1
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Roth-Walter F, Adcock IM, Benito-Villalvilla C, Bianchini R, Bjermer L, Caramori G, Cari L, Chung KF, Diamant Z, Eguiluz-Gracia I, Knol EF, Jesenak M, Levi-Schaffer F, Nocentini G, O'Mahony L, Palomares O, Redegeld F, Sokolowska M, Van Esch BCAM, Stellato C. Metabolic pathways in immune senescence and inflammaging: Novel therapeutic strategy for chronic inflammatory lung diseases. An EAACI position paper from the Task Force for Immunopharmacology. Allergy 2024; 79:1089-1122. [PMID: 38108546 DOI: 10.1111/all.15977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023]
Abstract
The accumulation of senescent cells drives inflammaging and increases morbidity of chronic inflammatory lung diseases. Immune responses are built upon dynamic changes in cell metabolism that supply energy and substrates for cell proliferation, differentiation, and activation. Metabolic changes imposed by environmental stress and inflammation on immune cells and tissue microenvironment are thus chiefly involved in the pathophysiology of allergic and other immune-driven diseases. Altered cell metabolism is also a hallmark of cell senescence, a condition characterized by loss of proliferative activity in cells that remain metabolically active. Accelerated senescence can be triggered by acute or chronic stress and inflammatory responses. In contrast, replicative senescence occurs as part of the physiological aging process and has protective roles in cancer surveillance and wound healing. Importantly, cell senescence can also change or hamper response to diverse therapeutic treatments. Understanding the metabolic pathways of senescence in immune and structural cells is therefore critical to detect, prevent, or revert detrimental aspects of senescence-related immunopathology, by developing specific diagnostics and targeted therapies. In this paper, we review the main changes and metabolic alterations occurring in senescent immune cells (macrophages, B cells, T cells). Subsequently, we present the metabolic footprints described in translational studies in patients with chronic asthma and chronic obstructive pulmonary disease (COPD), and review the ongoing preclinical studies and clinical trials of therapeutic approaches aiming at targeting metabolic pathways to antagonize pathological senescence. Because this is a recently emerging field in allergy and clinical immunology, a better understanding of the metabolic profile of the complex landscape of cell senescence is needed. The progress achieved so far is already providing opportunities for new therapies, as well as for strategies aimed at disease prevention and supporting healthy aging.
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Affiliation(s)
- F Roth-Walter
- Comparative Medicine, The Interuniversity Messerli Research Institute of the University of Veterinary Medicine Vienna, Medical University Vienna and University Vienna, Vienna, Austria
- Institute of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - I M Adcock
- Molecular Cell Biology Group, National Heart & Lung Institute, Imperial College London, London, UK
| | - C Benito-Villalvilla
- Department of Biochemistry and Molecular Biology, School of Chemistry, Complutense University of Madrid, Madrid, Spain
| | - R Bianchini
- Comparative Medicine, The Interuniversity Messerli Research Institute of the University of Veterinary Medicine Vienna, Medical University Vienna and University Vienna, Vienna, Austria
| | - L Bjermer
- Department of Respiratory Medicine and Allergology, Lung and Allergy research, Allergy, Asthma and COPD Competence Center, Lund University, Lund, Sweden
| | - G Caramori
- Department of Medicine and Surgery, University of Parma, Pneumologia, Italy
| | - L Cari
- Department of Medicine, Section of Pharmacology, University of Perugia, Perugia, Italy
| | - K F Chung
- Experimental Studies Medicine at National Heart & Lung Institute, Imperial College London & Royal Brompton & Harefield Hospital, London, UK
| | - Z Diamant
- Department of Respiratory Medicine and Allergology, Institute for Clinical Science, Skane University Hospital, Lund, Sweden
- Department of Respiratory Medicine, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czech Republic
- Department of Clinical Pharmacy & Pharmacology, University Groningen, University Medical Center Groningen and QPS-NL, Groningen, The Netherlands
| | - I Eguiluz-Gracia
- Allergy Unit, Hospital Regional Universitario de Málaga-Instituto de Investigación Biomédica de Málaga (IBIMA)-ARADyAL, Málaga, Spain
| | - E F Knol
- Departments of Center of Translational Immunology and Dermatology/Allergology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - M Jesenak
- Department of Paediatrics, Department of Pulmonology and Phthisiology, Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin, University Teaching Hospital, Martin, Slovakia
| | - F Levi-Schaffer
- Institute for Drug Research, Pharmacology Unit, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - G Nocentini
- Department of Medicine, Section of Pharmacology, University of Perugia, Perugia, Italy
| | - L O'Mahony
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - O Palomares
- Department of Biochemistry and Molecular Biology, School of Chemistry, Complutense University of Madrid, Madrid, Spain
| | - F Redegeld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - M Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF), University of Zürich, Davos, Switzerland
- Christine Kühne - Center for Allergy Research and Education (CK-CARE), Davos, Switzerland
| | - B C A M Van Esch
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - C Stellato
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
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2
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Cho SJ, Pronko A, Yang J, Stout-Delgado H. Impact of Senolytic Treatment on Gene Expression in Aged Lung. Int J Mol Sci 2023; 24:7628. [PMID: 37108795 PMCID: PMC10145650 DOI: 10.3390/ijms24087628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Cellular senescence plays a key role in mediating tissue remodeling and modulation of host responses to pathogenic stimuli. Our current study was designed to gain a better understanding of the impact of short-term senolytic treatment or inflammatory stimulation on lung senescence. The results of our study demonstrate that short term treatment of aged adult mice (20 months of age) with senolytics, quercetin, and dasatinib decreases p16 and p21 expression in lung tissue. Short-term treatment with senolytics also significantly improved the expression of genes associated with genomic instability, telomere attrition, mitochondrial dysfunction, DNA binding, and the inflammatory response. In contrast, in response to low-dose LPS administration, there was increased expression of genes associated with genomic instability, mitochondrial dysfunction, and heightened inflammatory responses in young adult murine lung (3 months of age). Taken together, the results of our current study illustrate the efficacy of senolytic treatment on modulating responses in aged lung and the potential role of chronic low dose inflammation on senescence induction in the lung.
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Affiliation(s)
| | | | | | - Heather Stout-Delgado
- Pulmonary and Critical Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
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3
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Scheid JF, Eraslan B, Hudak A, Brown EM, Sergio D, Delorey TM, Phillips D, Lefkovith A, Jess AT, Duck LW, Elson CO, Vlamakis H, Plichta DR, Deguine J, Ananthakrishnan AN, Graham DB, Regev A, Xavier RJ. Remodeling of colon plasma cell repertoire within ulcerative colitis patients. J Exp Med 2023; 220:e20220538. [PMID: 36752797 PMCID: PMC9949229 DOI: 10.1084/jem.20220538] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 10/03/2022] [Accepted: 01/11/2023] [Indexed: 02/09/2023] Open
Abstract
Plasma cells (PCs) constitute a significant fraction of colonic mucosal cells and contribute to inflammatory infiltrates in ulcerative colitis (UC). While gut PCs secrete bacteria-targeting IgA antibodies, their role in UC pathogenesis is unknown. We performed single-cell V(D)J- and RNA-seq on sorted B cells from the colon of healthy individuals and patients with UC. A large fraction of B cell clones is shared between different colon regions, but inflammation in UC broadly disrupts this landscape, causing transcriptomic changes characterized by an increase in the unfolded protein response (UPR) and antigen presentation genes, clonal expansion, and isotype skewing from IgA1 and IgA2 to IgG1. We also directly expressed and assessed the specificity of 152 mAbs from expanded PC clones. These mAbs show low polyreactivity and autoreactivity and instead target both shared bacterial antigens and specific bacterial strains. Altogether, our results characterize the microbiome-specific colon PC response and how its disruption might contribute to inflammation in UC.
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Affiliation(s)
- Johannes F. Scheid
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Basak Eraslan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew Hudak
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric M. Brown
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Dallis Sergio
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Toni M. Delorey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Alison T. Jess
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lennard W. Duck
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Charles O. Elson
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Ashwin N. Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Daniel B. Graham
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ramnik J. Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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4
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Abstract
Cellular senescence is a ubiquitous process with roles in tissue remodelling, including wound repair and embryogenesis. However, prolonged senescence can be maladaptive, leading to cancer development and age-related diseases. Cellular senescence involves cell-cycle arrest and the release of inflammatory cytokines with autocrine, paracrine and endocrine activities. Senescent cells also exhibit morphological alterations, including flattened cell bodies, vacuolization and granularity in the cytoplasm and abnormal organelles. Several biomarkers of cellular senescence have been identified, including SA-βgal, p16 and p21; however, few markers have high sensitivity and specificity. In addition to driving ageing, senescence of immune and parenchymal cells contributes to the development of a variety of diseases and metabolic disorders. In the kidney, senescence might have beneficial roles during development and recovery from injury, but can also contribute to the progression of acute kidney injury and chronic kidney disease. Therapies that target senescence, including senolytic and senomorphic drugs, stem cell therapies and other interventions, have been shown to extend lifespan and reduce tissue injury in various animal models. Early clinical trials confirm that senotherapeutic approaches could be beneficial in human disease. However, larger clinical trials are needed to translate these approaches to patient care.
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Affiliation(s)
- Weijun Huang
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
- Key Laboratory of Chinese Internal Medicine of Ministry of Education and Beijing, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, Beijing, China
| | - LaTonya J Hickson
- Division of Nephrology and Hypertension, Mayo Clinic, Jacksonville, FL, USA
| | - Alfonso Eirin
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - James L Kirkland
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - Lilach O Lerman
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA.
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5
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Scheid JF, Barnes CO, Eraslan B, Hudak A, Keeffe JR, Cosimi LA, Brown EM, Muecksch F, Weisblum Y, Zhang S, Delorey T, Woolley AE, Ghantous F, Park SM, Phillips D, Tusi B, Huey-Tubman KE, Cohen AA, Gnanapragasam PNP, Rzasa K, Hatziioanno T, Durney MA, Gu X, Tada T, Landau NR, West AP, Rozenblatt-Rosen O, Seaman MS, Baden LR, Graham DB, Deguine J, Bieniasz PD, Regev A, Hung D, Bjorkman PJ, Xavier RJ. B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV. Cell 2021; 184:3205-3221.e24. [PMID: 34015271 PMCID: PMC8064835 DOI: 10.1016/j.cell.2021.04.032] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/26/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023]
Abstract
Monoclonal antibodies (mAbs) are a focus in vaccine and therapeutic design to counteract severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants. Here, we combined B cell sorting with single-cell VDJ and RNA sequencing (RNA-seq) and mAb structures to characterize B cell responses against SARS-CoV-2. We show that the SARS-CoV-2-specific B cell repertoire consists of transcriptionally distinct B cell populations with cells producing potently neutralizing antibodies (nAbs) localized in two clusters that resemble memory and activated B cells. Cryo-electron microscopy structures of selected nAbs from these two clusters complexed with SARS-CoV-2 spike trimers show recognition of various receptor-binding domain (RBD) epitopes. One of these mAbs, BG10-19, locks the spike trimer in a closed conformation to potently neutralize SARS-CoV-2, the recently arising mutants B.1.1.7 and B.1.351, and SARS-CoV and cross-reacts with heterologous RBDs. Together, our results characterize transcriptional differences among SARS-CoV-2-specific B cells and uncover cross-neutralizing Ab targets that will inform immunogen and therapeutic design against coronaviruses.
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MESH Headings
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antigen-Antibody Complex/chemistry
- Antigen-Antibody Complex/metabolism
- Antigen-Antibody Reactions
- B-Lymphocytes/cytology
- B-Lymphocytes/metabolism
- B-Lymphocytes/virology
- COVID-19/pathology
- COVID-19/virology
- Cryoelectron Microscopy
- Crystallography, X-Ray
- Gene Expression Profiling
- Humans
- Immunoglobulin A/immunology
- Immunoglobulin Variable Region/chemistry
- Immunoglobulin Variable Region/genetics
- Protein Domains/immunology
- Protein Multimerization
- Protein Structure, Quaternary
- SARS-CoV-2/immunology
- SARS-CoV-2/isolation & purification
- SARS-CoV-2/metabolism
- Sequence Analysis, RNA
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
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Affiliation(s)
- Johannes F Scheid
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Basak Eraslan
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Andrew Hudak
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lisa A Cosimi
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eric M Brown
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Frauke Muecksch
- Laboratory of Molecular Virology, The Rockefeller University, New York, NY 10065, USA
| | - Yiska Weisblum
- Laboratory of Molecular Virology, The Rockefeller University, New York, NY 10065, USA
| | - Shuting Zhang
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Toni Delorey
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ann E Woolley
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Fadi Ghantous
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Sung-Moo Park
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Devan Phillips
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Betsabeh Tusi
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Alexander A Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Kara Rzasa
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Theodora Hatziioanno
- Laboratory of Molecular Virology, The Rockefeller University, New York, NY 10065, USA
| | - Michael A Durney
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Xiebin Gu
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Takuya Tada
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Nathaniel R Landau
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Orit Rozenblatt-Rosen
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Lindsey R Baden
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel B Graham
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jacques Deguine
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA
| | - Paul D Bieniasz
- Laboratory of Molecular Virology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Deborah Hung
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Ramnik J Xavier
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02142, USA; Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.
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6
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Agudelo M, Palus M, Keeffe JR, Bianchini F, Svoboda P, Salát J, Peace A, Gazumyan A, Cipolla M, Kapoor T, Guidetti F, Yao KH, Elsterová J, Teislerová D, Chrdle A, Hönig V, Oliveira T, West AP, Lee YE, Rice CM, MacDonald MR, Bjorkman PJ, Růžek D, Robbiani DF, Nussenzweig MC. Broad and potent neutralizing human antibodies to tick-borne flaviviruses protect mice from disease. J Exp Med 2021; 218:e20210236. [PMID: 33831141 PMCID: PMC8040517 DOI: 10.1084/jem.20210236] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/17/2021] [Accepted: 02/19/2021] [Indexed: 12/30/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) is an emerging human pathogen that causes potentially fatal disease with no specific treatment. Mouse monoclonal antibodies are protective against TBEV, but little is known about the human antibody response to infection. Here, we report on the human neutralizing antibody response to TBEV in a cohort of infected and vaccinated individuals. Expanded clones of memory B cells expressed closely related anti-envelope domain III (EDIII) antibodies in both groups of volunteers. However, the most potent neutralizing antibodies, with IC50s below 1 ng/ml, were found only in individuals who recovered from natural infection. These antibodies also neutralized other tick-borne flaviviruses, including Langat, louping ill, Omsk hemorrhagic fever, Kyasanur forest disease, and Powassan viruses. Structural analysis revealed a conserved epitope near the lateral ridge of EDIII adjoining the EDI-EDIII hinge region. Prophylactic or early therapeutic antibody administration was effective at low doses in mice that were lethally infected with TBEV.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Monoclonal/administration & dosage
- Antibodies, Monoclonal/genetics
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/administration & dosage
- Antibodies, Neutralizing/genetics
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/administration & dosage
- Antibodies, Viral/genetics
- Antibodies, Viral/immunology
- Cells, Cultured
- Cohort Studies
- Cross Reactions/immunology
- Encephalitis Viruses, Tick-Borne/drug effects
- Encephalitis Viruses, Tick-Borne/immunology
- Encephalitis Viruses, Tick-Borne/physiology
- Encephalitis, Tick-Borne/immunology
- Encephalitis, Tick-Borne/prevention & control
- Encephalitis, Tick-Borne/virology
- Epitopes/immunology
- Female
- Humans
- Immunoglobulin G/administration & dosage
- Immunoglobulin G/immunology
- Mice, Inbred BALB C
- Sequence Homology, Amino Acid
- Survival Analysis
- Viral Envelope Proteins/genetics
- Viral Envelope Proteins/immunology
- Mice
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Affiliation(s)
- Marianna Agudelo
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Martin Palus
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Veterinary Research Institute, Brno, Czech Republic
| | - Jennifer R. Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Filippo Bianchini
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Pavel Svoboda
- Veterinary Research Institute, Brno, Czech Republic
- Department of Pharmacology and Pharmacy, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Jiří Salát
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Veterinary Research Institute, Brno, Czech Republic
| | - Avery Peace
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Tania Kapoor
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Francesca Guidetti
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Kai-Hui Yao
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Jana Elsterová
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Veterinary Research Institute, Brno, Czech Republic
| | | | - Aleš Chrdle
- Hospital České Budějovice, České Budějovice, Czech Republic
- Faculty of Social and Health Sciences, University of South Bohemia, České Budějovice, Czech Republic
- Royal Liverpool University Hospital, Liverpool, UK
| | - Václav Hönig
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Veterinary Research Institute, Brno, Czech Republic
| | - Thiago Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Yu E. Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Margaret R. MacDonald
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA
| | - Daniel Růžek
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Veterinary Research Institute, Brno, Czech Republic
| | - Davide F. Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY
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7
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Wang Z, Schmidt F, Weisblum Y, Muecksch F, Barnes CO, Finkin S, Schaefer-Babajew D, Cipolla M, Gaebler C, Lieberman JA, Oliveira TY, Yang Z, Abernathy ME, Huey-Tubman KE, Hurley A, Turroja M, West KA, Gordon K, Millard KG, Ramos V, Da Silva J, Xu J, Colbert RA, Patel R, Dizon J, Unson-O'Brien C, Shimeliovich I, Gazumyan A, Caskey M, Bjorkman PJ, Casellas R, Hatziioannou T, Bieniasz PD, Nussenzweig MC. mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants. Nature 2021; 592:616-622. [PMID: 33567448 PMCID: PMC8503938 DOI: 10.1038/s41586-021-03324-6] [Citation(s) in RCA: 972] [Impact Index Per Article: 324.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/03/2021] [Indexed: 12/16/2022]
Abstract
Here we report on the antibody and memory B cell responses of a cohort of 20 volunteers who received the Moderna (mRNA-1273) or Pfizer-BioNTech (BNT162b2) vaccine against SARS-CoV-21-4. Eight weeks after the second injection of vaccine, volunteers showed high levels of IgM and IgG anti-SARS-CoV-2 spike protein (S) and receptor-binding-domain (RBD) binding titre. Moreover, the plasma neutralizing activity and relative numbers of RBD-specific memory B cells of vaccinated volunteers were equivalent to those of individuals who had recovered from natural infection5,6. However, activity against SARS-CoV-2 variants that encode E484K-, N501Y- or K417N/E484K/N501-mutant S was reduced by a small-but significant-margin. The monoclonal antibodies elicited by the vaccines potently neutralize SARS-CoV-2, and target a number of different RBD epitopes in common with monoclonal antibodies isolated from infected donors5-8. However, neutralization by 14 of the 17 most-potent monoclonal antibodies that we tested was reduced or abolished by the K417N, E484K or N501Y mutation. Notably, these mutations were selected when we cultured recombinant vesicular stomatitis virus expressing SARS-CoV-2 S in the presence of the monoclonal antibodies elicited by the vaccines. Together, these results suggest that the monoclonal antibodies in clinical use should be tested against newly arising variants, and that mRNA vaccines may need to be updated periodically to avoid a potential loss of clinical efficacy.
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MESH Headings
- 2019-nCoV Vaccine mRNA-1273
- Adult
- Aged
- Antibodies, Monoclonal/blood
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- B-Lymphocytes/immunology
- BNT162 Vaccine
- COVID-19/immunology
- COVID-19/virology
- COVID-19 Vaccines/genetics
- COVID-19 Vaccines/immunology
- Cryoelectron Microscopy
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/immunology
- Epitopes, B-Lymphocyte/ultrastructure
- Female
- Humans
- Immunization, Secondary
- Immunoglobulin G/blood
- Immunoglobulin G/immunology
- Immunoglobulin M/blood
- Immunoglobulin M/immunology
- Immunologic Memory/immunology
- Male
- Middle Aged
- Models, Molecular
- Mutation
- Neutralization Tests
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Vaccines, Synthetic/genetics
- Vaccines, Synthetic/immunology
- mRNA Vaccines
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Affiliation(s)
- Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Shlomo Finkin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | | | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Jenna A Lieberman
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Zhi Yang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Morgan E Abernathy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Arlene Hurley
- Hospital Program Direction, The Rockefeller University, New York, NY, USA
| | - Martina Turroja
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Kamille A West
- Department of Transfusion Medicine, National Institutes of Health Clinical Center, Bethesda, MD, USA
| | - Kristie Gordon
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Katrina G Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Justin Da Silva
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Jianliang Xu
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Robert A Colbert
- Pediatric Translational Research Branch and Office of the Clinical Director, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Roshni Patel
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Juan Dizon
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | | | - Irina Shimeliovich
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA.
- The NIH Regulome Project, National Institutes of Health, Bethesda, MD, USA.
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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8
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Wang Z, Schmidt F, Weisblum Y, Muecksch F, Barnes CO, Finkin S, Schaefer-Babajew D, Cipolla M, Gaebler C, Lieberman JA, Oliveira TY, Yang Z, Abernathy ME, Huey-Tubman KE, Hurley A, Turroja M, West KA, Gordon K, Millard KG, Ramos V, Da Silva J, Xu J, Colbert RA, Patel R, Dizon J, Unson-O'Brien C, Shimeliovich I, Gazumyan A, Caskey M, Bjorkman PJ, Casellas R, Hatziioannou T, Bieniasz PD, Nussenzweig MC. mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants. bioRxiv 2021. [PMID: 33501451 DOI: 10.1101/2021.01.15.426911] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
To date severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected over 100 million individuals resulting in over two million deaths. Many vaccines are being deployed to prevent coronavirus disease 2019 (COVID-19) including two novel mRNA-based vaccines 1,2 . These vaccines elicit neutralizing antibodies and appear to be safe and effective, but the precise nature of the elicited antibodies is not known 3-6 . Here we report on the antibody and memory B cell responses in a cohort of 20 volunteers who received either the Moderna (mRNA-1273) or Pfizer-BioNTech (BNT162b2) vaccines. Consistent with prior reports, 8 weeks after the second vaccine injection volunteers showed high levels of IgM, and IgG anti-SARS-CoV-2 spike protein (S) and receptor binding domain (RBD) binding titers 3,5,6 . Moreover, the plasma neutralizing activity, and the relative numbers of RBD-specific memory B cells were equivalent to individuals who recovered from natural infection 7,8 . However, activity against SARS-CoV-2 variants encoding E484K or N501Y or the K417N:E484K:N501Y combination was reduced by a small but significant margin. Consistent with these findings, vaccine-elicited monoclonal antibodies (mAbs) potently neutralize SARS-CoV-2, targeting a number of different RBD epitopes in common with mAbs isolated from infected donors. Structural analyses of mAbs complexed with S trimer suggest that vaccine- and virus-encoded S adopts similar conformations to induce equivalent anti-RBD antibodies. However, neutralization by 14 of the 17 most potent mAbs tested was reduced or abolished by either K417N, or E484K, or N501Y mutations. Notably, the same mutations were selected when recombinant vesicular stomatitis virus (rVSV)/SARS-CoV-2 S was cultured in the presence of the vaccine elicited mAbs. Taken together the results suggest that the monoclonal antibodies in clinical use should be tested against newly arising variants, and that mRNA vaccines may need to be updated periodically to avoid potential loss of clinical efficacy.
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9
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Robbiani DF, Gaebler C, Muecksch F, Lorenzi JCC, Wang Z, Cho A, Agudelo M, Barnes CO, Gazumyan A, Finkin S, Hägglöf T, Oliveira TY, Viant C, Hurley A, Hoffmann HH, Millard KG, Kost RG, Cipolla M, Gordon K, Bianchini F, Chen ST, Ramos V, Patel R, Dizon J, Shimeliovich I, Mendoza P, Hartweger H, Nogueira L, Pack M, Horowitz J, Schmidt F, Weisblum Y, Michailidis E, Ashbrook AW, Waltari E, Pak JE, Huey-Tubman KE, Koranda N, Hoffman PR, West AP, Rice CM, Hatziioannou T, Bjorkman PJ, Bieniasz PD, Caskey M, Nussenzweig MC. Convergent antibody responses to SARS-CoV-2 in convalescent individuals. Nature 2020; 584:437-442. [PMID: 32555388 PMCID: PMC7442695 DOI: 10.1038/s41586-020-2456-9] [Citation(s) in RCA: 1419] [Impact Index Per Article: 354.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 06/12/2020] [Indexed: 12/14/2022]
Abstract
During the coronavirus disease-2019 (COVID-19) pandemic, severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) has led to the infection of millions of people and has claimed hundreds of thousands of lives. The entry of the virus into cells depends on the receptor-binding domain (RBD) of the spike (S) protein of SARS-CoV-2. Although there is currently no vaccine, it is likely that antibodies will be essential for protection. However, little is known about the human antibody response to SARS-CoV-21-5. Here we report on 149 COVID-19-convalescent individuals. Plasma samples collected an average of 39 days after the onset of symptoms had variable half-maximal pseudovirus neutralizing titres; titres were less than 50 in 33% of samples, below 1,000 in 79% of samples and only 1% of samples had titres above 5,000. Antibody sequencing revealed the expansion of clones of RBD-specific memory B cells that expressed closely related antibodies in different individuals. Despite low plasma titres, antibodies to three distinct epitopes on the RBD neutralized the virus with half-maximal inhibitory concentrations (IC50 values) as low as 2 ng ml-1. In conclusion, most convalescent plasma samples obtained from individuals who recover from COVID-19 do not contain high levels of neutralizing activity. Nevertheless, rare but recurring RBD-specific antibodies with potent antiviral activity were found in all individuals tested, suggesting that a vaccine designed to elicit such antibodies could be broadly effective.
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Affiliation(s)
- Davide F Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Julio C C Lorenzi
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Marianna Agudelo
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Shlomo Finkin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Thomas Hägglöf
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Charlotte Viant
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Arlene Hurley
- Hospital Program Direction, The Rockefeller University, New York, NY, USA
| | - Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Katrina G Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Rhonda G Kost
- Center for Clinical Translational Science, The Rockefeller University, New York, NY, USA
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Kristie Gordon
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Filippo Bianchini
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Spencer T Chen
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Roshni Patel
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Juan Dizon
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Irina Shimeliovich
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Pilar Mendoza
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Harald Hartweger
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Lilian Nogueira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Maggi Pack
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Jill Horowitz
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Eleftherios Michailidis
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | - Alison W Ashbrook
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | | | - John E Pak
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Nicholas Koranda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Pauline R Hoffman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY, USA
| | | | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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10
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Robbiani DF, Gaebler C, Muecksch F, Lorenzi JCC, Wang Z, Cho A, Agudelo M, Barnes CO, Gazumyan A, Finkin S, Hagglof T, Oliveira TY, Viant C, Hurley A, Hoffmann HH, Millard KG, Kost RG, Cipolla M, Gordon K, Bianchini F, Chen ST, Ramos V, Patel R, Dizon J, Shimeliovich I, Mendoza P, Hartweger H, Nogueira L, Pack M, Horowitz J, Schmidt F, Weisblum Y, Michailidis E, Ashbrook AW, Waltari E, Pak JE, Huey-Tubman KE, Koranda N, Hoffman PR, West AP, Rice CM, Hatziioannou T, Bjorkman PJ, Bieniasz PD, Caskey M, Nussenzweig MC. Convergent Antibody Responses to SARS-CoV-2 Infection in Convalescent Individuals. bioRxiv 2020. [PMID: 32511384 PMCID: PMC7263513 DOI: 10.1101/2020.05.13.092619] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
During the COVID-19 pandemic, SARS-CoV-2 infected millions of people and claimed hundreds of thousands of lives. Virus entry into cells depends on the receptor binding domain (RBD) of the SARS-CoV-2 spike protein (S). Although there is no vaccine, it is likely that antibodies will be essential for protection. However, little is known about the human antibody response to SARS-CoV-21–5. Here we report on 149 COVID-19 convalescent individuals. Plasmas collected an average of 39 days after the onset of symptoms had variable half-maximal neutralizing titers ranging from undetectable in 33% to below 1:1000 in 79%, while only 1% showed titers >1:5000. Antibody cloning revealed expanded clones of RBD-specific memory B cells expressing closely related antibodies in different individuals. Despite low plasma titers, antibodies to three distinct epitopes on RBD neutralized at half-maximal inhibitory concentrations (IC50s) as low as single digit ng/mL. Thus, most convalescent plasmas obtained from individuals who recover from COVID-19 do not contain high levels of neutralizing activity. Nevertheless, rare but recurring RBD-specific antibodies with potent antiviral activity were found in all individuals tested, suggesting that a vaccine designed to elicit such antibodies could be broadly effective.
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Affiliation(s)
- Davide F Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Julio C C Lorenzi
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Marianna Agudelo
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Shlomo Finkin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thomas Hagglof
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Charlotte Viant
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Arlene Hurley
- Hospital Program Direction, The Rockefeller University, New York, NY 10065, USA
| | - Hans-Heinrich Hoffmann
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Katrina G Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Rhonda G Kost
- Hospital Clinical Research Office, The Rockefeller University, New York, NY 10065, USA
| | - Melissa Cipolla
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Kristie Gordon
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Filippo Bianchini
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Spencer T Chen
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Victor Ramos
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Roshni Patel
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Juan Dizon
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Irina Shimeliovich
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Pilar Mendoza
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Harald Hartweger
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Lilian Nogueira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Maggi Pack
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Jill Horowitz
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Eleftherios Michailidis
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Alison W Ashbrook
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Eric Waltari
- Chan Zuckerberg Biohub, 499 Illinois Street, San Francisco, CA 94158, USA
| | - John E Pak
- Chan Zuckerberg Biohub, 499 Illinois Street, San Francisco, CA 94158, USA
| | - Kathryn E Huey-Tubman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Nicholas Koranda
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Pauline R Hoffman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | | | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA.,Howard Hughes Medical Institute
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.,Howard Hughes Medical Institute
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11
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Lemaître J, Pavard S, Giraudeau M, Vincze O, Jennings G, Hamede R, Ujvari B, Thomas F. Eco‐evolutionary perspectives of the dynamic relationships linking senescence and cancer. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13394] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jean‐François Lemaître
- Université de Lyon, F‐69000, Lyon; Université Lyon 1; CNRS, UMR5558 Laboratoire de Biométrie et Biologie Évolutive F‐69622 Villeurbanne France
| | - Samuel Pavard
- Unité Eco-anthropologie (EA), Muséum National d’Histoire Naturelle, CNRS 7206 Université Paris Diderot Paris France
| | | | - Orsolya Vincze
- Hungarian Department of Biology and Ecology, Evolutionary Ecology Group Babeş‐Bolyai University Cluj‐Napoca Romania
- Department of Tisza Research MTA Centre for Ecological Research Debrecen Hungary
| | - Geordie Jennings
- Centre for Integrative Ecology, School of Life and Environmental Sciences Deakin University Waurn Ponds Victoria Australia
- School of Natural Sciences University of Tasmania Hobart Tasmania Australia
| | - Rodrigo Hamede
- Centre for Integrative Ecology, School of Life and Environmental Sciences Deakin University Waurn Ponds Victoria Australia
- School of Natural Sciences University of Tasmania Hobart Tasmania Australia
| | - Beata Ujvari
- Centre for Integrative Ecology, School of Life and Environmental Sciences Deakin University Waurn Ponds Victoria Australia
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12
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Dunn-walters DK, O’hare JS. Older Human B Cells and Antibodies. Handbook of Immunosenescence 2019. [DOI: 10.1007/978-3-319-99375-1_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
B cells have a number of different roles in the immune response. Their excellent antigen presentation potential can contribute to the activation of other cells of the immune system, and evidence is emerging that specialized subsets of these cells, that may be increased with age, can influence the cell-mediated immune system in antitumor responses. They can also regulate immune responses, to avoid autoreactivity and excessive inflammation. Deficiencies in regulatory B cells may be beneficial in cancer but will only exacerbate the inflammatory environment that is a hallmark of aging. The B cell role as antibody producers is particularly important, since antibodies perform numerous different functions in different environments. Although studying tissue responses in humans is not as easy as in mice, we do know that certain classes of antibodies are more suited to protecting the mucosal tissues (IgA) or responding to T-independent bacterial polysaccharide antigens (IgG2) so we can make some inference with respect to tissue-specific immunity from a study of peripheral blood. We can also make inferences about changes in B cell development with age by looking at the repertoire of different B cell populations to see how age affects the selection events that would normally occur to avoid autoreactivity, or increase specificity, to antigen.
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Devulapally PR, Bürger J, Mielke T, Konthur Z, Lehrach H, Yaspo ML, Glökler J, Warnatz HJ. Simple paired heavy- and light-chain antibody repertoire sequencing using endoplasmic reticulum microsomes. Genome Med 2018; 10:34. [PMID: 29703216 PMCID: PMC5921987 DOI: 10.1186/s13073-018-0542-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 04/12/2018] [Indexed: 12/21/2022] Open
Abstract
Existing methods for paired antibody heavy- and light-chain repertoire sequencing rely on specialized equipment and are limited by their commercial availability and high costs. Here, we report a novel simple and cost-effective emulsion-based single-cell paired antibody repertoire sequencing method that employs only basic laboratory equipment. We performed a proof-of-concept using mixed mouse hybridoma cells and we also showed that our method can be used for discovery of novel antigen-specific monoclonal antibodies by sequencing human CD19+ B cell IgM and IgG repertoires isolated from peripheral whole blood before and seven days after Td (Tetanus toxoid/Diphtheria toxoid) booster immunization. We anticipate broad applicability of our method for providing insights into adaptive immune responses associated with various diseases, vaccinations, and cancer immunotherapies.
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Affiliation(s)
- Praneeth Reddy Devulapally
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jörg Bürger
- Microscopy and Cryo-Electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin, Berlin, Germany
| | - Thorsten Mielke
- Microscopy and Cryo-Electron Microscopy Service Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Zoltán Konthur
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Hans Lehrach
- Alacris Theranostics GmbH, Berlin, Germany.,Dahlem Centre for Genome Research and Medical Systems Biology, Berlin, Germany
| | - Marie-Laure Yaspo
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, Berlin, Germany.,Alacris Theranostics GmbH, Berlin, Germany
| | - Jörn Glökler
- Department of Molecular Biotechnology and Functional Genomics, Institute of Applied Biosciences, Technical University of Applied Sciences Wildau, Wildau, Brandenburg, Germany
| | - Hans-Jörg Warnatz
- Otto Warburg Laboratory Gene Regulation and Systems Biology of Cancer, Max Planck Institute for Molecular Genetics, Berlin, Germany.
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14
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Robbiani DF, Bozzacco L, Keeffe JR, Khouri R, Olsen PC, Gazumyan A, Schaefer-Babajew D, Avila-Rios S, Nogueira L, Patel R, Azzopardi SA, Uhl LFK, Saeed M, Sevilla-Reyes EE, Agudelo M, Yao KH, Golijanin J, Gristick HB, Lee YE, Hurley A, Caskey M, Pai J, Oliveira T, Wunder EA, Sacramento G, Nery N, Orge C, Costa F, Reis MG, Thomas NM, Eisenreich T, Weinberger DM, de Almeida ARP, West AP, Rice CM, Bjorkman PJ, Reyes-Teran G, Ko AI, MacDonald MR, Nussenzweig MC. Recurrent Potent Human Neutralizing Antibodies to Zika Virus in Brazil and Mexico. Cell 2017; 169:597-609.e11. [PMID: 28475892 PMCID: PMC5492969 DOI: 10.1016/j.cell.2017.04.024] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 04/17/2017] [Accepted: 04/17/2017] [Indexed: 01/20/2023]
Abstract
Antibodies to Zika virus (ZIKV) can be protective. To examine the antibody response in individuals who develop high titers of anti-ZIKV antibodies, we screened cohorts in Brazil and Mexico for ZIKV envelope domain III (ZEDIII) binding and neutralization. We find that serologic reactivity to dengue 1 virus (DENV1) EDIII before ZIKV exposure is associated with increased ZIKV neutralizing titers after exposure. Antibody cloning shows that donors with high ZIKV neutralizing antibody titers have expanded clones of memory B cells that express the same immunoglobulin VH3-23/VK1-5 genes. These recurring antibodies cross-react with DENV1, but not other flaviviruses, neutralize both DENV1 and ZIKV, and protect mice against ZIKV challenge. Structural analyses reveal the mechanism of recognition of the ZEDIII lateral ridge by VH3-23/VK1-5 antibodies. Serologic testing shows that antibodies to this region correlate with serum neutralizing activity to ZIKV. Thus, high neutralizing responses to ZIKV are associated with pre-existing reactivity to DENV1 in humans.
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Affiliation(s)
- Davide F Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.
| | - Leonia Bozzacco
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ricardo Khouri
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia CEP 40296-710, Brazil
| | - Priscilla C Olsen
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | | | | | - Lilian Nogueira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Roshni Patel
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Stephanie A Azzopardi
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Lion F K Uhl
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Mohsan Saeed
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | | | - Marianna Agudelo
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Kai-Hui Yao
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Jovana Golijanin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Harry B Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yu E Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Arlene Hurley
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Joy Pai
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thiago Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Elsio A Wunder
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia CEP 40296-710, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA
| | - Gielson Sacramento
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia CEP 40296-710, Brazil
| | - Nivison Nery
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia CEP 40296-710, Brazil
| | - Cibele Orge
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia CEP 40296-710, Brazil
| | - Federico Costa
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia CEP 40296-710, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA; Faculdade de Medicina da Bahia and Instituto da Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia CEP 40296-710, Brazil
| | - Mitermayer G Reis
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia CEP 40296-710, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA; Faculdade de Medicina da Bahia and Instituto da Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia CEP 40296-710, Brazil
| | - Neena M Thomas
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thomas Eisenreich
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA
| | - Antonio R P de Almeida
- Faculdade de Medicina da Bahia and Instituto da Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia CEP 40296-710, Brazil
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Albert I Ko
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia CEP 40296-710, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA
| | - Margaret R MacDonald
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA.
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
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15
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Lee YN, Frugoni F, Dobbs K, Tirosh I, Du L, Ververs FA, Ru H, Ott de Bruin L, Adeli M, Bleesing JH, Buchbinder D, Butte MJ, Cancrini C, Chen K, Choo S, Elfeky RA, Finocchi A, Fuleihan RL, Gennery AR, El-Ghoneimy DH, Henderson LA, Al-Herz W, Hossny E, Nelson RP, Pai SY, Patel NC, Reda SM, Soler-Palacin P, Somech R, Palma P, Wu H, Giliani S, Walter JE, Notarangelo LD. Characterization of T and B cell repertoire diversity in patients with RAG deficiency. Sci Immunol 2016; 1:eaah6109. [PMID: 28783691 PMCID: PMC5586490 DOI: 10.1126/sciimmunol.aah6109] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/22/2016] [Indexed: 12/13/2022]
Abstract
Recombination-activating genes 1 and 2 (RAG1 and RAG2) play a critical role in T and B cell development by initiating the recombination process that controls the expression of T cell receptor (TCR) and immunoglobulin genes. Mutations in the RAG1 and RAG2 genes in humans cause a broad spectrum of phenotypes, including severe combined immunodeficiency (SCID) with lack of T and B cells, Omenn syndrome, leaky SCID, and combined immunodeficiency with granulomas or autoimmunity (CID-G/AI). Using next-generation sequencing, we analyzed the TCR and B cell receptor (BCR) repertoire in 12 patients with RAG mutations presenting with Omenn syndrome (n = 5), leaky SCID (n = 3), or CID-G/AI (n = 4). Restriction of repertoire diversity skewed usage of variable (V), diversity (D), and joining (J) segment genes, and abnormalities of CDR3 length distribution were progressively more prominent in patients with a more severe phenotype. Skewed usage of V, D, and J segment genes was present also within unique sequences, indicating a primary restriction of repertoire. Patients with Omenn syndrome had a high proportion of class-switched immunoglobulin heavy chain transcripts and increased somatic hypermutation rate, suggesting in vivo activation of these B cells. These data provide a framework to better understand the phenotypic heterogeneity of RAG deficiency.
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Affiliation(s)
- Yu Nee Lee
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Pediatric Department A and the Immunology Service, "Edmond and Lily Safra" Children's Hospital, Jeffrey Modell Foundation Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Francesco Frugoni
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kerry Dobbs
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Irit Tirosh
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Likun Du
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Francesca A Ververs
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Heng Ru
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Lisa Ott de Bruin
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mehdi Adeli
- Pediatrics Department, Weill Cornell Medical College, Hamad Medical Corporation, Doha, Qatar
| | - Jacob H Bleesing
- Division of Hematology/Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - David Buchbinder
- Division of Hematology, Children's Hospital Orange County, Orange County, CA 92868, USA
| | - Manish J Butte
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Caterina Cancrini
- DPUO, University Department of Pediatrics, Bambino Gesù Children's Hospital and University of Tor Vergata School of Medicine, Rome, Italy
| | - Karin Chen
- Division of Allergy, Immunology, and Rheumatology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Sharon Choo
- Department of Immunology, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Reem A Elfeky
- Department of Pediatric Allergy and Immunology, Children's Hospital, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Andrea Finocchi
- DPUO, University Department of Pediatrics, Bambino Gesù Children's Hospital and University of Tor Vergata School of Medicine, Rome, Italy
| | - Ramsay L Fuleihan
- Division of Allergy and Immunology, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Andrew R Gennery
- Department of Paediatric Immunology, Great North Children's Hospital, Newcastle Upon Tyne, U.K
- Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, U.K
| | - Dalia H El-Ghoneimy
- Department of Pediatric Allergy and Immunology, Children's Hospital, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Lauren A Henderson
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Waleed Al-Herz
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Elham Hossny
- Department of Pediatric Allergy and Immunology, Children's Hospital, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Robert P Nelson
- Division of Hematology and Oncology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Sung-Yun Pai
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Niraj C Patel
- Division of Infectious Disease and Immunology, Department of Pediatrics, Levine Children's Hospital, Carolinas Medical Center, Charlotte, NC 28203, USA
| | - Shereen M Reda
- Department of Pediatric Allergy and Immunology, Children's Hospital, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Pere Soler-Palacin
- Paediatric Infectious Diseases and Immunodeficiencies Unit, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Raz Somech
- Pediatric Department A and the Immunology Service, "Edmond and Lily Safra" Children's Hospital, Jeffrey Modell Foundation Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Paolo Palma
- DPUO, University Department of Pediatrics, Bambino Gesù Children's Hospital and University of Tor Vergata School of Medicine, Rome, Italy
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Silvia Giliani
- A. Nocivelli Institute for Molecular Medicine, Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
- Section of Medical Genetics, Department of Pathology, Spedali Civili di Bresia, Brescia, Italy
| | - Jolan E Walter
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Division of Pediatric Allergy/Immunology, University of South Florida, and Johns Hopkins All Children's Hospital, St. Petersburg, FL 33701, USA
| | - Luigi D Notarangelo
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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16
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Turchaninova MA, Davydov A, Britanova OV, Shugay M, Bikos V, Egorov ES, Kirgizova VI, Merzlyak EM, Staroverov DB, Bolotin DA, Mamedov IZ, Izraelson M, Logacheva MD, Kladova O, Plevova K, Pospisilova S, Chudakov DM. High-quality full-length immunoglobulin profiling with unique molecular barcoding. Nat Protoc 2016; 11:1599-616. [DOI: 10.1038/nprot.2016.093] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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17
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Scharf L, West AP, Sievers SA, Chen C, Jiang S, Gao H, Gray MD, McGuire AT, Scheid JF, Nussenzweig MC, Stamatatos L, Bjorkman PJ. Structural basis for germline antibody recognition of HIV-1 immunogens. eLife 2016; 5. [PMID: 26997349 PMCID: PMC4811768 DOI: 10.7554/elife.13783] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 03/05/2016] [Indexed: 01/16/2023] Open
Abstract
Efforts to elicit broadly neutralizing antibodies (bNAbs) against HIV-1 require understanding germline bNAb recognition of HIV-1 envelope glycoprotein (Env). The VRC01-class bNAb family derived from the VH1-2*02 germline allele arose in multiple HIV-1–infected donors, yet targets the CD4-binding site on Env with common interactions. Modified forms of the 426c Env that activate germline-reverted B cell receptors are candidate immunogens for eliciting VRC01-class bNAbs. We present structures of germline-reverted VRC01-class bNAbs alone and complexed with 426c-based gp120 immunogens. Germline bNAb–426c gp120 complexes showed preservation of VRC01-class signature residues and gp120 contacts, but detectably different binding modes compared to mature bNAb-gp120 complexes. Unlike typical antibody-antigen interactions, VRC01–class germline antibodies exhibited preformed antigen-binding conformations for recognizing immunogens. Affinity maturation introduced substitutions increasing induced-fit recognition and electropositivity, potentially to accommodate negatively-charged complex-type N-glycans on gp120. These results provide general principles relevant to the unusual evolution of VRC01–class bNAbs and guidelines for structure-based immunogen design. DOI:http://dx.doi.org/10.7554/eLife.13783.001 When human immunodeficiency virus-1 (HIV-1) infects humans it can cause a serious disease that damages the immune system. Currently there is no cure for this disease and there are no vaccines available to halt the spread of the virus. Researchers are hoping to be able to develop a single vaccine that can protect individuals against every form (or strain) of HIV-1, but this has proved difficult because many different versions of the virus exist. An effective vaccine triggers long-lasting immunity to a particular virus or microbe by activating the production of proteins called antibodies that identify and help to destroy the threat. Research has shown that most individuals infected with HIV-1 produce antibodies that can only recognize a few HIV strains. However, there are rare individuals who produce “broadly neutralizing antibodies”; that is, antibodies that can recognize and help to kill 90% or more of HIV-1 strains. Understanding how broadly neutralizing antibodies are produced in infected individuals may aid the development of a vaccine that can protect others from the many circulating strains of HIV. When an individual encounters a virus, immature antibodies are modified to generate mature antibodies that bind more effectively to specific virus proteins. Here, Scharf et al. investigated how a class of broadly neutralizing antibodies called VRC01-class antibodies, which bind to an HIV protein called gp120, are produced. The experiments used a technique called X-ray crystallography to reveal the three-dimensional structures of immature versions of these antibodies when they are bound to gp120. Scharf et al. discovered that, unlike most antibodies, the overall final structure of VRC01 antibodies is formed before the antibody matures. Instead of making large changes to the structure of these antibodies, the maturation process makes VRC01-class antibodies become more positively charged, which allows them to bind to gp120 proteins on a wider variety of HIV viruses. These findings suggest that it may be possible to use modified gp120 proteins in vaccines to trigger the production of broadly neutralizing antibodies against HIV. DOI:http://dx.doi.org/10.7554/eLife.13783.002
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Affiliation(s)
- Louise Scharf
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Stuart A Sievers
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Courtney Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Siduo Jiang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Han Gao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Matthew D Gray
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Andrew T McGuire
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Johannes F Scheid
- Laboratory of Molecular Immunology, The Rockefeller University, New York, United States
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, United States.,Howard Hughes Medical Institute, The Rockefeller University, New York, United States
| | - Leonidas Stamatatos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
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18
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Abstract
New high-throughput DNA sequencing (HTS) technologies developed in the past decade have begun to be applied to the study of the complex gene rearrangements that encode human antibodies. This article first reviews the genetic features of Ig loci and the HTS technologies that have been applied to human repertoire studies, then discusses key choices for experimental design and data analysis in these experiments and the insights gained in immunological and infectious disease studies with the use of these approaches.
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19
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Amaral AFS, Newson RB, Abramson MJ, Antó JM, Bono R, Corsico AG, de Marco R, Demoly P, Forsberg B, Gislason T, Heinrich J, Huerta I, Janson C, Jõgi R, Kim JL, Maldonado J, Martinez-Moratalla Rovira J, Neukirch C, Nowak D, Pin I, Probst-Hensch N, Raherison-Semjen C, Svanes C, Urrutia Landa I, van Ree R, Versteeg SA, Weyler J, Zock JP, Burney PGJ, Jarvis DL. Changes in IgE sensitization and total IgE levels over 20 years of follow-up. J Allergy Clin Immunol 2015; 137:1788-1795.e9. [PMID: 26586040 PMCID: PMC4889785 DOI: 10.1016/j.jaci.2015.09.037] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 08/21/2015] [Accepted: 09/30/2015] [Indexed: 11/29/2022]
Abstract
Background Cross-sectional studies have reported a lower prevalence of sensitization in older adults, but few longitudinal studies have examined whether this is an aging or a year-of-birth cohort effect. Objective We sought to assess changes in sensitization and total IgE levels in a cohort of European adults as they aged over a 20-year period. Methods Levels of serum specific IgE to common aeroallergens (house dust mite, cat, and grass) and total IgE levels were measured in 3206 adults from 25 centers in the European Community Respiratory Health Survey on 3 occasions over 20 years. Changes in sensitization and total IgE levels were analyzed by using regression analysis corrected for potential differences in laboratory equipment and by using inverse sampling probability weights to account for nonresponse. Results Over the 20-year follow-up, the prevalence of sensitization to at least 1 of the 3 allergens decreased from 29.4% to 24.8% (−4.6%; 95% CI, −7.0% to −2.1%). The prevalence of sensitization to house dust mite (−4.3%; 95% CI, −6.0% to −2.6%) and cat (−2.1%; 95% CI, −3.6% to −0.7%) decreased more than sensitization to grass (−0.6%; 95% CI, −2.5% to 1.3%). Age-specific prevalence of sensitization to house dust mite and cat did not differ between year-of-birth cohorts, but sensitization to grass was most prevalent in the most recent ones. Overall, total IgE levels decreased significantly (geometric mean ratio, 0.63; 95% CI, 0.58-0.68) at all ages in all year-of-birth cohorts. Conclusion Aging was associated with lower levels of sensitization, especially to house dust mite and cat, after the age of 20 years.
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Affiliation(s)
- André F S Amaral
- Respiratory Epidemiology, Occupational Medicine and Public Health, National Heart and Lung Institute, Imperial College, London, United Kingdom.
| | - Roger B Newson
- Respiratory Epidemiology, Occupational Medicine and Public Health, National Heart and Lung Institute, Imperial College, London, United Kingdom; Department of Primary Care and Public Health, School of Public Health, Imperial College, London, United Kingdom
| | - Michael J Abramson
- School of Public Health & Preventive Medicine, Monash University, Melbourne, Australia
| | - Josep M Antó
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain; IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Roberto Bono
- Department of Public Health and Pediatrics, University of Turin, Turin, Italy
| | - Angelo G Corsico
- Division of Respiratory Diseases, IRCCS Policlinico San Matteo Foundation-University of Pavia, Pavia, Italy
| | - Roberto de Marco
- Unit of Epidemiology and Medical Statistics, Department of Public Health and Community Medicine, University of Verona, Verona, Italy
| | - Pascal Demoly
- Department of Pulmonology, Division of Allergy, Arnaud de Villeneuve Hospital, CHU Montpellier, and EPAR Team-UMR-S 1136 INSERM, Paris, France
| | - Bertil Forsberg
- Division of Occupational and Environmental Medicine, Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Thorarinn Gislason
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland; Department of Respiratory Medicine and Sleep, Landspitali-The National University Hospital of Iceland, Reykjavik, Iceland
| | - Joachim Heinrich
- Institute of Epidemiology I, Helmholtz Zentrum, Munich, Germany; Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Inner City Clinic, University Hospital Munich, Ludwig-Maximilians-Universität of Munich, Munich, Germany
| | - Ismael Huerta
- Epidemiological Surveillance Section, Directorate General of Public Health, Department of Health of Asturias, Oviedo, Spain
| | - Christer Janson
- Department of Medical Sciences: Respiratory, Allergy and Sleep Research, Uppsala University, Uppsala, Sweden
| | - Rain Jõgi
- Tartu University Hospital, Lung Clinic, Tartu, Estonia
| | - Jeong-Lim Kim
- Department of Publich Health and Community Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - José Maldonado
- Unit of Clinical Management of Pneumology and Allergy, University Hospital of Huelva, Huelva, Spain
| | | | - Catherine Neukirch
- INSERM UMR1152, Paris, France; Université Paris Diderot Paris 7, UMR1152, Paris, France
| | - Dennis Nowak
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Inner City Clinic, University Hospital Munich, Ludwig-Maximilians-Universität of Munich, and the German Center for Lung Research, Munich, Germany
| | - Isabelle Pin
- Pédiatrie, Pole Couple Enfants, CHU de Grenoble, Grenoble, France; INSERM U823, Institut Albert Bonniot, Grenoble, France; Université Joseph Fourier, Grenoble, France
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | | | - Cecilie Svanes
- Centre for International Health, University of Bergen, Bergen, Norway; Department of Occupational Medicine, Haukeland University Hospital, Bergen, Norway
| | | | - Ronald van Ree
- Departments of Experimental Immunology and of Otorhinolaryngology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Serge A Versteeg
- Department of Experimental Immunology, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Joost Weyler
- Epidemiology and Social Medicine and the StatUA Statistics Centre, University of Antwerp, Antwerp, Belgium
| | - Jan-Paul Zock
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Peter G J Burney
- Respiratory Epidemiology, Occupational Medicine and Public Health, National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Deborah L Jarvis
- Respiratory Epidemiology, Occupational Medicine and Public Health, National Heart and Lung Institute, Imperial College, London, United Kingdom
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20
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Abstract
The development of high-throughput DNA sequencing technologies has enabled large-scale characterization of functional antibody repertoires, a new method of understanding protective and pathogenic immune responses. Important parameters to consider when sequencing antibody repertoires include the methodology, the B-cell population and clinical characteristics of the individuals analysed, and the bioinformatic analysis. Although focused sequencing of immunoglobulin heavy chains or complement determining regions can be utilized to monitor particular immune responses and B-cell malignancies, high-fidelity analysis of the full-length paired heavy and light chains expressed by individual B cells is critical for characterizing functional antibody repertoires. Bioinformatic identification of clonal antibody families and recombinant expression of representative members produces recombinant antibodies that can be used to identify the antigen targets of functional immune responses and to investigate the mechanisms of their protective or pathogenic functions. Integrated analysis of coexpressed functional genes provides the potential to further pinpoint the most important antibodies and clonal families generated during an immune response. Sequencing antibody repertoires is transforming our understanding of immune responses to autoimmunity, vaccination, infection and cancer. We anticipate that antibody repertoire sequencing will provide next-generation biomarkers, diagnostic tools and therapeutic antibodies for a spectrum of diseases, including rheumatic diseases.
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Affiliation(s)
- William H Robinson
- Division of Immunology and Rheumatology, CCSR 4135, 269 Campus Drive, Stanford, CA 94305, USA
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21
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Galson JD, Pollard AJ, Trück J, Kelly DF. Studying the antibody repertoire after vaccination: practical applications. Trends Immunol 2014; 35:319-31. [PMID: 24856924 DOI: 10.1016/j.it.2014.04.005] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 04/17/2014] [Accepted: 04/28/2014] [Indexed: 12/25/2022]
Abstract
Nearly all licensed vaccines have been developed to confer protection against infectious diseases by stimulating the production of antibodies by B cells, but the nature of a successful antibody response has been difficult to capture. Recent advances in next-generation sequencing (NGS) technology have allowed high-resolution characterization of the antibody repertoire, and of the changes that occur following vaccination. These approaches have yielded important insights into the B cell response, and have raised the possibility of using specific antibody sequences as measures of vaccine immunogenicity. Here, we review recent findings based on antibody repertoire sequencing, and discuss potential applications of these new technologies and of the analyses of the increasing volume of antibody sequence data in the context of vaccine development.
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Affiliation(s)
- Jacob D Galson
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK.
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK.
| | - Johannes Trück
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
| | - Dominic F Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, UK
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22
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Georgiou G, Ippolito GC, Beausang J, Busse CE, Wardemann H, Quake SR. The promise and challenge of high-throughput sequencing of the antibody repertoire. Nat Biotechnol 2014; 32:158-68. [PMID: 24441474 DOI: 10.1038/nbt.2782] [Citation(s) in RCA: 465] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 12/04/2013] [Indexed: 12/16/2022]
Abstract
Georgiou and colleagues discuss rapidly evolving methods for high-throughput sequencing of the antibody repertoire, and how the resulting data may be applied to answer basic and translational research questions. Efforts to determine the antibody repertoire encoded by B cells in the blood or lymphoid organs using high-throughput DNA sequencing technologies have been advancing at an extremely rapid pace and are transforming our understanding of humoral immune responses. Information gained from high-throughput DNA sequencing of immunoglobulin genes (Ig-seq) can be applied to detect B-cell malignancies with high sensitivity, to discover antibodies specific for antigens of interest, to guide vaccine development and to understand autoimmunity. Rapid progress in the development of experimental protocols and informatics analysis tools is helping to reduce sequencing artifacts, to achieve more precise quantification of clonal diversity and to extract the most pertinent biological information. That said, broader application of Ig-seq, especially in clinical settings, will require the development of a standardized experimental design framework that will enable the sharing and meta-analysis of sequencing data generated by different laboratories.
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23
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Luštrek M, Lorenz P, Kreutzer M, Qian Z, Steinbeck F, Wu D, Born N, Ziems B, Hecker M, Blank M, Shoenfeld Y, Cao Z, Glocker MO, Li Y, Fuellen G, Thiesen HJ. Epitope predictions indicate the presence of two distinct types of epitope-antibody-reactivities determined by epitope profiling of intravenous immunoglobulins. PLoS One 2013; 8:e78605. [PMID: 24244326 PMCID: PMC3823795 DOI: 10.1371/journal.pone.0078605] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 09/20/2013] [Indexed: 01/23/2023] Open
Abstract
Epitope-antibody-reactivities (EAR) of intravenous immunoglobulins (IVIGs) determined for 75,534 peptides by microarray analysis demonstrate that roughly 9% of peptides derived from 870 different human protein sequences react with antibodies present in IVIG. Computational prediction of linear B cell epitopes was conducted using machine learning with an ensemble of classifiers in combination with position weight matrix (PWM) analysis. Machine learning slightly outperformed PWM with area under the curve (AUC) of 0.884 vs. 0.849. Two different types of epitope-antibody recognition-modes (Type I EAR and Type II EAR) were found. Peptides of Type I EAR are high in tyrosine, tryptophan and phenylalanine, and low in asparagine, glutamine and glutamic acid residues, whereas for peptides of Type II EAR it is the other way around. Representative crystal structures present in the Protein Data Bank (PDB) of Type I EAR are PDB 1TZI and PDB 2DD8, while PDB 2FD6 and 2J4W are typical for Type II EAR. Type I EAR peptides share predicted propensities for being presented by MHC class I and class II complexes. The latter interaction possibly favors T cell-dependent antibody responses including IgG class switching. Peptides of Type II EAR are predicted not to be preferentially presented by MHC complexes, thus implying the involvement of T cell-independent IgG class switch mechanisms. The high extent of IgG immunoglobulin reactivity with human peptides implies that circulating IgG molecules are prone to bind to human protein/peptide structures under non-pathological, non-inflammatory conditions. A webserver for predicting EAR of peptide sequences is available at www.sysmed-immun.eu/EAR.
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Affiliation(s)
- Mitja Luštrek
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Universitätsmedizin, University of Rostock, Rostock, Germany
- Department of Intelligent Systems, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Peter Lorenz
- Institute of Immunology, Universitätsmedizin Rostock, University of Rostock, Rostock, Germany
| | - Michael Kreutzer
- Institute of Immunology, Universitätsmedizin Rostock, University of Rostock, Rostock, Germany
| | - Zilliang Qian
- Institute of Immunology, Universitätsmedizin Rostock, University of Rostock, Rostock, Germany
- Shanghai Institute for Biological Sciences, Shanghai, China
| | - Felix Steinbeck
- Institute of Immunology, Universitätsmedizin Rostock, University of Rostock, Rostock, Germany
| | - Di Wu
- Institute of Immunology, Universitätsmedizin Rostock, University of Rostock, Rostock, Germany
- Shanghai Institute for Biological Sciences, Shanghai, China
| | - Nadine Born
- Institute of Immunology, Universitätsmedizin Rostock, University of Rostock, Rostock, Germany
| | - Bjoern Ziems
- Gesellschaft für Individualisierte Medizin GmbH, Rostock, Germany
| | - Michael Hecker
- Steinbeis Transfer Center for Proteome Analysis, Rostock, Germany
| | - Miri Blank
- The Zabludovicz Center for Autoimmune Diseases, Sheba Medical Center, Ramat-Gan, Israel
| | - Yehuda Shoenfeld
- The Zabludovicz Center for Autoimmune Diseases, Sheba Medical Center, Ramat-Gan, Israel
| | - Zhiwei Cao
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | | | - Yixue Li
- Shanghai Institute for Biological Sciences, Shanghai, China
| | - Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, Universitätsmedizin, University of Rostock, Rostock, Germany
| | - Hans-Jürgen Thiesen
- Institute of Immunology, Universitätsmedizin Rostock, University of Rostock, Rostock, Germany
- * E-mail:
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24
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Mathonet P, Ullman CG. The application of next generation sequencing to the understanding of antibody repertoires. Front Immunol 2013; 4:265. [PMID: 24062737 PMCID: PMC3769625 DOI: 10.3389/fimmu.2013.00265] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Accepted: 08/19/2013] [Indexed: 01/01/2023] Open
Abstract
In the decade since the human genome sequence was declared complete, the development of next generation sequencing (NGS) or "deep" sequencing to deliver cost-effective genomic sequencing has influenced advances beyond its primary application and changed the research landscape in many other areas. This review will survey recent applications of NGS which have broadened the understanding of natural antibody repertoires (the "antibodyome") and how these evolve in response to viral infection. We will also report examples where deep sequencing of binding populations, derived from both natural and synthetic repertoires, have been used to benefit antibody engineering. This knowledge will ultimately lead to the design of more effective biological drugs and vaccines.
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25
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Abstract
The herpes zoster vaccine is made using high doses of live attenuated varicella/zoster virus. The vaccine is well tolerated and has few adverse effects: the most common one is pain at the injection site. Complications can occur mainly in persons who had prior zoster keratitis or uveitis. The vaccine can prevent this disease with low mortality but high morbidity.
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