T, Ralli-Jain P, Rosales D, Burton S, Aftab A, Karunakaran K, Pellegrini K, Kilembe W, Karita E, Gnanakaran S, Upadhyay AA, Bosinger SE, Derdeyn CA. High throughput analysis of B cell dynamics and neutralizing antibody development during immunization with a novel clade C HIV-1 envelope. PLoS Pathog 2023; 19:e1011717. [PMID: 37878666 PMCID: PMC10627474 DOI: 10.1371/journal.ppat.1011717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 11/06/2023] [Accepted: 09/26/2023] [Indexed: 10/27/2023] Open
Abstract
A protective HIV-1 vaccine has been hampered by a limited understanding of how B cells acquire neutralizing activity. Our previous vaccines expressing two different HIV-1 envelopes elicited robust antigen specific serum IgG titers in 20 rhesus macaques; yet serum from only two animals neutralized the autologous virus. Here, we used high throughput immunoglobulin receptor and single cell RNA sequencing to characterize the overall expansion, recall, and maturation of antigen specific B cells longitudinally over 90 weeks. Diversification and expansion of many B cell clonotypes occurred broadly in the absence of serum neutralization. However, in one animal that developed neutralization, two neutralizing B cell clonotypes arose from the same immunoglobulin germline and were tracked longitudinally. Early antibody variants with high identity to germline neutralized the autologous virus while later variants acquired somatic hypermutation and increased neutralization potency. The early engagement of precursors capable of neutralization with little to no SHM followed by prolonged affinity maturation allowed the two neutralizing lineages to successfully persist despite many other antigen specific B cells. The findings provide new insight into B cells responding to HIV-1 envelope during heterologous prime and boost immunization in rhesus macaques and the development of selected autologous neutralizing antibody lineages.
Collapse
Affiliation(s)
- Rohini Mopuri
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Sarah Welbourn
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Tysheena Charles
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Pooja Ralli-Jain
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - David Rosales
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Samantha Burton
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Areeb Aftab
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
| | - Kirti Karunakaran
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | - Kathryn Pellegrini
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
| | | | | | - Sandrasegaram Gnanakaran
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Amit A. Upadhyay
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Steven E. Bosinger
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Cynthia A. Derdeyn
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
- Infectious Diseases and Translational Medicine Unit, Washington National Primate Research Center, University of Washington, Seattle, Washington, United States of America
| |
Collapse
|
12
|
Sokal A, Barba-Spaeth G, Hunault L, Fernández I, Broketa M, Meola A, Fourati S, Azzaoui I, Vandenberghe A, Lagouge-Roussey P, Broutin M, Roeser A, Bouvier-Alias M, Crickx E, Languille L, Fournier M, Michel M, Godeau B, Gallien S, Melica G, Nguyen Y, Canoui-Poitrine F, Pirenne F, Megret J, Pawlotsky JM, Fillatreau S, Reynaud CA, Weill JC, Rey FA, Bruhns P, Mahévas M, Chappert P. SARS-CoV-2 Omicron BA.1 breakthrough infection drives late remodeling of the memory B cell repertoire in vaccinated individuals. Immunity 2023; 56:2137-2151.e7. [PMID: 37543032 DOI: 10.1016/j.immuni.2023.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/12/2023] [Accepted: 07/06/2023] [Indexed: 08/07/2023]
Abstract
How infection by a viral variant showing antigenic drift impacts a preformed mature human memory B cell (MBC) repertoire remains an open question. Here, we studied the MBC response up to 6 months after SARS-CoV-2 Omicron BA.1 breakthrough infection in individuals previously vaccinated with three doses of the COVID-19 mRNA vaccine. Longitudinal analysis, using single-cell multi-omics and functional analysis of monoclonal antibodies from RBD-specific MBCs, revealed that a BA.1 breakthrough infection mostly recruited pre-existing cross-reactive MBCs with limited de novo response against BA.1-restricted epitopes. Reorganization of clonal hierarchy and new rounds of germinal center reactions, however, combined to maintain diversity and induce progressive maturation of the MBC repertoire against common Hu-1 and BA.1, but not BA.5-restricted, SARS-CoV-2 Spike RBD epitopes. Such remodeling was further associated with a marked improvement in overall neutralizing breadth and potency. These findings have fundamental implications for the design of future vaccination booster strategies.
Collapse
Affiliation(s)
- Aurélien Sokal
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine interne, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris (AP-HP), Université de Paris Cité, Clichy, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Giovanna Barba-Spaeth
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Lise Hunault
- Institut Pasteur, Université de Paris Cité, INSERM UMR1222, Unit of Antibodies in Therapy and Pathology, Paris, France; Sorbonne University, ED394, Paris, France; Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), 75013 Paris, France
| | - Ignacio Fernández
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Matteo Broketa
- Institut Pasteur, Université de Paris Cité, INSERM UMR1222, Unit of Antibodies in Therapy and Pathology, Paris, France; Sorbonne University, ED394, Paris, France
| | - Annalisa Meola
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Slim Fourati
- Département de Virologie, Bactériologie, Hygiène et Mycologie-Parasitologie, Centre Hospitalier Universitaire Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France; INSERM U955, équipe 18. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Imane Azzaoui
- Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Alexis Vandenberghe
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Pauline Lagouge-Roussey
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Manon Broutin
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Anais Roeser
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Magali Bouvier-Alias
- Département de Virologie, Bactériologie, Hygiène et Mycologie-Parasitologie, Centre Hospitalier Universitaire Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France; INSERM U955, équipe 18. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Etienne Crickx
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Laetitia Languille
- Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Morgane Fournier
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Marc Michel
- Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Bertrand Godeau
- Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Sébastien Gallien
- Service de Maladies Infectieuses, Centre Hospitalier Universitaire Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Giovanna Melica
- Service de Maladies Infectieuses, Centre Hospitalier Universitaire Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Yann Nguyen
- Service de Médecine Interne, Centre Hospitalier Universitaire Cochin, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Florence Canoui-Poitrine
- Département de Santé Publique, Unité de Recherche Clinique (URC), CEpiA (Clinical Epidemiology and Ageing), EA 7376- Institut Mondor de Recherche Biomédicale (IMRB), Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France
| | - France Pirenne
- INSERM U955, équipe 18. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France; Etablissement Français du Sang (EFS) Ile de France, Créteil, France
| | - Jérôme Megret
- Plateforme de Cytométrie en Flux, Structure Fédérative de Recherche Necker, INSERM US24-CNRS UMS3633, Paris, France
| | - Jean-Michel Pawlotsky
- Département de Virologie, Bactériologie, Hygiène et Mycologie-Parasitologie, Centre Hospitalier Universitaire Henri Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Créteil, France; INSERM U955, équipe 18. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France
| | - Simon Fillatreau
- Institut Necker Enfants Malades (INEM), INSERM U1151/CNRS UMR 8253, Université de Paris, Paris, France
| | - Claude-Agnès Reynaud
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France
| | - Jean-Claude Weill
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France
| | - Félix A Rey
- Institut Pasteur, Université de Paris Cité, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Pierre Bruhns
- Institut Pasteur, Université de Paris Cité, INSERM UMR1222, Unit of Antibodies in Therapy and Pathology, Paris, France
| | - Matthieu Mahévas
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; Service de Médecine Interne, Centre Hospitalier Universitaire Henri-Mondor, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris-Est Créteil (UPEC), Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France.
| | - Pascal Chappert
- Institut Necker Enfants Malades, INSERM U1151/CNRS UMR 8253, Action thématique incitative sur programme-Avenir Team, Auto-Immune and Immune B cells, Université Paris Cité, Université Paris Est-Créteil, Créteil, France; INSERM U955, équipe 2. Institut Mondor de Recherche Biomédicale (IMRB), Université Paris-Est Créteil (UPEC), Créteil, France.
| |
Collapse
|
13
|
Lopes de Assis F, Hoehn KB, Zhang X, Kardava L, Smith CD, El Merhebi O, Buckner CM, Trihemasava K, Wang W, Seamon CA, Chen V, Schaughency P, Cheung F, Martins AJ, Chiang CI, Li Y, Tsang JS, Chun TW, Kleinstein SH, Moir S. Tracking B cell responses to the SARS-CoV-2 mRNA-1273 vaccine. Cell Rep 2023; 42:112780. [PMID: 37440409 PMCID: PMC10529190 DOI: 10.1016/j.celrep.2023.112780] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/15/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Protective immunity following vaccination is sustained by long-lived antibody-secreting cells and resting memory B cells (MBCs). Responses to two-dose SARS-CoV-2 mRNA-1273 vaccination are evaluated longitudinally by multimodal single-cell analysis in three infection-naïve individuals. Integrated surface protein, transcriptomics, and B cell receptor (BCR) repertoire analysis of sorted plasmablasts and spike+ (S-2P+) and S-2P- B cells reveal clonal expansion and accumulating mutations among S-2P+ cells. These cells are enriched in a cluster of immunoglobulin G-expressing MBCs and evolve along a bifurcated trajectory rooted in CXCR3+ MBCs. One branch leads to CD11c+ atypical MBCs while the other develops from CD71+ activated precursors to resting MBCs, the dominant population at month 6. Among 12 evolving S-2P+ clones, several are populated with plasmablasts at early timepoints as well as CD71+ activated and resting MBCs at later timepoints, and display intra- and/or inter-cohort BCR convergence. These relationships suggest a coordinated and predictable evolution of SARS-CoV-2 vaccine-generated MBCs.
Collapse
Affiliation(s)
- Felipe Lopes de Assis
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kenneth B Hoehn
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Xiaozhen Zhang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lela Kardava
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Connor D Smith
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Omar El Merhebi
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Clarisa M Buckner
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Krittin Trihemasava
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Wang
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Catherine A Seamon
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vicky Chen
- Integrated Data Sciences Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Schaughency
- Integrated Data Sciences Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Foo Cheung
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Andrew J Martins
- Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Chi-I Chiang
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA
| | - Yuxing Li
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA; Department of Microbiology and Immunology and Center for Biomolecular Therapeutics, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - John S Tsang
- NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD 20892, USA; Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD 20892, USA
| | - Tae-Wook Chun
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steven H Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA; Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA; Department of Immunobiology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Susan Moir
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| |
Collapse
|
14
|
Faliti CE, Anam FA, Cheedarla N, Woodruff MC, Usman SY, Runnstrom MC, Van TT, Kyu S, Ahmed H, Morrison-Porter A, Quehl H, Haddad NS, Chen W, Cheedarla S, Neish AS, Roback JD, Antia R, Khosroshahi A, Lee FEH, Sanz I. Poor immunogenicity upon SARS-CoV-2 mRNA vaccinations in autoimmune SLE patients is associated with pronounced EF-mediated responses and anti-BAFF/Belimumab treatment. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.08.23291159. [PMID: 37398319 PMCID: PMC10312827 DOI: 10.1101/2023.06.08.23291159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Novel mRNA vaccines have resulted in a reduced number of SARS-CoV-2 infections and hospitalizations. Yet, there is a paucity of studies regarding their effectiveness on immunocompromised autoimmune subjects. In this study, we enrolled subjects naïve to SARS-CoV-2 infections from two cohorts of healthy donors (HD, n=56) and systemic lupus erythematosus (SLE, n=69). Serological assessments of their circulating antibodies revealed a significant reduction of potency and breadth of neutralization in the SLE group, only partially rescued by a 3rd booster dose. Immunological memory responses in the SLE cohort were characterized by a reduced magnitude of spike-reactive B and T cell responses that were strongly associated with poor seroconversion. Vaccinated SLE subjects were defined by a distinct expansion and persistence of a DN2 spike-reactive memory B cell pool and a contraction of spike-specific memory cTfh cells, contrasting with the sustained germinal center (GC)-driven activity mediated by mRNA vaccination in the healthy population. Among the SLE-associated factors that dampened the vaccine responses, treatment with the monoclonal antibody anti-BAFF/Belimumab (a lupus FDA-approved B cell targeting agent) profoundly affected the vaccine responsiveness by restricting the de novo B cell responses and promoting stronger extra-follicular (EF)-mediated responses that were associated with poor immunogenicity and impaired immunological memory. In summary, this study interrogates antigen-specific responses and characterized the immune cell landscape associated with mRNA vaccination in SLE. The identification of factors associated with reduced vaccine efficacy illustrates the impact of SLE B cell biology on mRNA vaccine responses and provides guidance for the management of boosters and recall vaccinations in SLE patients according to their disease endotype and modality of treatment.
Collapse
Affiliation(s)
- Caterina E. Faliti
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Fabliha A. Anam
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Narayanaiah Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Matthew C. Woodruff
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Sabeena Y. Usman
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Martin C. Runnstrom
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Trinh T.P. Van
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - Shuya Kyu
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Andrea Morrison-Porter
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Hannah Quehl
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Natalie S. Haddad
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, USA
- MicroB-plex, Atlanta, GA, USA
| | | | - Suneethamma Cheedarla
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Andrew S. Neish
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - John D. Roback
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Arezou Khosroshahi
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| | - F. Eun-Hyung Lee
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Emory University, Atlanta, GA, USA
| | - Ignacio Sanz
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA
- Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
| |
Collapse
|
15
|
Mazzolini A, Mora T, Walczak AM. Inspecting the interaction between human immunodeficiency virus and the immune system through genetic turnover. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220056. [PMID: 37004725 PMCID: PMC10067267 DOI: 10.1098/rstb.2022.0056] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/15/2022] [Indexed: 04/04/2023] Open
Abstract
Chronic infections of the human immunodeficiency virus (HIV) create a very complex coevolutionary process, where the virus tries to escape the continuously adapting host immune system. Quantitative details of this process are largely unknown and could help in disease treatment and vaccine development. Here we study a longitudinal dataset of ten HIV-infected people, where both the B-cell receptors and the virus are deeply sequenced. We focus on simple measures of turnover, which quantify how much the composition of the viral strains and the immune repertoire change between time points. At the single-patient level, the viral-host turnover rates do not show any statistically significant correlation, however, they correlate if one increases the amount of statistics by aggregating the information across patients. We identify an anti-correlation: large changes in the viral pool composition come with small changes in the B-cell receptor repertoire. This result seems to contradict the naïve expectation that when the virus mutates quickly, the immune repertoire needs to change to keep up. However, a simple model of antagonistically evolving populations can explain this signal. If it is sampled at intervals comparable with the sweep time, one population has had time to sweep while the second cannot start a counter-sweep, leading to the observed anti-correlation. This article is part of the theme issue 'Interdisciplinary approaches to predicting evolutionary biology'.
Collapse
Affiliation(s)
- Andrea Mazzolini
- Laboratoire de physique de l’École normale supérieure, PSL Université, CNRS, Sorbonne Université and Université Paris Cité, 75005 Paris, France
| | - Thierry Mora
- Laboratoire de physique de l’École normale supérieure, PSL Université, CNRS, Sorbonne Université and Université Paris Cité, 75005 Paris, France
| | - Aleksandra M. Walczak
- Laboratoire de physique de l’École normale supérieure, PSL Université, CNRS, Sorbonne Université and Université Paris Cité, 75005 Paris, France
| |
Collapse
|
16
|
Chernyshev M, Sakharkar M, Connor RI, Dugan HL, Sheward DJ, Rappazzo CG, Stålmarck A, Forsell MNE, Wright PF, Corcoran M, Murrell B, Walker LM, Karlsson Hedestam GB. Vaccination of SARS-CoV-2-infected individuals expands a broad range of clonally diverse affinity-matured B cell lineages. Nat Commun 2023; 14:2249. [PMID: 37076511 PMCID: PMC10115384 DOI: 10.1038/s41467-023-37972-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 04/03/2023] [Indexed: 04/21/2023] Open
Abstract
Vaccination of SARS-CoV-2 convalescent individuals generates broad and potent antibody responses. Here, we isolate 459 spike-specific monoclonal antibodies (mAbs) from two individuals who were infected with the index variant of SARS-CoV-2 and later boosted with mRNA-1273. We characterize mAb genetic features by sequence assignments to the donors' personal immunoglobulin genotypes and assess antibody neutralizing activities against index SARS-CoV-2, Beta, Delta, and Omicron variants. The mAbs used a broad range of immunoglobulin heavy chain (IGH) V genes in the response to all sub-determinants of the spike examined, with similar characteristics observed in both donors. IGH repertoire sequencing and B cell lineage tracing at longitudinal time points reveals extensive evolution of SARS-CoV-2 spike-binding antibodies from acute infection until vaccination five months later. These results demonstrate that highly polyclonal repertoires of affinity-matured memory B cells are efficiently recalled by vaccination, providing a basis for the potent antibody responses observed in convalescent persons following vaccination.
Collapse
Affiliation(s)
- Mark Chernyshev
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Ruth I Connor
- Department of Pediatrics, Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | | | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Aron Stålmarck
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Peter F Wright
- Department of Pediatrics, Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Laura M Walker
- Adimab LLC, Lebanon, NH, 03766, USA.
- Invivyd Inc, Waltham, MA, 02451, USA.
| | | |
Collapse
|
17
|
Cohn H, Bloom N, Cai G, Clark J, Tarke A, Bermúdez-González MC, Altman D, Lugo LA, Lobo FP, Marquez S, Chen JQ, Ren W, Qin L, Crotty S, Krammer F, Grifoni A, Sette A, Simon V, Coelho CH. Mpox vaccine and infection-driven human immune signatures. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.07.23286701. [PMID: 36945651 PMCID: PMC10029032 DOI: 10.1101/2023.03.07.23286701] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Background Mpox (formerly known as monkeypox) outbreaks outside endemic areas peaked in July 2022, infecting > 85,000 people and raising concerns about our preparedness against this emerging viral pathogen. Licensed and approved for mpox, the JYNNEOS vaccine has fewer side effects than previous smallpox vaccines and demonstrated efficacy against mpox infection in humans. Comparing JYNNEOS vaccine- and mpox-induced immunity is imperative to evaluate JYNNEOS' immunogenicity and inform vaccine administration and design. Methods We examined the polyclonal serum (ELISA) and single B cell (heavy chain gene and transcriptome data) antibody repertoires and T cells (AIM and ICS assays) induced by the JYNNEOS vaccine as well as mpox infection. Findings Gene-level plasmablast and antibody responses were negligible and JYNNEOS vaccinee sera displayed minimal binding to recombinant mpox proteins and native proteins from the 2022 outbreak strain. In contrast, recent mpox infection (within 20-102 days) induced robust serum antibody responses to A29L, A35R, A33R, B18R, and A30L, and to native mpox proteins, compared to vaccinees. JYNNEOS vaccine recipients presented comparable CD4 and CD8 T cell responses against orthopox peptides to those observed after mpox infection. Interpretation JYNNEOS immunization does not elicit a robust B cell response, and its immunogenicity may be mediated by T cells. Funding Research reported in this publication was supported, in part, by the National Cancer Institute of the National Institutes of Health under Award Number U54CA267776, U19AI168631(VS), as well as institutional funds from the Icahn School of Medicine.
Collapse
|
18
|
King SM, Bryan SP, Hilchey SP, Wang J, Zand MS. First Impressions Matter: Immune Imprinting and Antibody Cross-Reactivity in Influenza and SARS-CoV-2. Pathogens 2023; 12:169. [PMID: 36839441 PMCID: PMC9967769 DOI: 10.3390/pathogens12020169] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/24/2023] Open
Abstract
Many rigorous studies have shown that early childhood infections leave a lasting imprint on the immune system. The understanding of this phenomenon has expanded significantly since 1960, when Dr. Thomas Francis Jr first coined the term "original antigenic sin", to account for all previous pathogen exposures, rather than only the first. Now more commonly referred to as "immune imprinting", this effect most often focuses on how memory B-cell responses are shaped by prior antigen exposure, and the resultant antibodies produced after subsequent exposure to antigenically similar pathogens. Although imprinting was originally observed within the context of influenza viral infection, it has since been applied to the pandemic coronavirus SARS-CoV-2. To fully comprehend how imprinting affects the evolution of antibody responses, it is necessary to compare responses elicited by pathogenic strains that are both antigenically similar and dissimilar to strains encountered previously. To accomplish this, we must be able to measure the antigenic distance between strains, which can be easily accomplished using data from multidimensional immunological assays. The knowledge of imprinting, combined with antigenic distance measures, may allow for improvements in vaccine design and development for both influenza and SARS-CoV-2 viruses.
Collapse
Affiliation(s)
- Samantha M. King
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Shane P. Bryan
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Shannon P. Hilchey
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Jiong Wang
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Martin S. Zand
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY 14642, USA
- Clinical and Translational Science Institute, University of Rochester Medical Center, Rochester, NY 14618, USA
| |
Collapse
|
19
|
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.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Georgii A Bazykin
- Institute of Translational Medicine, Pirogov Russian National Research Medical University
| | | |
Collapse
|
20
|
Effects of Prior Infection with SARS-CoV-2 on B Cell Receptor Repertoire Response during Vaccination. Vaccines (Basel) 2022; 10:vaccines10091477. [PMID: 36146555 PMCID: PMC9506540 DOI: 10.3390/vaccines10091477] [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: 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.
Collapse
|
21
|
Lee JH, Sutton HJ, Cottrell CA, Phung I, Ozorowski G, Sewall LM, Nedellec R, Nakao C, Silva M, Richey ST, Torres JL, Lee WH, Georgeson E, Kubitz M, Hodges S, Mullen TM, Adachi Y, Cirelli KM, Kaur A, Allers C, Fahlberg M, Grasperge BF, Dufour JP, Schiro F, Aye PP, Kalyuzhniy O, Liguori A, Carnathan DG, Silvestri G, Shen X, Montefiori DC, Veazey RS, Ward AB, Hangartner L, Burton DR, Irvine DJ, Schief WR, Crotty S. Long-primed germinal centres with enduring affinity maturation and clonal migration. Nature 2022; 609:998-1004. [PMID: 36131022 PMCID: PMC9491273 DOI: 10.1038/s41586-022-05216-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 08/09/2022] [Indexed: 02/06/2023]
Abstract
Germinal centres are the engines of antibody evolution. Here, using human immunodeficiency virus (HIV) Env protein immunogen priming in rhesus monkeys followed by a long period without further immunization, we demonstrate germinal centre B (BGC) cells that last for at least 6 months. A 186-fold increase in BGC cells was present by week 10 compared with conventional immunization. Single-cell transcriptional profiling showed that both light- and dark-zone germinal centre states were sustained. Antibody somatic hypermutation of BGC cells continued to accumulate throughout the 29-week priming period, with evidence of selective pressure. Env-binding BGC cells were still 49-fold above baseline at 29 weeks, which suggests that they could remain active for even longer periods of time. High titres of HIV-neutralizing antibodies were generated after a single booster immunization. Fully glycosylated HIV trimer protein is a complex antigen, posing considerable immunodominance challenges for B cells1,2. Memory B cells generated under these long priming conditions had higher levels of antibody somatic hypermutation, and both memory B cells and antibodies were more likely to recognize non-immunodominant epitopes. Numerous BGC cell lineage phylogenies spanning more than the 6-month germinal centre period were identified, demonstrating continuous germinal centre activity and selection for at least 191 days with no further antigen exposure. A long-prime, slow-delivery (12 days) immunization approach holds promise for difficult vaccine targets and suggests that patience can have great value for tuning of germinal centres to maximize antibody responses.
Collapse
Affiliation(s)
- Jeong Hyun Lee
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Henry J Sutton
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
| | - Christopher A Cottrell
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ivy Phung
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Gabriel Ozorowski
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Leigh M Sewall
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rebecca Nedellec
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Catherine Nakao
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Murillo Silva
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sara T Richey
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Erik Georgeson
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Michael Kubitz
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sam Hodges
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Tina-Marie Mullen
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Yumiko Adachi
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kimberly M Cirelli
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
| | - Amitinder Kaur
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Carolina Allers
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Marissa Fahlberg
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Brooke F Grasperge
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Jason P Dufour
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Faith Schiro
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Pyone P Aye
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Oleksandr Kalyuzhniy
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Alessia Liguori
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Diane G Carnathan
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Emory National Primate Research Center and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Guido Silvestri
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Emory National Primate Research Center and Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Xiaoying Shen
- Department of Surgery, Laboratory for AIDS Vaccine Research & Development, Duke University Medical Center, Duke University, Durham, NC, USA
| | - David C Montefiori
- Department of Surgery, Laboratory for AIDS Vaccine Research & Development, Duke University Medical Center, Duke University, Durham, NC, USA
| | - Ronald S Veazey
- Tulane National Primate Research Center, Tulane School of Medicine, Covington, LA, USA
| | - Andrew B Ward
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Lars Hangartner
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Dennis R Burton
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Darrell J Irvine
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - William R Schief
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Consortium for HIV/AIDS Vaccine Development, The Scripps Research Institute, La Jolla, CA, USA.
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
22
|
Weber CR, Rubio T, Wang L, Zhang W, Robert PA, Akbar R, Snapkov I, Wu J, Kuijjer ML, Tarazona S, Conesa A, Sandve GK, Liu X, Reddy ST, Greiff V. Reference-based comparison of adaptive immune receptor repertoires. CELL REPORTS METHODS 2022; 2:100269. [PMID: 36046619 PMCID: PMC9421535 DOI: 10.1016/j.crmeth.2022.100269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 04/01/2022] [Accepted: 07/19/2022] [Indexed: 11/26/2022]
Abstract
B and T cell receptor (immune) repertoires can represent an individual's immune history. While current repertoire analysis methods aim to discriminate between health and disease states, they are typically based on only a limited number of parameters. Here, we introduce immuneREF: a quantitative multidimensional measure of adaptive immune repertoire (and transcriptome) similarity that allows interpretation of immune repertoire variation by relying on both repertoire features and cross-referencing of simulated and experimental datasets. To quantify immune repertoire similarity landscapes across health and disease, we applied immuneREF to >2,400 datasets from individuals with varying immune states (healthy, [autoimmune] disease, and infection). We discovered, in contrast to the current paradigm, that blood-derived immune repertoires of healthy and diseased individuals are highly similar for certain immune states, suggesting that repertoire changes to immune perturbations are less pronounced than previously thought. In conclusion, immuneREF enables the population-wide study of adaptive immune response similarity across immune states.
Collapse
Affiliation(s)
- Cédric R. Weber
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Teresa Rubio
- Laboratory of Neurobiology, Centro Investigación Príncipe Felipe, Valencia, Spain
| | - Longlong Wang
- BGI-Shenzhen, Shenzhen, China
- BGI-Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Wei Zhang
- BGI-Shenzhen, Shenzhen, China
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Philippe A. Robert
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Rahmad Akbar
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Igor Snapkov
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
| | | | - Marieke L. Kuijjer
- Centre for Molecular Medicine Norway, University of Oslo, Oslo, Norway
- Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
- Leiden Center for Computational Oncology, Leiden University Medical Center, Leiden, the Netherlands
| | - Sonia Tarazona
- Departamento de Estadística e Investigación Operativa Aplicadas y Calidad, Universitat Politècnica de València, Valencia, Spain
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council, Valencia, Spain
| | - Geir K. Sandve
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Xiao Liu
- BGI-Shenzhen, Shenzhen, China
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Sai T. Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Victor Greiff
- Department of Immunology and Oslo University Hospital, University of Oslo, Oslo, Norway
| |
Collapse
|
23
|
Abstract
The SARS-CoV-2 pandemic has demonstrated the importance of studying antiviral immunity within sites of infection to gain insights into mechanisms for immune protection and disease pathology. As SARS-CoV-2 is tropic to the respiratory tract, many studies of airway washes, lymph node aspirates, and postmortem lung tissue have revealed site-specific immune dynamics that are associated with the protection or immunopathology but are not readily observed in circulation. This review summarizes the growing body of work identifying immune processes in tissues and their interplay with immune responses in circulation during acute SARS-CoV-2 infection, severe disease, and memory persistence. Establishment of tissue resident immunity also may have implications for vaccination and the durability of immune memory and protection.
Collapse
Affiliation(s)
- Ksenia Rybkina
- Department of Microbiology and ImmunologyColumbia University Vagelos College of Physicians and SurgeonsNew YorkNew YorkUSA
| | - Julia Davis‐Porada
- Department of Microbiology and ImmunologyColumbia University Vagelos College of Physicians and SurgeonsNew YorkNew YorkUSA
| | - Donna L. Farber
- Department of Microbiology and ImmunologyColumbia University Vagelos College of Physicians and SurgeonsNew YorkNew YorkUSA
- Department of SurgeryColumbia University Irving Medical CenterNew YorkNew YorkUSA
| |
Collapse
|
24
|
Xu Q, Milanez-Almeida P, Martins AJ, Radtke AJ, Hoehn KB, Chen J, Liu C, Tang J, Grubbs G, Stein S, Ramelli S, Kabat J, Behzadpour H, Karkanitsa M, Spathies J, Kalish H, Kardava L, Kirby M, Cheung F, Preite S, Duncker PC, Romero N, Preciado D, Gitman L, Koroleva G, Smith G, Shaffer A, McBain IT, Pittaluga S, Germain RN, Apps R, Sadtler K, Moir S, Chertow DS, Kleinstein SH, Khurana S, Tsang JS, Mudd P, Schwartzberg PL, Manthiram K. Robust, persistent adaptive immune responses to SARS-CoV-2 in the oropharyngeal lymphoid tissue of children. RESEARCH SQUARE 2022:rs.3.rs-1276578. [PMID: 35350206 PMCID: PMC8963700 DOI: 10.21203/rs.3.rs-1276578/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
SARS-CoV-2 infection triggers adaptive immune responses from both T and B cells. However, most studies focus on peripheral blood, which may not fully reflect immune responses in lymphoid tissues at the site of infection. To evaluate both local and systemic adaptive immune responses to SARS-CoV-2, we collected peripheral blood, tonsils, and adenoids from 110 children undergoing tonsillectomy/adenoidectomy during the COVID-19 pandemic and found 24 with evidence of prior SARS-CoV-2 infection, including detectable neutralizing antibodies against multiple viral variants. We identified SARS-CoV-2-specific germinal center (GC) and memory B cells; single cell BCR sequencing showed that these virus-specific B cells were class-switched and somatically hypermutated, with overlapping clones in the adenoids and tonsils. Oropharyngeal tissues from COVID-19-convalescent children showed persistent expansion of GC and anti-viral lymphocyte populations associated with an IFN-γ-type response, with particularly prominent changes in the adenoids, as well as evidence of persistent viral RNA in both tonsil and adenoid tissues of many participants. Our results show robust, tissue-specific adaptive immune responses to SARS-CoV-2 in the upper respiratory tract of children weeks to months after acute infection, providing evidence of persistent localized immunity to this respiratory virus.
Collapse
Affiliation(s)
- Qin Xu
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD
| | | | | | - Andrea J. Radtke
- Center for Advanced Tissue Imaging, LISB, NIAID, NIH Bethesda, MD
| | | | - Jinguo Chen
- Center for Human Immunology, NIAID, NIH, Bethesda, MD
| | - Can Liu
- Multiscale Systems Biology Section, LISB, NIAID, NIH, Bethesda, MD
| | - Juanjie Tang
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), Silver Spring, MD
| | - Gabrielle Grubbs
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), Silver Spring, MD
| | - Sydney Stein
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center (CC), NIH, Bethesda, MD
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD
| | - Sabrina Ramelli
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center (CC), NIH, Bethesda, MD
| | - Juraj Kabat
- Center for Advanced Tissue Imaging, LISB, NIAID, NIH Bethesda, MD
| | - Hengameh Behzadpour
- Division of Pediatric Otolaryngology, Children’s National Hospital, Washington, DC
| | - Maria Karkanitsa
- Laboratory of Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering (NIBIB), NIH, Bethesda, MD
| | - Jacquelyn Spathies
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, NIBIB, NIH, Bethesda, MD
| | - Heather Kalish
- Trans-NIH Shared Resource on Biomedical Engineering and Physical Science, NIBIB, NIH, Bethesda, MD
| | - Lela Kardava
- B-cell Immunology Section, Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD
| | - Martha Kirby
- National Human Genome Research Institute (NHGRI), NIH, Bethesda, MD
| | - Foo Cheung
- Center for Human Immunology, NIAID, NIH, Bethesda, MD
| | - Silvia Preite
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD
| | | | - Nahir Romero
- Division of Otolaryngology, Department of Surgery, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Diego Preciado
- Division of Pediatric Otolaryngology, Children’s National Hospital, Washington, DC
- Division of Otolaryngology, Department of Surgery, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Lyuba Gitman
- Division of Pediatric Otolaryngology, Children’s National Hospital, Washington, DC
- Division of Otolaryngology, Department of Surgery, George Washington University School of Medicine and Health Sciences, Washington, DC
| | | | - Grace Smith
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, MD
| | - Arthur Shaffer
- Lymphoid Malignancies Branch, Center for Cancer Research, NCI, NIH, Bethesda, MD
| | - Ian T. McBain
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD
| | - Stefania Pittaluga
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute (NCI), NIH, Bethesda, MD
| | - Ronald N. Germain
- Center for Advanced Tissue Imaging, LISB, NIAID, NIH Bethesda, MD
- Lymphocyte Biology Section, LISB, NIAID, NIH, Bethesda, MD
| | - Richard Apps
- Center for Human Immunology, NIAID, NIH, Bethesda, MD
| | - Kaitlyn Sadtler
- Laboratory of Immuno-Engineering, National Institute of Biomedical Imaging and Bioengineering (NIBIB), NIH, Bethesda, MD
| | - Susan Moir
- B-cell Immunology Section, Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD
| | - Daniel S. Chertow
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center (CC), NIH, Bethesda, MD
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD
| | - Steven H. Kleinstein
- Department of Pathology, Yale School of Medicine, New Haven, CT
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT
- Department of Immunobiology, Yale School of Medicine, New Haven, CT
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research (CBER), Food and Drug Administration (FDA), Silver Spring, MD
| | - John S. Tsang
- Center for Human Immunology, NIAID, NIH, Bethesda, MD
- Multiscale Systems Biology Section, LISB, NIAID, NIH, Bethesda, MD
| | - Pamela Mudd
- Division of Pediatric Otolaryngology, Children’s National Hospital, Washington, DC
- Division of Otolaryngology, Department of Surgery, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Pamela L. Schwartzberg
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD
- National Human Genome Research Institute (NHGRI), NIH, Bethesda, MD
| | - Kalpana Manthiram
- Cell Signaling and Immunity Section, Laboratory of Immune System Biology (LISB), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD
| |
Collapse
|
25
|
Abstract
The germinal centre (GC) response is critical for the generation of affinity-matured plasma cells and memory B cells capable of mediating long-term protective immunity. Understanding whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or vaccination elicits a GC response has profound implications for the capacity of responding B cells to contribute to protection against infection. However, direct assessment of the GC response in humans remains a major challenge. Here we summarize emerging evidence for the importance of the GC response in the establishment of durable and broad immunity against SARS-CoV-2 and discuss new approaches to modulate the GC response to better protect against newly emerging SARS-CoV-2 variants. We also discuss new findings showing that the GC B cell response persists in the draining lymph nodes for at least 6 months in some individuals following vaccination with SARS-CoV-2 mRNA-based vaccines.
Collapse
Affiliation(s)
- Brian J Laidlaw
- Division of Allergy and Immunology, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
| | - Ali H Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
- The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA.
- Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA.
| |
Collapse
|