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Martini V, Silvestri Y, Ciurea A, Möller B, Danelon G, Flamigni F, Jarrossay D, Kwee I, Foglierini M, Rinaldi A, Cecchinato V, Uguccioni M. Patients with ankylosing spondylitis present a distinct CD8 T cell subset with osteogenic and cytotoxic potential. RMD Open 2024; 10:e003926. [PMID: 38395454 PMCID: PMC10895246 DOI: 10.1136/rmdopen-2023-003926] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
OBJECTIVES Ankylosing spondylitis (AS) is a chronic inflammatory rheumatic disease affecting mainly the axial skeleton. Peripheral involvement (arthritis, enthesitis and dactylitis) and extra-musculoskeletal manifestations, including uveitis, psoriasis and bowel inflammation, occur in a relevant proportion of patients. AS is responsible for chronic and severe back pain caused by local inflammation that can lead to osteoproliferation and ultimately spinal fusion. The association of AS with the human leucocyte antigen-B27 gene, together with elevated levels of chemokines, CCL17 and CCL22, in the sera of patients with AS, led us to study the role of CCR4+ T cells in the disease pathogenesis. METHODS CD8+CCR4+ T cells isolated from the blood of patients with AS (n=76) or healthy donors were analysed by multiparameter flow cytometry, and gene expression was evaluated by RNA sequencing. Patients with AS were stratified according to the therapeutic regimen and current disease score. RESULTS CD8+CCR4+ T cells display a distinct effector phenotype and upregulate the inflammatory chemokine receptors CCR1, CCR5, CX3CR1 and L-selectin CD62L, indicating an altered migration ability. CD8+CCR4+ T cells expressing CX3CR1 present an enhanced cytotoxic profile, expressing both perforin and granzyme B. RNA-sequencing pathway analysis revealed that CD8+CCR4+ T cells from patients with active disease significantly upregulate genes promoting osteogenesis, a core process in AS pathogenesis. CONCLUSIONS Our results shed light on a new molecular mechanism by which T cells may selectively migrate to inflammatory loci, promote new bone formation and contribute to the pathological ossification process observed in AS.
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Affiliation(s)
- Veronica Martini
- Institute for Research in Biomedicine, Universitá della Svizzera italiana, Bellinzona, Switzerland
| | - Ylenia Silvestri
- Institute for Research in Biomedicine, Universitá della Svizzera italiana, Bellinzona, Switzerland
| | - Adrian Ciurea
- Department of Rheumatology, University of Zurich, University Hospital Zurich, Zurich, Switzerland
| | - Burkhard Möller
- Department of Rheumatology and Immunology, Inselspital-University Hospital Bern, University of Bern, Bern, Switzerland
| | - Gabriela Danelon
- Institute for Research in Biomedicine, Universitá della Svizzera italiana, Bellinzona, Switzerland
| | - Flavio Flamigni
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - David Jarrossay
- Institute for Research in Biomedicine, Universitá della Svizzera italiana, Bellinzona, Switzerland
| | - Ivo Kwee
- Institute for Research in Biomedicine, Universitá della Svizzera italiana, Bellinzona, Switzerland
| | - Mathilde Foglierini
- Institute for Research in Biomedicine, Universitá della Svizzera italiana, Bellinzona, Switzerland
| | - Andrea Rinaldi
- Institute of Oncology Research, Universitá della Svizzera italiana, Bellinzona, Switzerland
| | - Valentina Cecchinato
- Institute for Research in Biomedicine, Universitá della Svizzera italiana, Bellinzona, Switzerland
| | - Mariagrazia Uguccioni
- Institute for Research in Biomedicine, Universitá della Svizzera italiana, Bellinzona, Switzerland
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2
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Banga R, Procopio FA, Lana E, Gladkov GT, Roseto I, Parsons EM, Lian X, Armani-Tourret M, Bellefroid M, Gao C, Kauzlaric A, Foglierini M, Alfageme-Abello O, Sluka SHM, Munoz O, Mastrangelo A, Fenwick C, Muller Y, Mkindi CG, Daubenberger C, Cavassini M, Trunfio R, Déglise S, Corpataux JM, Delorenzi M, Lichterfeld M, Pantaleo G, Perreau M. Lymph node dendritic cells harbor inducible replication-competent HIV despite years of suppressive ART. Cell Host Microbe 2023; 31:1714-1731.e9. [PMID: 37751747 PMCID: PMC11068440 DOI: 10.1016/j.chom.2023.08.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 02/13/2023] [Revised: 06/02/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023]
Abstract
Although gut and lymph node (LN) memory CD4 T cells represent major HIV and simian immunodeficiency virus (SIV) tissue reservoirs, the study of the role of dendritic cells (DCs) in HIV persistence has long been limited to the blood due to difficulties to access lymphoid tissue samples. In this study, we show that LN migratory and resident DC subpopulations harbor distinct phenotypic and transcriptomic profiles. Interestingly, both LN DC subpopulations contain HIV intact provirus and inducible replication-competent HIV despite the expression of the antiviral restriction factor SAMHD1. Notably, LN DC subpopulations isolated from HIV-infected individuals treated for up to 14 years are transcriptionally silent but harbor replication-competent virus that can be induced upon TLR7/8 stimulation. Taken together, these results uncover a potential important contribution of LN DCs to HIV infection in the presence of ART.
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Affiliation(s)
- Riddhima Banga
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Francesco Andrea Procopio
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Erica Lana
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | | | | | - Elizabeth M Parsons
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiaodong Lian
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | - Ce Gao
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Annamaria Kauzlaric
- Translational Bioinformatics and Statistics Department of Oncology, University of Lausanne Swiss Cancer Center, Lausanne, Switzerland
| | - Mathilde Foglierini
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Oscar Alfageme-Abello
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Susanna H M Sluka
- Newborn Screening Switzerland, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Olivia Munoz
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Andrea Mastrangelo
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Craig Fenwick
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Yannick Muller
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Catherine Gerald Mkindi
- Ifakara Health Institute, Bagamoyo, United Republic of Tanzania; Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Claudia Daubenberger
- Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, 4001 Basel, Switzerland
| | - Matthias Cavassini
- Services of Infectious Diseases, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Rafael Trunfio
- Services of Vascular Surgery, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Sébastien Déglise
- Services of Vascular Surgery, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Jean-Marc Corpataux
- Services of Vascular Surgery, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Mauro Delorenzi
- Translational Bioinformatics and Statistics Department of Oncology, University of Lausanne Swiss Cancer Center, Lausanne, Switzerland
| | - Mathias Lichterfeld
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
| | - Giuseppe Pantaleo
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland; Swiss Vaccine Research Institute, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
| | - Matthieu Perreau
- Services of Immunology and Allergy, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland.
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3
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Fallet B, Foglierini M, Porret R, Alcaraz A, Sauvage C, Jenelten R, Caplanusi T, Gilliet M, Perez L, Fenwick C, Genolet R, Harari A, Bobisse S, Gotardo R, Pantaleo G, Muller YD. Intradermal skin test with mRNA vaccines as a surrogate marker of T cell immunity in immunocompromised patients. J Infect 2023:S0163-4453(23)00329-8. [PMID: 37321353 DOI: 10.1016/j.jinf.2023.06.005] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023]
Abstract
OBJECTIVES Intradermal skin test (IDT) with mRNA vaccines may represent a simple, reliable, and affordable tool to measure T cell response in immunocompromised patients who failed to mount serological responses following vaccination with mRNA covid-19 vaccines. METHODS We compared anti-SARS-CoV-2 antibodies and cellular responses in vaccinated immunocompromised patients (n=58), healthy seronegative naive controls (NC, n=8), and healthy seropositive vaccinated controls (VC, n=32) by Luminex, spike-induced IFN-γ Elispot and an IDT. A skin biopsy 24h after IDT and single-cell RNAseq was performed in three vaccinated volunteers. RESULTS Twenty-five percent of seronegative NC had a positive Elispot (2/8) and IDT (1/4), compared to 95% (20/21) and 93% (28/30) in seropositive VC, respectively. Single-cell RNAseq data in the skin of VC showed a predominant mixed population of effector helper and cytotoxic T cells. The TCR repertoire revealed 18/1064 clonotypes with known specificities against SARS-CoV-2, among which six were spike-specific. Seronegative immunocompromised patients with positive Elispot and IDT were in 83% (5/6) treated with B cell-depleting reagents, while those with negative IDT were all transplant recipients. CONCLUSIONS Our results indicate that delayed local reaction to IDT reflects vaccine-induced T-cell immunity opening new perspectives to monitor seronegative patients and elderly populations with waning immunity.
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Affiliation(s)
- Benedict Fallet
- Division of Immunology and Allergy, University Hospital of Lausanne, Switzerland
| | - Mathilde Foglierini
- Division of Immunology and Allergy, University Hospital of Lausanne, Switzerland
| | - Raphael Porret
- Division of Immunology and Allergy, University Hospital of Lausanne, Switzerland
| | - Ana Alcaraz
- Division of Immunology and Allergy, University Hospital of Lausanne, Switzerland
| | - Christophe Sauvage
- Center for Cell Immunotherapy, Department of Oncology and Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne, Lausanne CH-1066, Switzerland
| | - Raphael Jenelten
- Department of Dermatology and venereology, University Hospital of Lausanne, Switzerland
| | - Teofila Caplanusi
- Department of Dermatology and venereology, University Hospital of Lausanne, Switzerland
| | - Michel Gilliet
- Department of Dermatology and venereology, University Hospital of Lausanne, Switzerland; University of Lausanne, Faculty of Biology and Medicine, Lausanne, Switzerland
| | - Laurent Perez
- Division of Immunology and Allergy, University Hospital of Lausanne, Switzerland; University of Lausanne, Faculty of Biology and Medicine, Lausanne, Switzerland
| | - Craig Fenwick
- Division of Immunology and Allergy, University Hospital of Lausanne, Switzerland
| | - Raphael Genolet
- Center for Cell Immunotherapy, Department of Oncology and Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne, Lausanne CH-1066, Switzerland
| | - Alexandre Harari
- Center for Cell Immunotherapy, Department of Oncology and Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne, Lausanne CH-1066, Switzerland; University of Lausanne, Faculty of Biology and Medicine, Lausanne, Switzerland
| | - Sara Bobisse
- Center for Cell Immunotherapy, Department of Oncology and Ludwig Institute for Cancer Research, Lausanne Branch, University of Lausanne, Lausanne CH-1066, Switzerland
| | - Raphael Gotardo
- Biomedical Data Science Center, University Hospital of Lausanne, Switzerland; University of Lausanne, Faculty of Biology and Medicine, Lausanne, Switzerland; Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Giuseppe Pantaleo
- Division of Immunology and Allergy, University Hospital of Lausanne, Switzerland; University of Lausanne, Faculty of Biology and Medicine, Lausanne, Switzerland
| | - Yannick D Muller
- Division of Immunology and Allergy, University Hospital of Lausanne, Switzerland; University of Lausanne, Faculty of Biology and Medicine, Lausanne, Switzerland.
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4
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Hu M, Notarbartolo S, Foglierini M, Jovic S, Mele F, Jarrossay D, Lanzavecchia A, Cassotta A, Sallusto F. Clonal composition and persistence of antigen-specific circulating T follicular helper cells. Eur J Immunol 2023; 53:e2250190. [PMID: 36480793 PMCID: PMC10107804 DOI: 10.1002/eji.202250190] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/16/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
T follicular helper (TFH ) cells play an essential role in promoting B cell responses and antibody affinity maturation in germinal centers (GC). A subset of memory CD4+ T cells expressing the chemokine receptor CXCR5 has been described in human blood as phenotypically and clonally related to GC TFH cells. However, the antigen specificity and relationship of these circulating TFH (cTFH ) cells with other memory CD4+ T cells remain poorly defined. Combining antigenic stimulation and T cell receptor (TCR) Vβ sequencing, we found T cells specific to tetanus toxoid (TT), influenza vaccine (Flu), or Candida albicans (C.alb) in both cTFH and non-cTFH subsets, although with different frequencies and effector functions. Interestingly, cTFH and non-cTFH cells specific for C.alb or TT had a largely overlapping TCR Vβ repertoire while the repertoire of Flu-specific cTFH and non-cTFH cells was distinct. Furthermore, Flu-specific but not C.alb-specific PD-1+ cTFH cells had a "GC TFH -like" phenotype, with overexpression of IL21, CXCL13, and BCL6. Longitudinal analysis of serial blood donations showed that Flu-specific cTFH and non-cTFH cells persisted as stable repertoires for years. Collectively, our study provides insights on the relationship of cTFH with non-cTFH cells and on the heterogeneity and persistence of antigen-specific human cTFH cells.
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Affiliation(s)
- Mengyun Hu
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.,Present address: Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Stanford, CA, USA
| | - Samuele Notarbartolo
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.,Present address: National Institute of Molecular Genetics, Milano, Italy
| | - Mathilde Foglierini
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.,Present address: Service d'immunologie et d'allergie, CHUV, Lausanne, Switzerland
| | - Sandra Jovic
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Federico Mele
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - David Jarrossay
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | | | - Antonino Cassotta
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.,Institute of Microbiology, ETH Zurich, Zurich, Switzerland
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5
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Antonello P, Pizzagalli DU, Foglierini M, Melgrati S, Radice E, Thelen S, Thelen M. ACKR3 promotes CXCL12/CXCR4-mediated cell-to-cell-induced lymphoma migration through LTB4 production. Front Immunol 2023; 13:1067885. [PMID: 36713377 PMCID: PMC9878562 DOI: 10.3389/fimmu.2022.1067885] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/22/2022] [Indexed: 01/14/2023] Open
Abstract
Chemotaxis is an essential physiological process, often harnessed by tumors for metastasis. CXCR4, its ligand CXCL12 and the atypical receptor ACKR3 are overexpressed in many human cancers. Interfering with this axis by ACKR3 deletion impairs lymphoma cell migration towards CXCL12. Here, we propose a model of how ACKR3 controls the migration of the diffused large B-cell lymphoma VAL cells in vitro and in vivo in response to CXCL12. VAL cells expressing full-length ACKR3, but not a truncated version missing the C-terminus, can support the migration of VAL cells lacking ACKR3 (VAL-ko) when allowed to migrate together. This migration of VAL-ko cells is pertussis toxin-sensitive suggesting the involvement of a Gi-protein coupled receptor. RNAseq analysis indicate the expression of chemotaxis-mediating LTB4 receptors in VAL cells. We found that LTB4 acts synergistically with CXCL12 in stimulating the migration of VAL cells. Pharmacologic or genetic inhibition of BLT1R markedly reduces chemotaxis towards CXCL12 suggesting that LTB4 enhances in a contact-independent manner the migration of lymphoma cells. The results unveil a novel mechanism of cell-to-cell-induced migration of lymphoma.
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Affiliation(s)
- Paola Antonello
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
- Graduate School of Cellular and Molecular Sciences, University of Bern, Bern, Switzerland
| | - Diego U. Pizzagalli
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
- Università della Svizzera italiana, Euler Institute, Lugano-Viganello, Switzerland
| | - Mathilde Foglierini
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Serena Melgrati
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
- Graduate School of Cellular and Molecular Sciences, University of Bern, Bern, Switzerland
| | - Egle Radice
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Sylvia Thelen
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Marcus Thelen
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
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6
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Low JS, Jerak J, Tortorici MA, McCallum M, Pinto D, Cassotta A, Foglierini M, Mele F, Abdelnabi R, Weynand B, Noack J, Montiel-Ruiz M, Bianchi S, Benigni F, Sprugasci N, Joshi A, Bowen JE, Stewart C, Rexhepaj M, Walls AC, Jarrossay D, Morone D, Paparoditis P, Garzoni C, Ferrari P, Ceschi A, Neyts J, Purcell LA, Snell G, Corti D, Lanzavecchia A, Veesler D, Sallusto F. ACE2-binding exposes the SARS-CoV-2 fusion peptide to broadly neutralizing coronavirus antibodies. Science 2022; 377:735-742. [PMID: 35857703 PMCID: PMC9348755 DOI: 10.1126/science.abq2679] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [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: 03/28/2022] [Accepted: 07/03/2022] [Indexed: 12/14/2022]
Abstract
The coronavirus spike glycoprotein attaches to host receptors and mediates viral fusion. Using a broad screening approach, we isolated seven monoclonal antibodies (mAbs) that bind to all human-infecting coronavirus spike proteins from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immune donors. These mAbs recognize the fusion peptide and acquire affinity and breadth through somatic mutations. Despite targeting a conserved motif, only some mAbs show broad neutralizing activity in vitro against alpha- and betacoronaviruses, including animal coronaviruses WIV-1 and PDF-2180. Two selected mAbs also neutralize Omicron BA.1 and BA.2 authentic viruses and reduce viral burden and pathology in vivo. Structural and functional analyses showed that the fusion peptide-specific mAbs bound with different modalities to a cryptic epitope hidden in prefusion stabilized spike, which became exposed upon binding of angiotensin-converting enzyme 2 (ACE2) or ACE2-mimicking mAbs.
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Affiliation(s)
- Jun Siong Low
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
- Institute of Microbiology, ETH Zürich, 8093 Zurich, Switzerland
| | - Josipa Jerak
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
- Institute of Microbiology, ETH Zürich, 8093 Zurich, Switzerland
| | | | - Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Dora Pinto
- Humabs BioMed SA (subsidiary of Vir Biotechnology), 6500 Bellinzona, Switzerland
| | - Antonino Cassotta
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Mathilde Foglierini
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Federico Mele
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Rana Abdelnabi
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
| | - Birgit Weynand
- KU Leuven Department of Imaging and Pathology, Translational Cell and Tissue Research, B-3000 Leuven, Belgium
| | - Julia Noack
- Vir Biotechnology, San Francisco, CA 94158, USA
| | | | - Siro Bianchi
- Humabs BioMed SA (subsidiary of Vir Biotechnology), 6500 Bellinzona, Switzerland
| | - Fabio Benigni
- Humabs BioMed SA (subsidiary of Vir Biotechnology), 6500 Bellinzona, Switzerland
| | - Nicole Sprugasci
- Humabs BioMed SA (subsidiary of Vir Biotechnology), 6500 Bellinzona, Switzerland
| | - Anshu Joshi
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - John E. Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Megi Rexhepaj
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Alexandra C. Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - David Jarrossay
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Diego Morone
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Philipp Paparoditis
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
| | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco; 6900 Lugano, Switzerland
| | - Paolo Ferrari
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland
- Department of Internal Medicine, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland
- Prince of Wales Hospital Clinical School, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Alessandro Ceschi
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, 6900 Lugano, Switzerland
- Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland
- Clinical Trial Unit, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, B-3000 Leuven, Belgium
- Global Virus Network, Baltimore, MD 21201, USA
| | | | | | - Davide Corti
- Humabs BioMed SA (subsidiary of Vir Biotechnology), 6500 Bellinzona, Switzerland
| | - Antonio Lanzavecchia
- Humabs BioMed SA (subsidiary of Vir Biotechnology), 6500 Bellinzona, Switzerland
- National Institute of Molecular Genetics, 20122 Milano, Italy
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland
- Institute of Microbiology, ETH Zürich, 8093 Zurich, Switzerland
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7
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Fenwick C, Turelli P, Perez L, Pellaton C, Esteves-Leuenberger L, Farina A, Campos J, Lana E, Fiscalini F, Raclot C, Pojer F, Lau K, Demurtas D, Descatoire M, Joo VS, Foglierini M, Noto A, Abdelnabi R, Foo CS, Vangeel L, Neyts J, Du W, Bosch BJ, Veldman G, Leyssen P, Thiel V, LeGrand R, Lévy Y, Trono D, Pantaleo G. A highly potent antibody effective against SARS-CoV-2 variants of concern. Cell Rep 2021; 37:109814. [PMID: 34599871 PMCID: PMC8452523 DOI: 10.1016/j.celrep.2021.109814] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/09/2021] [Accepted: 09/17/2021] [Indexed: 12/11/2022] Open
Abstract
Control of the ongoing SARS-CoV-2 pandemic is endangered by the emergence of viral variants with increased transmission efficiency, resistance to marketed therapeutic antibodies, and reduced sensitivity to vaccine-induced immunity. Here, we screen B cells from COVID-19 donors and identify P5C3, a highly potent and broadly neutralizing monoclonal antibody with picomolar neutralizing activity against all SARS-CoV-2 variants of concern (VOCs) identified to date. Structural characterization of P5C3 Fab in complex with the spike demonstrates a neutralizing activity defined by a large buried surface area, highly overlapping with the receptor-binding domain (RBD) surface necessary for ACE2 interaction. We further demonstrate that P5C3 shows complete prophylactic protection in the SARS-CoV-2-infected hamster challenge model. These results indicate that P5C3 opens exciting perspectives either as a prophylactic agent in immunocompromised individuals with poor response to vaccination or as combination therapy in SARS-CoV-2-infected individuals.
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Affiliation(s)
- Craig Fenwick
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Priscilla Turelli
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Laurent Perez
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Céline Pellaton
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Line Esteves-Leuenberger
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Alex Farina
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jérémy Campos
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Erica Lana
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Flurin Fiscalini
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Charlène Raclot
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Florence Pojer
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Kelvin Lau
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Davide Demurtas
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Marc Descatoire
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Victor S Joo
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Mathilde Foglierini
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Alessandra Noto
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Rana Abdelnabi
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
| | - Caroline S Foo
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
| | - Laura Vangeel
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
| | - Wenjuan Du
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Berend-Jan Bosch
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | | | - Pieter Leyssen
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, 3000 Leuven, Belgium
| | - Volker Thiel
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Roger LeGrand
- CEA, Université Paris Sud 11, INSERM U1184, Center for Immunology of Viral Infections and Autoimmune Diseases, IDMIT Department, IBFJ, Fontenay-aux-Roses, France
| | - Yves Lévy
- VRI, Université Paris-Est Créteil, Faculté de Médicine, INSERM U955, 94010 Créteil, France; INSERM U955, Equipe 16, Créteil, France; AP-HP, Ho^pital Henri-Mondor Albert-Chenevier, Service d'Immunologie Clinique et Maladies Infectieuses, Créteil, France
| | - Didier Trono
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
| | - Giuseppe Pantaleo
- Service of Immunology and Allergy, Department of Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland; VRI, Université Paris-Est Créteil, Faculté de Médicine, INSERM U955, 94010 Créteil, France; Swiss Vaccine Research Institute, Lausanne University Hospital and University of Lausanne, Switzerland.
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8
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Cheung CSF, Fruehwirth A, Paparoditis PCG, Shen CH, Foglierini M, Joyce MG, Leung K, Piccoli L, Rawi R, Silacci-Fregni C, Tsybovsky Y, Verardi R, Wang L, Wang S, Yang ES, Zhang B, Zhang Y, Chuang GY, Corti D, Mascola JR, Shapiro L, Kwong PD, Lanzavecchia A, Zhou T. Identification and Structure of a Multidonor Class of Head-Directed Influenza-Neutralizing Antibodies Reveal the Mechanism for Its Recurrent Elicitation. Cell Rep 2021; 32:108088. [PMID: 32877670 DOI: 10.1016/j.celrep.2020.108088] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 05/12/2020] [Accepted: 08/07/2020] [Indexed: 12/11/2022] Open
Abstract
Multidonor antibodies are of interest for vaccine design because they can in principle be elicited in the general population by a common set of immunogens. For influenza, multidonor antibodies have been observed against the hemagglutinin (HA) stem, but not the immunodominant HA head. Here, we identify and characterize a multidonor antibody class (LPAF-a class) targeting the HA head. This class exhibits potent viral entry inhibition against H1N1 A/California/04/2009 (CA09) virus. LPAF-a class antibodies derive from the HV2-70 gene and contain a "Tyr-Gly-Asp"-motif, which occludes the HA-sialic acid binding site as revealed by a co-crystal structure with HA. Both germline-reverted and mature LPAF antibodies potently neutralize CA09 virus and have nanomolar affinities for CA09 HA. Moreover, increased frequencies for LPFA-a class antibodies are observed in humans after a single vaccination. Overall, this work highlights the identification of a multidonor class of head-directed influenza-neutralizing antibodies and delineates the mechanism of their recurrent elicitation in humans.
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Affiliation(s)
- Crystal Sao-Fong Cheung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexander Fruehwirth
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | | | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mathilde Foglierini
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - M Gordon Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Luca Piccoli
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chiara Silacci-Fregni
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Raffaello Verardi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Davide Corti
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland.
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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9
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Low JS, Vaqueirinho D, Mele F, Foglierini M, Jerak J, Perotti M, Jarrossay D, Jovic S, Perez L, Cacciatore R, Terrot T, Pellanda AF, Biggiogero M, Garzoni C, Ferrari P, Ceschi A, Lanzavecchia A, Sallusto F, Cassotta A. Clonal analysis of immunodominance and cross-reactivity of the CD4 T cell response to SARS-CoV-2. Science 2021; 372:1336-1341. [PMID: 34006597 PMCID: PMC8168615 DOI: 10.1126/science.abg8985] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [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: 02/03/2021] [Accepted: 05/13/2021] [Indexed: 12/14/2022]
Abstract
The identification of CD4+ T cell epitopes is instrumental for the design of subunit vaccines for broad protection against coronaviruses. Here we demonstrate in COVID-19-recovered individuals a robust CD4+ T cell response to naturally processed SARS-CoV-2 spike (S) and nucleoprotein (N), including effector, helper, and memory T cells. By characterizing 2943 S-reactive T cell clones from 34 individuals, we found that 34% of clones and 93% of individuals recognized a conserved immunodominant S346-365 region within the RBD comprising nested HLA-DR- and HLA-DP-restricted epitopes. Using pre- and post-COVID-19 samples and S proteins from endemic coronaviruses, we identify cross-reactive T cells targeting multiple S protein sites. The immunodominant and cross-reactive epitopes identified can inform vaccination strategies to counteract emerging SARS-CoV-2 variants.
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Affiliation(s)
- Jun Siong Low
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Daniela Vaqueirinho
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Federico Mele
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Mathilde Foglierini
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Josipa Jerak
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Michela Perotti
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - David Jarrossay
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Sandra Jovic
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Laurent Perez
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Rosalia Cacciatore
- Laboratory of Immunogenetics, Department of Transfusion Medicine and Immuno-Hematology, Fondazione I.R.C.C.S. Policlinico S. Matteo, 27100 Pavia, Italy
| | - Tatiana Terrot
- Clinical Trial Unit, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland
| | | | - Maira Biggiogero
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Paolo Ferrari
- Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland.,Department of Internal Medicine, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland.,Prince of Wales Hospital Clinical School, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Alessandro Ceschi
- Clinical Trial Unit, Ente Ospedaliero Cantonale, 6500 Bellinzona, Switzerland.,Faculty of Biomedical Sciences, Università della Svizzera italiana, 6900 Lugano, Switzerland.,Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Sciences of Southern Switzerland, Ente Ospedaliero Cantonale, 6900 Lugano, Switzerland.,Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, 8091 Zurich, Switzerland
| | | | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland. .,Institute of Microbiology, ETH Zürich, 8093 Zurich, Switzerland
| | - Antonino Cassotta
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland.
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10
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Radice E, Ameti R, Melgrati S, Foglierini M, Antonello P, Stahl RAK, Thelen S, Jarrossay D, Thelen M. Marginal Zone Formation Requires ACKR3 Expression on B Cells. Cell Rep 2021; 32:107951. [PMID: 32755592 DOI: 10.1016/j.celrep.2020.107951] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 05/12/2020] [Accepted: 07/02/2020] [Indexed: 12/27/2022] Open
Abstract
The marginal zone (MZ) contributes to the highly organized spleen microarchitecture. We show that expression of atypical chemokine receptor 3 (ACKR3) defines two equal-sized populations of mouse MZ B cells (MZBs). ACKR3 is required for development of a functional MZ and for positioning of MZBs. Deletion of ACKR3 on B cells distorts the MZ, and MZBs fail to deliver antigens to follicles, reducing humoral responses. Reconstitution of MZ-deficient CD19ko mice shows that ACKR3- MZBs can differentiate into ACKR3+ MZBs, but not vice versa. The lack of a MZ is rescued by adoptive transfer of ACKR3-sufficient, and less by ACKR3-deficient, follicular B cells (FoBs); hence, ACKR3 expression is crucial for establishment of the MZ. The inability of CD19ko mice to respond to T-independent antigen is rescued when ACKR3-proficient, but not ACKR3-deficient, FoBs are transferred. Accordingly, ACKR3-deficient FoBs are able to reconstitute the MZ if the niche is pre-established by ACKR3-proficient MZBs.
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Affiliation(s)
- Egle Radice
- Università della Svizzera Italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, 6500 Bellinzona, Switzerland; Graduate School of Cellular and Molecular Sciences, University of Bern, 3012 Bern, Switzerland
| | - Rafet Ameti
- Università della Svizzera Italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, 6500 Bellinzona, Switzerland; Graduate School of Cellular and Molecular Sciences, University of Bern, 3012 Bern, Switzerland
| | - Serena Melgrati
- Università della Svizzera Italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, 6500 Bellinzona, Switzerland; Graduate School of Cellular and Molecular Sciences, University of Bern, 3012 Bern, Switzerland
| | - Mathilde Foglierini
- Università della Svizzera Italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, 6500 Bellinzona, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Paola Antonello
- Università della Svizzera Italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, 6500 Bellinzona, Switzerland; Graduate School of Cellular and Molecular Sciences, University of Bern, 3012 Bern, Switzerland
| | - Rolf A K Stahl
- III Medizinische Klinik, University Hospital Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Sylvia Thelen
- Università della Svizzera Italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, 6500 Bellinzona, Switzerland
| | - David Jarrossay
- Università della Svizzera Italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, 6500 Bellinzona, Switzerland
| | - Marcus Thelen
- Università della Svizzera Italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, 6500 Bellinzona, Switzerland.
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11
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Chen Y, Xu K, Piccoli L, Foglierini M, Tan J, Jin W, Gorman J, Tsybovsky Y, Zhang B, Traore B, Silacci-Fregni C, Daubenberger C, Crompton PD, Geiger R, Sallusto F, Kwong PD, Lanzavecchia A. Structural basis of malaria RIFIN binding by LILRB1-containing antibodies. Nature 2021; 592:639-643. [PMID: 33790470 PMCID: PMC8068667 DOI: 10.1038/s41586-021-03378-6] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/19/2021] [Indexed: 02/02/2023]
Abstract
Some Plasmodium falciparum repetitive interspersed families of polypeptides (RIFINs)-variant surface antigens that are expressed on infected erythrocytes1-bind to the inhibitory receptor LAIR1, and insertion of DNA that encodes LAIR1 into immunoglobulin genes generates RIFIN-specific antibodies2,3. Here we address the general relevance of this finding by searching for antibodies that incorporate LILRB1, another inhibitory receptor that binds to β2 microglobulin and RIFINs through their apical domains4,5. By screening plasma from a cohort of donors from Mali, we identified individuals with LILRB1-containing antibodies. B cell clones isolated from three donors showed large DNA insertions in the switch region that encodes non-apical LILRB1 extracellular domain 3 and 4 (D3D4) or D3 alone in the variable-constant (VH-CH1) elbow. Through mass spectrometry and binding assays, we identified a large set of RIFINs that bind to LILRB1 D3. Crystal and cryo-electron microscopy structures of a RIFIN in complex with either LILRB1 D3D4 or a D3D4-containing antibody Fab revealed a mode of RIFIN-LILRB1 D3 interaction that is similar to that of RIFIN-LAIR1. The Fab showed an unconventional triangular architecture with the inserted LILRB1 domains opening up the VH-CH1 elbow without affecting VH-VL or CH1-CL pairing. Collectively, these findings show that RIFINs bind to LILRB1 through D3 and illustrate, with a naturally selected example, the general principle of creating novel antibodies by inserting receptor domains into the VH-CH1 elbow.
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Affiliation(s)
- Yiwei Chen
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Kai Xu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Luca Piccoli
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Mathilde Foglierini
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Joshua Tan
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Wenjie Jin
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Boubacar Traore
- Malaria Research and Training Center, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Chiara Silacci-Fregni
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Claudia Daubenberger
- Swiss Tropical and Public Health Institute, University of Basel, Basel, Switzerland
| | - Peter D Crompton
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Roger Geiger
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.
- Humabs BioMed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
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12
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Cassotta A, Paparoditis P, Geiger R, Mettu RR, Landry SJ, Donati A, Benevento M, Foglierini M, Lewis DJM, Lanzavecchia A, Sallusto F. Deciphering and predicting CD4+ T cell immunodominance of influenza virus hemagglutinin. J Exp Med 2021; 217:151933. [PMID: 32644114 PMCID: PMC7537397 DOI: 10.1084/jem.20200206] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 02/05/2020] [Revised: 04/21/2020] [Accepted: 05/29/2020] [Indexed: 01/07/2023] Open
Abstract
The importance of CD4+ T helper (Th) cells is well appreciated in view of their essential role in the elicitation of antibody and cytotoxic T cell responses. However, the mechanisms that determine the selection of immunodominant epitopes within complex protein antigens remain elusive. Here, we used ex vivo stimulation of memory T cells and screening of naive and memory T cell libraries, combined with T cell cloning and TCR sequencing, to dissect the human naive and memory CD4+ T cell repertoire against the influenza pandemic H1 hemagglutinin (H1-HA). We found that naive CD4+ T cells have a broad repertoire, being able to recognize naturally processed as well as cryptic peptides spanning the whole H1-HA sequence. In contrast, memory Th cells were primarily directed against just a few immunodominant peptides that were readily detected by mass spectrometry–based MHC-II peptidomics and predicted by structural accessibility analysis. Collectively, these findings reveal the presence of a broad repertoire of naive T cells specific for cryptic H1-HA peptides and demonstrate that antigen processing represents a major constraint determining immunodominance.
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Affiliation(s)
- Antonino Cassotta
- Institute for Research in Biomedicine, Università della Svizzera italiana, Faculty of Biomedical Sciences, Bellinzona, Switzerland.,Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Philipp Paparoditis
- Institute for Research in Biomedicine, Università della Svizzera italiana, Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Roger Geiger
- Institute for Research in Biomedicine, Università della Svizzera italiana, Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Ramgopal R Mettu
- Department of Computer Science, Tulane University, New Orleans, LA
| | - Samuel J Landry
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA
| | - Alessia Donati
- Institute for Research in Biomedicine, Università della Svizzera italiana, Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Marco Benevento
- Institute for Research in Biomedicine, Università della Svizzera italiana, Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Mathilde Foglierini
- Institute for Research in Biomedicine, Università della Svizzera italiana, Faculty of Biomedical Sciences, Bellinzona, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - David J M Lewis
- Surrey Clinical Research Centre, University of Surrey, Guildford, UK
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera italiana, Faculty of Biomedical Sciences, Bellinzona, Switzerland
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, Faculty of Biomedical Sciences, Bellinzona, Switzerland.,Institute of Microbiology, ETH Zürich, Zürich, Switzerland
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13
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Foglierini M, Pappas L, Lanzavecchia A, Corti D, Perez L. AncesTree: An interactive immunoglobulin lineage tree visualizer. PLoS Comput Biol 2020; 16:e1007731. [PMID: 32649725 PMCID: PMC7375605 DOI: 10.1371/journal.pcbi.1007731] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 02/13/2020] [Revised: 07/22/2020] [Accepted: 06/14/2020] [Indexed: 12/22/2022] Open
Abstract
High-throughput sequencing of human immunoglobulin genes allows analysis of antibody repertoires and the reconstruction of clonal lineage evolution. The study of antibodies (Abs) affinity maturation is of specific interest to understand the generation of Abs with high affinity or broadly neutralizing activities. Moreover, phylogenic analysis enables the identification of the key somatic mutations required to achieve optimal antigen binding. The Immcantation framework provides a start-to-finish set of analytical methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) data. Furthermore, Immcantation's Change-O package has developed IgPhyML, an algorithm designed to build specifically immunoglobulin (Ig) phylogenic trees. Meanwhile Phylip, an algorithm that has been originally developed for applications in ecology and macroevolution, can also be used for the phylogenic reconstruction of antibodies maturation pathway. To complement Ig lineages made by IgPhyML or Dnaml (Phylip), we developed AncesTree, a graphic user interface (GUI) that aims to give researchers the opportunity to interactively explore antibodies clonal evolution. AncesTree displays interactive immunoglobulins phylogenic tree, Ig related mutations and sequence alignments using additional information coming from specialized antibody tools. The GUI is a Java standalone application allowing interaction with Ig tree that can run under Windows, Linux and Mac OS.
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Affiliation(s)
- Mathilde Foglierini
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Leontios Pappas
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Antonio Lanzavecchia
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Davide Corti
- Humabs Biomed SA, Vir Biotechnology, Bellinzona, Switzerland
| | - Laurent Perez
- Università della Svizzera italiana, Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
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14
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Cassotta A, Mikol V, Bertrand T, Pouzieux S, Le Parc J, Ferrari P, Dumas J, Auer M, Deisenhammer F, Gastaldi M, Franciotta D, Silacci-Fregni C, Fernandez Rodriguez B, Giacchetto-Sasselli I, Foglierini M, Jarrossay D, Geiger R, Sallusto F, Lanzavecchia A, Piccoli L. A single T cell epitope drives the neutralizing anti-drug antibody response to natalizumab in multiple sclerosis patients. Nat Med 2019; 25:1402-1407. [PMID: 31501610 PMCID: PMC6795539 DOI: 10.1038/s41591-019-0568-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [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: 04/18/2019] [Accepted: 07/29/2019] [Indexed: 01/08/2023]
Abstract
Natalizumab (NZM), a humanized monoclonal IgG4 antibody to α4
integrins, is used to treat patients with relapsing-remitting multiple sclerosis
(MS)1,2, but in about 6% of the cases persistent
neutralizing anti-drug antibodies (ADAs) are induced leading to therapy
discontinuation3,4. To understand the basis of the
ADA response and the mechanism of ADA-mediated neutralization, we performed an
in-depth analysis of the B and T cell responses in two patients. By
characterizing a large panel of NZM-specific monoclonal antibodies, we found
that, in both patients, the response was polyclonal and targeted different
epitopes of the NZM idiotype. The neutralizing activity was acquired through
somatic mutations and correlated with a slow dissociation rate, a finding that
was supported by structural data. Interestingly, in both patients, the analysis
of the CD4+ T cell response, combined with mass spectrometry-based
peptidomics, revealed a single immunodominant T cell epitope spanning the
FR2-CDR2 region of the NZM light chain. Moreover, a CDR2-modified version of NZM
was not recognized by T cells, while retaining binding to α4 integrins.
Collectively, our integrated analysis identifies the basis of T-B collaboration
that leads to ADA-mediated therapeutic resistance and delineates an approach to
design novel deimmunized antibodies for autoimmune disease and cancer
treatment.
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Affiliation(s)
- Antonino Cassotta
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.,Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Vincent Mikol
- Research Platform, Sanofi R&D, Vitry-sur-Seine, France
| | | | | | | | - Paul Ferrari
- Research Platform, Sanofi R&D, Vitry-sur-Seine, France
| | - Jacques Dumas
- Research Platform, Sanofi R&D, Vitry-sur-Seine, France
| | - Michael Auer
- Department of Neurology, Innsbruck Medical University, Innsbruck, Austria
| | | | - Matteo Gastaldi
- Laboratory of Neuroimmunology, IRCCS Mondino Foundation, Pavia, Italy
| | - Diego Franciotta
- Laboratory of Neuroimmunology, IRCCS Mondino Foundation, Pavia, Italy
| | - Chiara Silacci-Fregni
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | | | | | - Mathilde Foglierini
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - David Jarrossay
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Roger Geiger
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.,Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Luca Piccoli
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland.
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15
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Abstract
Human cytomegalovirus (HCMV) is the leading viral cause of congenital birth defects and is responsible for morbidity and mortality in immunosuppressed individuals. Considerable efforts have been deployed over the last decade to develop a vaccine capable of preventing HCMV infection. However, in recent clinical trials, vaccines showed at best modest efficacy in preventing infection. These findings might be explained by the high level of sequence polymorphism at the genomic level. To investigate if genomic variation also leads to antigenic variation, we performed a bioinformatic sequence analysis and evaluated the percentage of conservation at the amino acid level of all the proteins present in the virion envelope. Using more than two hundred sequences per envelope glycoprotein and analyzing their degree of conservation, we observe that antigenic variation is in large part limited to three proteins. In addition, we demonstrate that the two leading vaccine candidates, the pentamer and gB complexes, are well conserved at the amino acid level. These results suggest that despite genomic polymorphism, antigenic variability is not involved in the modest efficacy observed in the recent clinical trials for a HCMV vaccine. We therefore propose that next-generation vaccines should focus on stabilizing and refining the gB domains needed to induce a protective humoral response.
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Affiliation(s)
- Mathilde Foglierini
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Jessica Marcandalli
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Laurent Perez
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
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16
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Aschenbrenner D, Foglierini M, Jarrossay D, Hu D, Weiner HL, Kuchroo VK, Lanzavecchia A, Notarbartolo S, Sallusto F. Publisher Correction: An immunoregulatory and tissue-residency program modulated by c-MAF in human T H17 cells. Nat Immunol 2018; 20:109. [PMID: 30448856 DOI: 10.1038/s41590-018-0264-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this article initially published, in the legend to Fig. 1b, the description of the frequency of TH17-IL-10+ clones was incomplete for the first group; this should read as follows: "...13 experiments with clones isolated from CCR6+CCR4+CXCR3- T cells...". Also, the label along the vertical axis of the bottom right plot in Figure 5b was incomplete; the correct label is 'IFN-γ+ cells (%)'. Finally, in the first sentence of the final paragraph of the final Results subsection, the description of the regions analyzed was incorrect; that sentence should begin: "DNA motif-enrichment analysis of the subset-specific H3K27ac-positive regions...". The errors have been corrected in the HTML and PDF versions of the article.
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Affiliation(s)
- Dominik Aschenbrenner
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, Bellinzona, Switzerland.,Translational Gastroenterology Unit, NDM Experimental Medicine, University of Oxford, Oxford, UK
| | - Mathilde Foglierini
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, Bellinzona, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - David Jarrossay
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Dan Hu
- Ann Romney Center for Neurologic Diseases and Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Howard L Weiner
- Ann Romney Center for Neurologic Diseases and Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Vijay K Kuchroo
- Ann Romney Center for Neurologic Diseases and Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Samuele Notarbartolo
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, Bellinzona, Switzerland.
| | - Federica Sallusto
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, Bellinzona, Switzerland. .,Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
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17
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Latorre D, Kallweit U, Armentani E, Foglierini M, Mele F, Cassotta A, Jovic S, Jarrossay D, Mathis J, Zellini F, Becher B, Lanzavecchia A, Khatami R, Manconi M, Tafti M, Bassetti CL, Sallusto F. T cells in patients with narcolepsy target self-antigens of hypocretin neurons. Nature 2018; 562:63-68. [PMID: 30232458 DOI: 10.1038/s41586-018-0540-1] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 08/10/2018] [Indexed: 11/09/2022]
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18
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Aschenbrenner D, Foglierini M, Jarrossay D, Hu D, Weiner HL, Kuchroo VK, Lanzavecchia A, Notarbartolo S, Sallusto F. An immunoregulatory and tissue-residency program modulated by c-MAF in human T H17 cells. Nat Immunol 2018; 19:1126-1136. [PMID: 30201991 DOI: 10.1038/s41590-018-0200-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Accepted: 07/22/2018] [Indexed: 12/11/2022]
Abstract
Different types of effector and memory T lymphocytes are induced and maintained in protective or pathological immune responses. Here we characterized two human CD4+ TH17 helper cell subsets that, in the recently activated state, could be distinguished on the basis of their expression of the anti-inflammatory cytokine IL-10. IL-10+ TH17 cells upregulated a variety of genes encoding immunoregulatory molecules, as well as genes whose expression is characteristic of tissue-resident T cells. In contrast, IL-10- TH17 cells maintained a pro-inflammatory gene-expression profile and upregulated the expression of homing receptors that guide recirculation from tissues to blood. Expression of the transcription factor c-MAF was selectively upregulated in IL-10+ TH17 cells, and it was bound to a large set of enhancer-like regions and modulated the immunoregulatory and tissue-residency program. Our results identify c-MAF as a relevant factor that drives two highly divergent post-activation fates of human TH17 cells and provide a framework with which to investigate the role of these cells in physiology and immunopathology.
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Affiliation(s)
- Dominik Aschenbrenner
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, Bellinzona, Switzerland.,Translational Gastroenterology Unit, NDM Experimental Medicine, University of Oxford, Oxford, UK
| | - Mathilde Foglierini
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, Bellinzona, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - David Jarrossay
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Dan Hu
- Ann Romney Center for Neurologic Diseases and Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Howard L Weiner
- Ann Romney Center for Neurologic Diseases and Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Vijay K Kuchroo
- Ann Romney Center for Neurologic Diseases and Evergrande Center for Immunologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, Bellinzona, Switzerland
| | - Samuele Notarbartolo
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, Bellinzona, Switzerland.
| | - Federica Sallusto
- Institute for Research in Biomedicine, Faculty of Biomedical Sciences, Università della Svizzera italiana, Bellinzona, Switzerland. .,Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
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19
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Martinez-Martin N, Marcandalli J, Huang CS, Arthur CP, Perotti M, Foglierini M, Ho H, Dosey AM, Shriver S, Payandeh J, Leitner A, Lanzavecchia A, Perez L, Ciferri C. An Unbiased Screen for Human Cytomegalovirus Identifies Neuropilin-2 as a Central Viral Receptor. Cell 2018; 174:1158-1171.e19. [PMID: 30057110 DOI: 10.1016/j.cell.2018.06.028] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 06/01/2018] [Accepted: 06/13/2018] [Indexed: 02/09/2023]
Abstract
Characterizing cell surface receptors mediating viral infection is critical for understanding viral tropism and developing antiviral therapies. Nevertheless, due to challenges associated with detecting protein interactions on the cell surface, the host receptors of many human pathogens remain unknown. Here, we build a library consisting of most single transmembrane human receptors and implement a workflow for unbiased and high-sensitivity detection of receptor-ligand interactions. We apply this technology to elucidate the long-sought receptor of human cytomegalovirus (HCMV), the leading viral cause of congenital birth defects. We identify neuropilin-2 (Nrp2) as the receptor for HCMV-pentamer infection in epithelial/endothelial cells and uncover additional HCMV interactors. Using a combination of biochemistry, cell-based assays, and electron microscopy, we characterize the pentamer-Nrp2 interaction and determine the architecture of the pentamer-Nrp2 complex. This work represents an important approach to the study of host-pathogen interactions and provides a framework for understanding HCMV infection, neutralization, and the development of novel anti-HCMV therapies.
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Affiliation(s)
| | - Jessica Marcandalli
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland
| | | | | | - Michela Perotti
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland; Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Mathilde Foglierini
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland; Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Hoangdung Ho
- Structural Biology, Genentech, South San Francisco, CA, USA
| | - Annie M Dosey
- Structural Biology, Genentech, South San Francisco, CA, USA
| | | | - Jian Payandeh
- Structural Biology, Genentech, South San Francisco, CA, USA
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Antonio Lanzavecchia
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland; Institute of Microbiology, ETH Zürich, Zürich, Switzerland
| | - Laurent Perez
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Bellinzona, Switzerland.
| | - Claudio Ciferri
- Structural Biology, Genentech, South San Francisco, CA, USA.
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20
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Sallusto F, Cassotta A, Hoces D, Foglierini M, Lanzavecchia A. Do Memory CD4 T Cells Keep Their Cell-Type Programming: Plasticity versus Fate Commitment? T-Cell Heterogeneity, Plasticity, and Selection in Humans. Cold Spring Harb Perspect Biol 2018; 10:cshperspect.a029421. [PMID: 28432133 DOI: 10.1101/cshperspect.a029421] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The wide range of effector and memory T cells is instrumental for immune regulation and tailored mechanisms of protection against pathogens. Here, we will focus on human CD4 T cells and discuss T-cell plasticity and intraclonal diversification in the context of a progressive and selective model of CD4 T-cell differentiation.
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Affiliation(s)
- Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland.,Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Antonino Cassotta
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland.,Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Daniel Hoces
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Mathilde Foglierini
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
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21
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Wang J, Bardelli M, Espinosa DA, Pedotti M, Ng TS, Bianchi S, Simonelli L, Lim EXY, Foglierini M, Zatta F, Jaconi S, Beltramello M, Cameroni E, Fibriansah G, Shi J, Barca T, Pagani I, Rubio A, Broccoli V, Vicenzi E, Graham V, Pullan S, Dowall S, Hewson R, Jurt S, Zerbe O, Stettler K, Lanzavecchia A, Sallusto F, Cavalli A, Harris E, Lok SM, Varani L, Corti D. A Human Bi-specific Antibody against Zika Virus with High Therapeutic Potential. Cell 2017; 171:229-241.e15. [PMID: 28938115 PMCID: PMC5673489 DOI: 10.1016/j.cell.2017.09.002] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [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: 01/17/2017] [Revised: 06/14/2017] [Accepted: 08/31/2017] [Indexed: 11/15/2022]
Abstract
Zika virus (ZIKV), a mosquito-borne flavivirus, causes devastating congenital birth defects. We isolated a human monoclonal antibody (mAb), ZKA190, that potently cross-neutralizes multi-lineage ZIKV strains. ZKA190 is highly effective in vivo in preventing morbidity and mortality of ZIKV-infected mice. NMR and cryo-electron microscopy show its binding to an exposed epitope on DIII of the E protein. ZKA190 Fab binds all 180 E protein copies, altering the virus quaternary arrangement and surface curvature. However, ZIKV escape mutants emerged in vitro and in vivo in the presence of ZKA190, as well as of other neutralizing mAbs. To counter this problem, we developed a bispecific antibody (FIT-1) comprising ZKA190 and a second mAb specific for DII of E protein. In addition to retaining high in vitro and in vivo potencies, FIT-1 robustly prevented viral escape, warranting its development as a ZIKV immunotherapy.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Monoclonal/administration & dosage
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/therapeutic use
- Antibodies, Neutralizing/administration & dosage
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/therapeutic use
- Antibodies, Viral/administration & dosage
- Antibodies, Viral/chemistry
- Antibodies, Viral/therapeutic use
- Cryoelectron Microscopy
- Epitopes
- Humans
- Magnetic Resonance Spectroscopy
- Mice
- Models, Molecular
- Sequence Alignment
- Viral Envelope Proteins/chemistry
- Zika Virus/chemistry
- Zika Virus/immunology
- Zika Virus Infection/therapy
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Affiliation(s)
- Jiaqi Wang
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore
| | - Marco Bardelli
- Insitute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Diego A Espinosa
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, 185 Li Ka Shing Center, 1951 Oxford Street, Berkeley, California, 94720-3370, USA
| | - Mattia Pedotti
- Insitute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Thiam-Seng Ng
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore
| | - Siro Bianchi
- Humabs BioMed SA a subsidiary of Vir Biotechnology, Inc., Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Luca Simonelli
- Insitute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Elisa X Y Lim
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore
| | - Mathilde Foglierini
- Insitute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Fabrizia Zatta
- Humabs BioMed SA a subsidiary of Vir Biotechnology, Inc., Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Stefano Jaconi
- Humabs BioMed SA a subsidiary of Vir Biotechnology, Inc., Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Martina Beltramello
- Humabs BioMed SA a subsidiary of Vir Biotechnology, Inc., Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs BioMed SA a subsidiary of Vir Biotechnology, Inc., Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Guntur Fibriansah
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore
| | - Jian Shi
- Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore; CryoEM unit, Department of Biological Sciences, National University of Singapore, Singapore 117557
| | - Taylor Barca
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, 185 Li Ka Shing Center, 1951 Oxford Street, Berkeley, California, 94720-3370, USA
| | - Isabel Pagani
- Viral Pathogens and Biosafety Unit, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Alicia Rubio
- Viral Pathogens and Biosafety Unit, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Vania Broccoli
- Viral Pathogens and Biosafety Unit, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy; CNR-Institute of Neuroscience, Via Vanvitelli 32, 20129, Milan, Italy
| | - Elisa Vicenzi
- Viral Pathogens and Biosafety Unit, San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Victoria Graham
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Steven Pullan
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Stuart Dowall
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Roger Hewson
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Simon Jurt
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Karin Stettler
- Humabs BioMed SA a subsidiary of Vir Biotechnology, Inc., Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Antonio Lanzavecchia
- Insitute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Federica Sallusto
- Insitute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Andrea Cavalli
- Insitute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, 185 Li Ka Shing Center, 1951 Oxford Street, Berkeley, California, 94720-3370, USA
| | - Shee-Mei Lok
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore.
| | - Luca Varani
- Insitute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland.
| | - Davide Corti
- Humabs BioMed SA a subsidiary of Vir Biotechnology, Inc., Via Mirasole 1, 6500 Bellinzona, Switzerland.
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22
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Pieper K, Tan J, Piccoli L, Foglierini M, Barbieri S, Chen Y, Silacci-Fregni C, Wolf T, Jarrossay D, Anderle M, Abdi A, Ndungu FM, Doumbo OK, Traore B, Tran TM, Jongo S, Zenklusen I, Crompton PD, Daubenberger C, Bull PC, Sallusto F, Lanzavecchia A. Public antibodies to malaria antigens generated by two LAIR1 insertion modalities. Nature 2017; 548:597-601. [PMID: 28847005 PMCID: PMC5635981 DOI: 10.1038/nature23670] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [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: 04/04/2017] [Accepted: 07/25/2017] [Indexed: 01/07/2023]
Abstract
We previously described two donors in whom the extracellular domain of LAIR1, a
collagen-binding inhibitory receptor encoded on chromosome 191, was inserted between the V and the DJ segments of an antibody. This
insertion generated, through somatic mutations, broadly reactive antibodies against
RIFINs, a type of variant antigen expressed on the surface of Plasmodium
falciparum-infected erythrocytes (IEs)2.
To investigate how frequently such antibodies are produced in response to malaria
infection, we screened plasma from two large cohorts of individuals living in
malaria-endemic regions. We report that 5-10% of malaria-exposed individuals, but none of
the European blood donors tested, have high levels of LAIR1-containing antibodies that
dominate the response to IEs without conferring enhanced protection against febrile
malaria. By analyzing the antibody-producing B cell clones at the protein, cDNA and gDNA
level, we characterized additional LAIR1 insertions between the V and DJ
segments and discovered a second insertion modality whereby the LAIR1
exon encoding the extracellular domain and flanking intronic sequences are inserted into
the switch region. By exon shuffling, this mechanism leads to the production of bispecific
antibodies in which the LAIR1 domain is precisely positioned at the elbow between the VH
and CH1 domains. Additionally, in one donor the gDNA encoding the VH and CH1 domains was
deleted, leading to the production of a camel-like LAIR1-containing antibody. Sequencing
of the switch regions of memory B cells from European blood donors revealed frequent
templated inserts originating from transcribed genes that, in rare cases, comprised exons
with orientation and frame compatible with expression. Collectively, these results reveal
different modalities of LAIR1 insertion that lead to public and dominant
antibodies against IEs and suggest that insertion of templated DNA represents an
additional mechanism of antibody diversification that can be selected in the immune
response against pathogens and exploited for B cell engineering.
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Affiliation(s)
- Kathrin Pieper
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Joshua Tan
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland.,Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
| | - Luca Piccoli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Mathilde Foglierini
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Sonia Barbieri
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Yiwei Chen
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland.,Institute for Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Chiara Silacci-Fregni
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Tobias Wolf
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland.,Institute for Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - David Jarrossay
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Marica Anderle
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Abdirahman Abdi
- KEMRI-Wellcome Trust Research Programme, CGMRC, PO Box 230, 80108 Kilifi, Kenya
| | - Francis M Ndungu
- KEMRI-Wellcome Trust Research Programme, CGMRC, PO Box 230, 80108 Kilifi, Kenya
| | - Ogobara K Doumbo
- Malaria Research and Training Centre, University of Sciences, Technique, and Technology of Bamako, 91094 Bamako, Mali
| | - Boubacar Traore
- Malaria Research and Training Centre, University of Sciences, Technique, and Technology of Bamako, 91094 Bamako, Mali
| | - Tuan M Tran
- Division of Infectious Diseases, Department of Medicine, Indiana University School of Medicine, 46202 Indianapolis, Indiana, USA
| | - Said Jongo
- Ifakara Health Institute, Bagamoyo Clinical Trial Unit, P.O. Box 74, Bagamoyo, Tanzania
| | - Isabelle Zenklusen
- Swiss Tropical and Public Health Institute, Clinical Immunology Unit, 4002 Basel, Switzerland.,University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Peter D Crompton
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852, USA
| | - Claudia Daubenberger
- Swiss Tropical and Public Health Institute, Clinical Immunology Unit, 4002 Basel, Switzerland.,University of Basel, Petersplatz 1, 4003 Basel, Switzerland
| | - Peter C Bull
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland.,Institute for Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland.,Institute for Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
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23
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Kallewaard NL, Corti D, Collins PJ, Neu U, McAuliffe JM, Benjamin E, Wachter-Rosati L, Palmer-Hill FJ, Yuan AQ, Walker PA, Vorlaender MK, Bianchi S, Guarino B, De Marco A, Vanzetta F, Agatic G, Foglierini M, Pinna D, Fernandez-Rodriguez B, Fruehwirth A, Silacci C, Ogrodowicz RW, Martin SR, Sallusto F, Suzich JA, Lanzavecchia A, Zhu Q, Gamblin SJ, Skehel JJ. Structure and Function Analysis of an Antibody Recognizing All Influenza A Subtypes. Cell 2016; 166:596-608. [PMID: 27453466 PMCID: PMC4967455 DOI: 10.1016/j.cell.2016.05.073] [Citation(s) in RCA: 268] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/04/2016] [Accepted: 05/25/2016] [Indexed: 01/12/2023]
Abstract
Influenza virus remains a threat because of its ability to evade vaccine-induced immune responses due to antigenic drift. Here, we describe the isolation, evolution, and structure of a broad-spectrum human monoclonal antibody (mAb), MEDI8852, effectively reacting with all influenza A hemagglutinin (HA) subtypes. MEDI8852 uses the heavy-chain VH6-1 gene and has higher potency and breadth when compared to other anti-stem antibodies. MEDI8852 is effective in mice and ferrets with a therapeutic window superior to that of oseltamivir. Crystallographic analysis of Fab alone or in complex with H5 or H7 HA proteins reveals that MEDI8852 binds through a coordinated movement of CDRs to a highly conserved epitope encompassing a hydrophobic groove in the fusion domain and a large portion of the fusion peptide, distinguishing it from other structurally characterized cross-reactive antibodies. The unprecedented breadth and potency of neutralization by MEDI8852 support its development as immunotherapy for influenza virus-infected humans.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Monoclonal/chemistry
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/isolation & purification
- Antibodies, Monoclonal, Humanized
- Antibodies, Neutralizing/chemistry
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/isolation & purification
- Antibodies, Viral/chemistry
- Antibodies, Viral/immunology
- Antibodies, Viral/isolation & purification
- Antibody Specificity
- Binding Sites, Antibody
- Crystallography, X-Ray
- Epitopes/immunology
- Ferrets
- Humans
- Influenza Vaccines
- Alphainfluenzavirus/immunology
- Mice
- Orthomyxoviridae Infections/prevention & control
- Protein Conformation
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Affiliation(s)
- Nicole L Kallewaard
- Department of Infectious Disease and Vaccines, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Davide Corti
- Humabs BioMed SA, Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Patrick J Collins
- Mill Hill Laboratory, The Francis Crick Institute, London NW7 1AA, UK
| | - Ursula Neu
- Mill Hill Laboratory, The Francis Crick Institute, London NW7 1AA, UK
| | - Josephine M McAuliffe
- Department of Infectious Disease and Vaccines, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Ebony Benjamin
- Department of Infectious Disease and Vaccines, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Leslie Wachter-Rosati
- Department of Infectious Disease and Vaccines, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Frances J Palmer-Hill
- Department of Infectious Disease and Vaccines, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Andy Q Yuan
- Department of Antibody Discovery and Protein Engineering, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Philip A Walker
- Structural Biology Science Technology Platform, Mill Hill Laboratory, Francis Crick Institute, London NW7 1AA, UK
| | | | - Siro Bianchi
- Humabs BioMed SA, Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Barbara Guarino
- Humabs BioMed SA, Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Anna De Marco
- Humabs BioMed SA, Via Mirasole 1, 6500 Bellinzona, Switzerland
| | | | - Gloria Agatic
- Humabs BioMed SA, Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Mathilde Foglierini
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Debora Pinna
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | | | - Alexander Fruehwirth
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Chiara Silacci
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - Roksana W Ogrodowicz
- Structural Biology Science Technology Platform, Mill Hill Laboratory, Francis Crick Institute, London NW7 1AA, UK
| | - Stephen R Martin
- Structural Biology Science Technology Platform, Mill Hill Laboratory, Francis Crick Institute, London NW7 1AA, UK
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland
| | - JoAnn A Suzich
- Department of Infectious Disease and Vaccines, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera italiana, 6500 Bellinzona, Switzerland; Institute for Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Qing Zhu
- Department of Infectious Disease and Vaccines, MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA.
| | - Steven J Gamblin
- Mill Hill Laboratory, The Francis Crick Institute, London NW7 1AA, UK
| | - John J Skehel
- Mill Hill Laboratory, The Francis Crick Institute, London NW7 1AA, UK.
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24
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Stettler K, Beltramello M, Espinosa DA, Graham V, Cassotta A, Bianchi S, Vanzetta F, Minola A, Jaconi S, Mele F, Foglierini M, Pedotti M, Simonelli L, Dowall S, Atkinson B, Percivalle E, Simmons CP, Varani L, Blum J, Baldanti F, Cameroni E, Hewson R, Harris E, Lanzavecchia A, Sallusto F, Corti D. Specificity, cross-reactivity, and function of antibodies elicited by Zika virus infection. Science 2016; 353:823-6. [PMID: 27417494 DOI: 10.1126/science.aaf8505] [Citation(s) in RCA: 584] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 07/05/2016] [Indexed: 12/29/2022]
Abstract
Zika virus (ZIKV), a mosquito-borne flavivirus with homology to Dengue virus (DENV), has become a public health emergency. By characterizing memory lymphocytes from ZIKV-infected patients, we dissected ZIKV-specific and DENV-cross-reactive immune responses. Antibodies to nonstructural protein 1 (NS1) were largely ZIKV-specific and were used to develop a serological diagnostic tool. In contrast, antibodies against E protein domain I/II (EDI/II) were cross-reactive and, although poorly neutralizing, potently enhanced ZIKV and DENV infection in vitro and lethally enhanced DENV disease in mice. Memory T cells against NS1 or E proteins were poorly cross-reactive, even in donors preexposed to DENV. The most potent neutralizing antibodies were ZIKV-specific and targeted EDIII or quaternary epitopes on infectious virus. An EDIII-specific antibody protected mice from lethal ZIKV infection, illustrating the potential for antibody-based therapy.
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Affiliation(s)
- Karin Stettler
- Humabs BioMed SA, Via Mirasole 1, 6500 Bellinzona, Switzerland
| | | | - Diego A Espinosa
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Victoria Graham
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Antonino Cassotta
- Institute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland. Institute for Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Siro Bianchi
- Humabs BioMed SA, Via Mirasole 1, 6500 Bellinzona, Switzerland
| | | | - Andrea Minola
- Humabs BioMed SA, Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Stefano Jaconi
- Humabs BioMed SA, Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Federico Mele
- Institute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Mathilde Foglierini
- Institute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Luca Simonelli
- Institute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Stuart Dowall
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Barry Atkinson
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Elena Percivalle
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, Pavia, Italy
| | - Cameron P Simmons
- Centre for Tropical Medicine, Nuffield Department of Medicine, University of Oxford, UK. Oxford University Clinical Research Unit, Center for Tropical Medicine, Ho Chi Minh City, Vietnam. Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute, 792 Elizabeth Street, Melbourne VIC 3000, Australia
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Johannes Blum
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002 Basel, Switzerland. University of Basel, Petersgraben 4, 4031 Basel, Switzerland
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, Pavia, Italy
| | | | - Roger Hewson
- National Infection Service, Public Health England, Porton Down, Salisbury, Wiltshire, UK
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland. Institute for Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland.
| | - Davide Corti
- Humabs BioMed SA, Via Mirasole 1, 6500 Bellinzona, Switzerland.
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25
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Kabanova A, Marcandalli J, Zhou T, Bianchi S, Baxa U, Tsybovsky Y, Lilleri D, Silacci-Fregni C, Foglierini M, Fernandez-Rodriguez BM, Druz A, Zhang B, Geiger R, Pagani M, Sallusto F, Kwong PD, Corti D, Lanzavecchia A, Perez L. Platelet-derived growth factor-α receptor is the cellular receptor for human cytomegalovirus gHgLgO trimer. Nat Microbiol 2016; 1:16082. [PMID: 27573107 PMCID: PMC4918640 DOI: 10.1038/nmicrobiol.2016.82] [Citation(s) in RCA: 135] [Impact Index Per Article: 16.9] [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: 12/02/2015] [Accepted: 04/26/2016] [Indexed: 12/25/2022]
Abstract
Human cytomegalovirus encodes at least 25 membrane glycoproteins that are found in the viral envelope(1). While gB represents the fusion protein, two glycoprotein complexes control the tropism of the virus: the gHgLgO trimer is involved in the infection of fibroblasts, and the gHgLpUL128L pentamer is required for infection of endothelial, epithelial and myeloid cells(2-5). Two reports suggested that gB binds to ErbB1 and PDGFRα (refs 6,7); however, these results do not explain the tropism of the virus and were recently challenged(8,9). Here, we provide a 19 Å reconstruction for the gHgLgO trimer and show that it binds with high affinity through the gO subunit to PDGFRα, which is expressed on fibroblasts but not on epithelial cells. We also provide evidence that the trimer is essential for viral entry in both fibroblasts and epithelial cells. Furthermore, we identify the pentamer, which is essential for infection of epithelial cells, as a trigger for the ErbB pathway. These findings help explain the broad tropism of human cytomegalovirus and indicate that PDGFRα and the viral gO subunit could be targeted by novel anti-viral therapies.
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Affiliation(s)
- Anna Kabanova
- Institute for Research in Biomedicine, University of Italian Switzerland, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Jessica Marcandalli
- Institute for Research in Biomedicine, University of Italian Switzerland, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Siro Bianchi
- Humabs BioMed SA, Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Ulrich Baxa
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Daniele Lilleri
- Laboratori Sperimentali di Ricerca-Area Trapiantologica, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Chiara Silacci-Fregni
- Institute for Research in Biomedicine, University of Italian Switzerland, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Mathilde Foglierini
- Institute for Research in Biomedicine, University of Italian Switzerland, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | | | - Aliaksandr Druz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Roger Geiger
- Institute for Research in Biomedicine, University of Italian Switzerland, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
- Institute for Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Massimiliano Pagani
- Istituto Nazionale Genetica Molecolare ‘Romeo ed Enrica Invernizzi’, Milano, Italy
| | - Federica Sallusto
- Institute for Research in Biomedicine, University of Italian Switzerland, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Davide Corti
- Humabs BioMed SA, Via Mirasole 1, 6500 Bellinzona, Switzerland
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, University of Italian Switzerland, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
- Institute for Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland
| | - Laurent Perez
- Institute for Research in Biomedicine, University of Italian Switzerland, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland
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26
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De Benedictis P, Minola A, Rota Nodari E, Aiello R, Zecchin B, Salomoni A, Foglierini M, Agatic G, Vanzetta F, Lavenir R, Lepelletier A, Bentley E, Weiss R, Cattoli G, Capua I, Sallusto F, Wright E, Lanzavecchia A, Bourhy H, Corti D. Development of broad-spectrum human monoclonal antibodies for rabies post-exposure prophylaxis. EMBO Mol Med 2016; 8:407-21. [PMID: 26992832 PMCID: PMC4818751 DOI: 10.15252/emmm.201505986] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 02/08/2016] [Accepted: 02/15/2016] [Indexed: 12/25/2022] Open
Abstract
Currently available rabies post-exposure prophylaxis (PEP) for use in humans includes equine or human rabies immunoglobulins (RIG). The replacement of RIG with an equally or more potent and safer product is strongly encouraged due to the high costs and limited availability of existing RIG. In this study, we identified two broadly neutralizing human monoclonal antibodies that represent a valid and affordable alternative to RIG in rabies PEP. Memory B cells from four selected vaccinated donors were immortalized and monoclonal antibodies were tested for neutralizing activity and epitope specificity. Two antibodies, identified as RVC20 and RVC58 (binding to antigenic site I and III, respectively), were selected for their potency and broad-spectrum reactivity. In vitro, RVC20 and RVC58 were able to neutralize all 35 rabies virus (RABV) and 25 non-RABV lyssaviruses. They showed higher potency and breath compared to antibodies under clinical development (namely CR57, CR4098, and RAB1) and commercially available human RIG. In vivo, the RVC20-RVC58 cocktail protected Syrian hamsters from a lethal RABV challenge and did not affect the endogenous hamster post-vaccination antibody response.
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MESH Headings
- Animals
- Antibodies, Monoclonal/administration & dosage
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/isolation & purification
- Antibodies, Neutralizing/administration & dosage
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/isolation & purification
- Antibodies, Viral/administration & dosage
- Antibodies, Viral/immunology
- Antibodies, Viral/isolation & purification
- Disease Models, Animal
- Humans
- Immunization, Passive/methods
- Immunologic Factors/administration & dosage
- Immunologic Factors/immunology
- Immunologic Factors/isolation & purification
- Mesocricetus
- Post-Exposure Prophylaxis/methods
- Rabies/prevention & control
- Rabies virus/immunology
- Survival Analysis
- Treatment Outcome
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Affiliation(s)
- Paola De Benedictis
- FAO and National Reference Centre for Rabies, National Reference Centre and OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padua, Italy
| | | | - Elena Rota Nodari
- FAO and National Reference Centre for Rabies, National Reference Centre and OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padua, Italy
| | - Roberta Aiello
- FAO and National Reference Centre for Rabies, National Reference Centre and OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padua, Italy
| | - Barbara Zecchin
- FAO and National Reference Centre for Rabies, National Reference Centre and OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padua, Italy
| | - Angela Salomoni
- FAO and National Reference Centre for Rabies, National Reference Centre and OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padua, Italy
| | - Mathilde Foglierini
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | | | | | - Rachel Lavenir
- Institut Pasteur, Unit of Lyssavirus Dynamics and Host Adaptation National Reference Centre for Rabies World Health Organization Collaborating Centre for Reference and Research on Rabies, Paris Cedex 15, France
| | - Anthony Lepelletier
- Institut Pasteur, Unit of Lyssavirus Dynamics and Host Adaptation National Reference Centre for Rabies World Health Organization Collaborating Centre for Reference and Research on Rabies, Paris Cedex 15, France
| | - Emma Bentley
- Viral Pseudotype Unit, Faculty of Science and Technology, University of Westminster, London, UK
| | - Robin Weiss
- Division of Infection and Immunity, University College London, London, UK
| | - Giovanni Cattoli
- FAO and National Reference Centre for Rabies, National Reference Centre and OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padua, Italy
| | - Ilaria Capua
- FAO and National Reference Centre for Rabies, National Reference Centre and OIE Collaborating Centre for Diseases at the Animal-Human Interface, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Padua, Italy
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Edward Wright
- Viral Pseudotype Unit, Faculty of Science and Technology, University of Westminster, London, UK
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Hervé Bourhy
- Institut Pasteur, Unit of Lyssavirus Dynamics and Host Adaptation National Reference Centre for Rabies World Health Organization Collaborating Centre for Reference and Research on Rabies, Paris Cedex 15, France
| | - Davide Corti
- Humabs BioMed SA, Bellinzona, Switzerland Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
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27
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Preite S, Baumjohann D, Foglierini M, Basso C, Ronchi F, Fernandez Rodriguez BM, Corti D, Lanzavecchia A, Sallusto F. Somatic mutations and affinity maturation are impaired by excessive numbers of T follicular helper cells and restored by Treg cells or memory T cells. Eur J Immunol 2015; 45:3010-21. [PMID: 26332258 PMCID: PMC5054911 DOI: 10.1002/eji.201545920] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [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: 07/13/2015] [Revised: 08/13/2015] [Accepted: 08/25/2015] [Indexed: 01/25/2023]
Abstract
We previously reported that Cd3e‐deficient mice adoptively transferred with CD4+ T cells generate high numbers of T follicular helper (Tfh) cells, which go on to induce a strong B‐cell and germinal center (GC) reaction. Here, we show that in this system, GC B cells display an altered distribution between the dark and light zones, and express low levels of activation‐induced cytidine deaminase. Furthermore, GC B cells from Cd3e–/– mice accumulate fewer somatic mutations as compared with GC B cells from wild‐type mice, and exhibit impaired affinity maturation and reduced differentiation into long‐lived plasma cells. Reconstitution of Cd3e–/– mice with regulatory T (Treg) cells restored Tfh‐cell numbers, GC B‐cell numbers and B‐cell distribution within dark and light zones, and the rate of antibody somatic mutations. Tfh‐cell numbers and GC B‐cell numbers and dynamics were also restored by pre‐reconstitution of Cd3e–/– mice with Cxcr5–/– Treg cells or non‐regulatory, memory CD4+ T cells. Taken together, these findings underline the importance of a quantitatively regulated Tfh‐cell response for an efficient and long‐lasting serological response.
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Affiliation(s)
- Silvia Preite
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Dirk Baumjohann
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Mathilde Foglierini
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Camilla Basso
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Francesca Ronchi
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | | | - Davide Corti
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland.,Institute of Microbiology, ETH Zürich, Zurich, Switzerland
| | - Federica Sallusto
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
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Becattini S, Latorre D, Mele F, Foglierini M, De Gregorio C, Cassotta A, Fernandez B, Kelderman S, Schumacher TN, Corti D, Lanzavecchia A, Sallusto F. Functional heterogeneity of human memory CD4+ T cell clones primed by pathogens or vaccines. Science 2014; 347:400-6. [DOI: 10.1126/science.1260668] [Citation(s) in RCA: 250] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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29
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Kiel C, Foglierini M, Kuemmerer N, Beltrao P, Serrano L. A genome-wide Ras-effector interaction network. J Mol Biol 2007; 370:1020-32. [PMID: 17544445 DOI: 10.1016/j.jmb.2007.05.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Revised: 05/01/2007] [Accepted: 05/03/2007] [Indexed: 11/18/2022]
Abstract
Here using structural information and protein design tools we have drawn the network of interactions between 20 Ras subfamily proteins with 50 putative Ras binding domains. To validate this network we have cloned six poorly characterized Ras binding domains (RBD) and two Ras proteins (RERG, DiRas1). These, together with previously described RBD domains, Ras and Rap proteins have been analyzed in 70 pull-down experiments. Comparing our interaction network with these and previous pull-down experiments (total of 150 cases) shows a very high accuracy for distinguishing between binders and non-binders ( approximately 0.80). Bioinformatics information was integrated to distinguish those in vitro interactions that are more likely to be relevant in vivo. We proposed several new interactions between Ras family members and effector domains that are of relevance in understanding the physiological role of these proteins. More broadly our results demonstrate that (domain-domain) interaction specificities between members of protein families can be accurately predicted using structural information.
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Affiliation(s)
- Christina Kiel
- Structural and computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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Ander M, Beltrao P, Di Ventura B, Ferkinghoff-Borg J, Foglierini M, Kaplan A, Lemerle C, Tomás-Oliveira I, Serrano L. SmartCell, a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks. ACTA ACUST UNITED AC 2006; 1:129-38. [PMID: 17052123 DOI: 10.1049/sb:20045017] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SmartCell has been developed to be a general framework for modelling and simulation of diffusion-reaction networks in a whole-cell context. It supports localisation and diffusion by using a mesoscopic stochastic reaction model. The SmartCell package can handle any cell geometry, considers different cell compartments, allows localisation of species, supports DNA transcription and translation, membrane diffusion and multistep reactions, as well as cell growth. Moreover, different temporal and spatial constraints can be applied to the model. A GUI interface that facilitates model making is also available. In this work we discuss limitations and advantages arising from the approach used in SmartCell and determine the impact of localisation on the behaviour of simple well-defined networks, previously analysed with differential equations. Our results show that this factor might play an important role in the response of networks and cannot be neglected in cell simulations.
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Affiliation(s)
- M Ander
- IBM Life Sciences, Stockholm, Sweden
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31
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Dublanche Y, Michalodimitrakis K, Kümmerer N, Foglierini M, Serrano L. Noise in transcription negative feedback loops: simulation and experimental analysis. Mol Syst Biol 2006; 2:41. [PMID: 16883354 PMCID: PMC1681513 DOI: 10.1038/msb4100081] [Citation(s) in RCA: 177] [Impact Index Per Article: 9.8] [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: 01/11/2006] [Accepted: 06/14/2006] [Indexed: 11/15/2022] Open
Abstract
Negative feedback loops have been invoked as a way to control and decrease transcriptional noise. Here, we have built three circuits to test the effect of negative feedback loops on transcriptional noise of an autoregulated gene encoding a transcription factor (TF) and a downstream gene (DG), regulated by this TF. Experimental analysis shows that self-repression decreases noise compared to expression from a non-regulated promoter. Interestingly enough, we find that noise minimization by negative feedback loop is optimal within a range of repression strength. Repression values outside this range result in noise increase producing a U-shaped behaviour. This behaviour is the result of external noise probably arising from plasmid fluctuations as shown by simulation of the network. Regarding the target gene of a self-repressed TF (sTF), we find a strong decrease of noise when repression by the sTF is strong and a higher degree of noise anti-correlation between sTF and its target. Simulations of the circuits indicate that the main source of noise in these circuits could come from plasmid variation and therefore that negative feedback loops play an important role in suppressing both external and internal noise. An important observation is that DG expression without negative feedback exhibits bimodality at intermediate TF repression values. This bimodal behaviour seems to be the result of external noise as it can only be found in those simulations that include plasmid variation.
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Affiliation(s)
- Yann Dublanche
- European Molecular Biology Laboratory (EMBL), Heildelberg, Germany
| | | | - Nico Kümmerer
- European Molecular Biology Laboratory (EMBL), Heildelberg, Germany
| | | | - Luis Serrano
- European Molecular Biology Laboratory (EMBL), Heildelberg, Germany
- European Molecular Biology Laboratory (EMBL), SCB, Meyerhofstrasse 1, 69117 Heildelberg, Germany. Tel.: +49 6 221387320; Fax: +49 6 221387306; E-mail:
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von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P. STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res 2005; 33:D433-7. [PMID: 15608232 PMCID: PMC539959 DOI: 10.1093/nar/gki005] [Citation(s) in RCA: 1036] [Impact Index Per Article: 54.5] [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] [Indexed: 12/29/2022] Open
Abstract
A full description of a protein's function requires knowledge of all partner proteins with which it specifically associates. From a functional perspective, 'association' can mean direct physical binding, but can also mean indirect interaction such as participation in the same metabolic pathway or cellular process. Currently, information about protein association is scattered over a wide variety of resources and model organisms. STRING aims to simplify access to this information by providing a comprehensive, yet quality-controlled collection of protein-protein associations for a large number of organisms. The associations are derived from high-throughput experimental data, from the mining of databases and literature, and from predictions based on genomic context analysis. STRING integrates and ranks these associations by benchmarking them against a common reference set, and presents evidence in a consistent and intuitive web interface. Importantly, the associations are extended beyond the organism in which they were originally described, by automatic transfer to orthologous protein pairs in other organisms, where applicable. STRING currently holds 730,000 proteins in 180 fully sequenced organisms, and is available at http://string.embl.de/.
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Affiliation(s)
- Christian von Mering
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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