1
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Marcotte H, Cao Y, Zuo F, Simonelli L, Sammartino JC, Pedotti M, Sun R, Cassaniti I, Hagbom M, Piralla A, Yang J, Du L, Percivalle E, Bertoglio F, Schubert M, Abolhassani H, Sherina N, Guerra C, Borte S, Rezaei N, Kumagai-Braesch M, Xue Y, Su C, Yan Q, He P, Grönwall C, Klareskog L, Calzolai L, Cavalli A, Wang Q, Robbiani DF, Hust M, Shi Z, Feng L, Svensson L, Chen L, Bao L, Baldanti F, Xiao J, Qin C, Hammarström L, Yang X, Varani L, Xie XS, Pan-Hammarström Q. Conversion of monoclonal IgG to dimeric and secretory IgA restores neutralizing ability and prevents infection of Omicron lineages. Proc Natl Acad Sci U S A 2024; 121:e2315354120. [PMID: 38194459 PMCID: PMC10801922 DOI: 10.1073/pnas.2315354120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 01/11/2024] Open
Abstract
The emergence of Omicron lineages and descendent subvariants continues to present a severe threat to the effectiveness of vaccines and therapeutic antibodies. We have previously suggested that an insufficient mucosal immunoglobulin A (IgA) response induced by the mRNA vaccines is associated with a surge in breakthrough infections. Here, we further show that the intramuscular mRNA and/or inactivated vaccines cannot sufficiently boost the mucosal secretory IgA response in uninfected individuals, particularly against the Omicron variant. We thus engineered and characterized recombinant monomeric, dimeric, and secretory IgA1 antibodies derived from four neutralizing IgG monoclonal antibodies (mAbs 01A05, rmAb23, DXP-604, and XG014) targeting the receptor-binding domain of the spike protein. Compared to their parental IgG antibodies, dimeric and secretory IgA1 antibodies showed a higher neutralizing activity against different variants of concern (VOCs), in part due to an increased avidity. Importantly, the dimeric or secretory IgA1 form of the DXP-604 antibody significantly outperformed its parental IgG antibody, and neutralized the Omicron lineages BA.1, BA.2, and BA.4/5 with a 25- to 75-fold increase in potency. In human angiotensin converting enzyme 2 (ACE2) transgenic mice, a single intranasal dose of the dimeric IgA DXP-604 conferred prophylactic and therapeutic protection against Omicron BA.5. Thus, dimeric or secretory IgA delivered by nasal administration may potentially be exploited for the treatment and prevention of Omicron infection, thereby providing an alternative tool for combating immune evasion by the current circulating subvariants and, potentially, future VOCs.
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Affiliation(s)
- Harold Marcotte
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm17165, Sweden
| | - Yunlong Cao
- Changping Laboratory, Beijing102206, People’s Republic of China
- School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing100871, People’s Republic of China
| | - Fanglei Zuo
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm17165, Sweden
| | - Luca Simonelli
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona6500, Switzerland
| | - Josè Camilla Sammartino
- Microbiology and Virology Department, Fondazione Istituto di ricovero e cura a carattere scientifico (IRCCS) Policlinico San Matteo, Pavia27100, Italy
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona6500, Switzerland
| | - Rui Sun
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm17165, Sweden
| | - Irene Cassaniti
- Microbiology and Virology Department, Fondazione Istituto di ricovero e cura a carattere scientifico (IRCCS) Policlinico San Matteo, Pavia27100, Italy
| | - Marie Hagbom
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping 58185, Sweden
| | - Antonio Piralla
- Microbiology and Virology Department, Fondazione Istituto di ricovero e cura a carattere scientifico (IRCCS) Policlinico San Matteo, Pavia27100, Italy
| | - Jinxuan Yang
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming650023, People’s Republic of China
| | - Likun Du
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm17165, Sweden
| | - Elena Percivalle
- Microbiology and Virology Department, Fondazione Istituto di ricovero e cura a carattere scientifico (IRCCS) Policlinico San Matteo, Pavia27100, Italy
| | - Federico Bertoglio
- Department of Medical Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig38106, Germany
| | - Maren Schubert
- Department of Medical Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig38106, Germany
| | - Hassan Abolhassani
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm17165, Sweden
| | - Natalia Sherina
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm17165, Sweden
| | - Concetta Guerra
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona6500, Switzerland
| | - Stephan Borte
- Department of Laboratory Medicine, Hospital St. Georg, Leipzig04129, Germany
- ImmunoDeficiencyCenter Leipzig, Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiency Diseases, Hospital St. Georg, Leipzig04129, Germany
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences, Tehran14194, Iran
| | - Makiko Kumagai-Braesch
- Division of Transplantation Surgery, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm14186, Sweden
| | - Yintong Xue
- Department of Immunology, Peking University Health Science Center, Beijing100191, People’s Republic of China
| | - Chen Su
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, People’s Republic of China
| | - Qihong Yan
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences,Guangzhou510530, People’s Republic of China
| | - Ping He
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences,Guangzhou510530, People’s Republic of China
| | - Caroline Grönwall
- Division of Rheumatology, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm17176, Sweden
| | - Lars Klareskog
- Division of Rheumatology, Department of Medicine Solna, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm17176, Sweden
- Rheumatology Unit, Karolinska University Hospital, Stockholm17176, Sweden
| | - Luigi Calzolai
- European Commission, Joint Research Centre, Ispra21027, Italy
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona6500, Switzerland
| | - Qiao Wang
- Key Laboratory of Medical Molecular Virology (Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences), Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, 200032 Shanghai200032, People’s Republic of China
| | - Davide F. Robbiani
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona6500, Switzerland
| | - Michael Hust
- Department of Medical Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig38106, Germany
| | - Zhengli Shi
- State Key laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei430071, People’s Republic of China
| | - Liqiang Feng
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences,Guangzhou510530, People’s Republic of China
| | - Lennart Svensson
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping 58185, Sweden
- Division of Infectious Diseases, Department of Medicine, Karolinska Institute, Stockholm17177, Sweden
| | - Ling Chen
- Guangzhou Laboratory, Guangzhou510005, People’s Republic of China
| | - Linlin Bao
- Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, National Health Commission Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing100021, People’s Republic of China
- National Center of Technology Innovation for Animal Model, Beijing102206, People’s Republic of China
| | - Fausto Baldanti
- Microbiology and Virology Department, Fondazione Istituto di ricovero e cura a carattere scientifico (IRCCS) Policlinico San Matteo, Pavia27100, Italy
- Department of Clinical, Surgical, Diagnostic and Paediatric Sciences, University of Pavia, Pavia27100, Italy
| | - Junyu Xiao
- Changping Laboratory, Beijing102206, People’s Republic of China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, People’s Republic of China
| | - Chuan Qin
- Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious Diseases, National Health Commission Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing100021, People’s Republic of China
- National Center of Technology Innovation for Animal Model, Beijing102206, People’s Republic of China
| | - Lennart Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm17165, Sweden
| | - Xinglou Yang
- Yunnan Key Laboratory of Biodiversity Information, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming650023, People’s Republic of China
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona6500, Switzerland
| | - Xiaoliang Sunney Xie
- Changping Laboratory, Beijing102206, People’s Republic of China
- School of Life Sciences, Biomedical Pioneering Innovation Center, Peking University, Beijing100871, People’s Republic of China
| | - Qiang Pan-Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm17165, Sweden
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2
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Guerrini G, Mehn D, Fumagalli F, Gioria S, Pedotti M, Simonelli L, Bianchini F, Robbiani DF, Varani L, Calzolai L. Analytical Ultracentrifugation Detects Quaternary Rearrangements and Antibody-Induced Conformational Selection of the SARS-CoV-2 Spike Trimer. Int J Mol Sci 2023; 24:14875. [PMID: 37834322 PMCID: PMC10573103 DOI: 10.3390/ijms241914875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/19/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Analytical ultracentrifugation (AUC) analysis shows that the SARS-CoV-2 trimeric Spike (S) protein adopts different quaternary conformations in solution. The relative abundance of the "open" and "close" conformations is temperature-dependent, and samples with different storage temperature history have different open/close distributions. Neutralizing antibodies (NAbs) targeting the S receptor binding domain (RBD) do not alter the conformer populations; by contrast, a NAb targeting a cryptic conformational epitope skews the Spike trimer toward an open conformation. The results highlight AUC, which is typically applied for molecular mass determination of biomolecules as a powerful tool for detecting functionally relevant quaternary protein conformations.
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Affiliation(s)
- Giuditta Guerrini
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Dora Mehn
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Francesco Fumagalli
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Sabrina Gioria
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Luca Simonelli
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Filippo Bianchini
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Davide F. Robbiani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, 6500 Bellinzona, Switzerland; (M.P.); (L.S.); (F.B.); (D.F.R.)
| | - Luigi Calzolai
- European Commission, Joint Research Centre (JRC), 21027 Ispra, Italy; (G.G.); (D.M.); (F.F.); (S.G.)
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3
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Peissert F, Pedotti M, Corbellari R, Simonelli L, De Gasparo R, Tamagnini E, Plüss L, Elsayed A, Matasci M, De Luca R, Cassaniti I, Sammartino JC, Piralla A, Baldanti F, Neri D, Varani L. Adapting Neutralizing Antibodies to Viral Variants by Structure-Guided Affinity Maturation Using Phage Display Technology. Glob Chall 2023; 7:2300088. [PMID: 37829677 PMCID: PMC10566804 DOI: 10.1002/gch2.202300088] [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] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Indexed: 10/14/2023]
Abstract
Neutralizing monoclonal antibodies have achieved great efficacy and safety for the treatment of numerous infectious diseases. However, their neutralization potency is often rapidly lost when the target antigen mutates. Instead of isolating new antibodies each time a pathogen variant arises, it can be attractive to adapt existing antibodies, making them active against the new variant. Potential benefits of this approach include reduced development time, cost, and regulatory burden. Here a methodology is described to rapidly evolve neutralizing antibodies of proven activity, improving their function against new pathogen variants without losing efficacy against previous ones. The reported procedure is based on structure-guided affinity maturation using combinatorial mutagenesis and phage display technology. Its use against the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is demonstrated, but it is suitable for any other pathogen. As proof of concept, the method is applied to CoV-X2, a human bispecific antibody that binds with high affinity to the early SARS-CoV-2 variants but lost neutralization potency against Delta. Antibodies emerging from the affinity maturation selection exhibit significantly improved neutralization potency against Delta and no loss of efficacy against the other viral sequences tested. These results illustrate the potential application of structure-guided affinity maturation in facilitating the rapid adaptation of neutralizing antibodies to pathogen variants.
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Affiliation(s)
| | - Mattia Pedotti
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
| | | | - Luca Simonelli
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
| | - Raoul De Gasparo
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
| | - Elia Tamagnini
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
| | - Louis Plüss
- Philochem AGLibernstrasse 3Otelfingen8112Switzerland
| | | | | | | | - Irene Cassaniti
- Molecular Virology UnitMicrobiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPavia27100Italy
| | - Jose’ Camilla Sammartino
- Molecular Virology UnitMicrobiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPavia27100Italy
| | - Antonio Piralla
- Molecular Virology UnitMicrobiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPavia27100Italy
| | - Fausto Baldanti
- Molecular Virology UnitMicrobiology and Virology DepartmentFondazione IRCCS Policlinico San MatteoPavia27100Italy
- Department of Clinical Surgical Diagnostic and Pediatric SciencesUniversità degli Studi di PaviaPavia27100Italy
| | - Dario Neri
- Philochem AGLibernstrasse 3Otelfingen8112Switzerland
- Philogen SpALocalità Bellaria 35Sovicille (SI)53018Italy
| | - Luca Varani
- Institute for Research in BiomedicineUniversità della Svizzera italiana (USI)Bellinzona6500Switzerland
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4
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García-Vega M, Melgoza-González EA, Hernández-Valenzuela S, Hinojosa-Trujillo D, Reséndiz-Sandoval M, Llamas-Covarrubias MA, Loza-López M, Valenzuela O, Soto-Gaxiola A, Hernández-Oñate MA, Mata-Haro V, Cassaniti I, Sammartino JC, Ferrari A, Simonelli L, Pedotti M, Sun R, Zuo F, Baldanti F, Varani L, Marcotte H, Pan-Hammarström Q, Hernández J. 19n01, a broadly neutralizing antibody against Omicron BA.1, BA.2, BA.4/5, and other SARS-CoV-2 variants of concern. iScience 2023; 26:106562. [PMID: 37063467 PMCID: PMC10066585 DOI: 10.1016/j.isci.2023.106562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 11/21/2022] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
This study reports the isolation and characterization of a human monoclonal antibody (mAb) called 19n01. This mAb was isolated by using single-cell RNAseq of B cells from donors infected with the ancestral strain. This mAb possesses a potent and broad capacity to bind and neutralize all previously circulating variants of concern (VOCs), including Omicron sublineages BA.1, BA.2, and BA.4/5. The pseudovirus neutralization assay revealed robust neutralization capacity against the G614 strain, BA.1, BA.2, and BA.4/5, with inhibitory concentration (IC50) values ranging from 0.0035 to 0.0164 μg/mL. The microneutralization assay using the G614 strain and VOCs demonstrated IC50 values of 0.013-0.267 μg/mL. Biophysical and structural analysis showed that 19n01 cross-competes with ACE2 binding to the receptor-binding domain (RBD) and the kinetic parameters confirmed the high affinity against the Omicron sublineages (KD of 61 and 30 nM for BA.2 and BA.4/5, respectively). These results suggest that the 19n01 is a remarkably potent and broadly reactive mAb.
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Affiliation(s)
- Melissa García-Vega
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Sonora, Mexico
| | - Edgar A. Melgoza-González
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Sonora, Mexico
| | - Sofía Hernández-Valenzuela
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Sonora, Mexico
| | - Diana Hinojosa-Trujillo
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Sonora, Mexico
| | - Mónica Reséndiz-Sandoval
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Sonora, Mexico
| | | | - Martín Loza-López
- Laboratory of Functional Analysis in silico, The University of Tokyo, Shirokanedai, Tokyo, Japan
| | - Olivia Valenzuela
- Departamento de Ciencias Químico Biológicas, División de Ciencias de la Salud, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Alan Soto-Gaxiola
- Hospital General del Estado de Sonora “Dr. Ernesto Ramos Bours”, Secretaria de Salud del Estado de Sonora, Hermosillo, Sonora, Mexico
| | - Miguel A. Hernández-Oñate
- Laboratorio de Fisiología y Biología Molecular de Plantas, Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Sonora, Mexico
| | - Verónica Mata-Haro
- Laboratorio de Microbiología e Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Sonora, Mexico
| | - Irene Cassaniti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | | | - Alessandro Ferrari
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Luca Simonelli
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Rui Sun
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fanglei Zuo
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fausto Baldanti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Clinical, Surgical, Diagnostics and Pediatric Sciences, University of Pavia, Pavia, Italy
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Harold Marcotte
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Qiang Pan-Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jesús Hernández
- Laboratorio de Inmunología, Centro de Investigación en Alimentación y Desarrollo, A.C. Hermosillo, Sonora, Mexico
- Corresponding author
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5
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Bianchini F, Crivelli V, Abernathy ME, Guerra C, Palus M, Muri J, Marcotte H, Piralla A, Pedotti M, De Gasparo R, Simonelli L, Matkovic M, Toscano C, Biggiogero M, Calvaruso V, Svoboda P, Cervantes Rincón T, Fava T, Podešvová L, Shanbhag AA, Celoria A, Sgrignani J, Stefanik M, Hönig V, Pranclova V, Michalcikova T, Prochazka J, Guerrini G, Mehn D, Ciabattini A, Abolhassani H, Jarrossay D, Uguccioni M, Medaglini D, Pan-Hammarström Q, Calzolai L, Fernandez D, Baldanti F, Franzetti-Pellanda A, Garzoni C, Sedlacek R, Ruzek D, Varani L, Cavalli A, Barnes CO, Robbiani DF. Human neutralizing antibodies to cold linear epitopes and subdomain 1 of the SARS-CoV-2 spike glycoprotein. Sci Immunol 2023; 8:eade0958. [PMID: 36701425 PMCID: PMC9972897 DOI: 10.1126/sciimmunol.ade0958] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 01/23/2023] [Indexed: 01/27/2023]
Abstract
Emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants diminishes the efficacy of vaccines and antiviral monoclonal antibodies. Continued development of immunotherapies and vaccine immunogens resilient to viral evolution is therefore necessary. Using coldspot-guided antibody discovery, a screening approach that focuses on portions of the virus spike glycoprotein that are both functionally relevant and averse to change, we identified human neutralizing antibodies to highly conserved viral epitopes. Antibody fp.006 binds the fusion peptide and cross-reacts against coronaviruses of the four genera, including the nine human coronaviruses, through recognition of a conserved motif that includes the S2' site of proteolytic cleavage. Antibody hr2.016 targets the stem helix and neutralizes SARS-CoV-2 variants. Antibody sd1.040 binds to subdomain 1, synergizes with antibody rbd.042 for neutralization, and, similar to fp.006 and hr2.016, protects mice expressing human angiotensin-converting enzyme 2 against infection when present as a bispecific antibody. Thus, coldspot-guided antibody discovery reveals donor-derived neutralizing antibodies that are cross-reactive with Orthocoronavirinae, including SARS-CoV-2 variants.
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Affiliation(s)
- Filippo Bianchini
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Virginia Crivelli
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | | | - Concetta Guerra
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Martin Palus
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences; Ceske Budejovice, Czech Republic
- Veterinary Research Institute; Brno, Czech Republic
| | - Jonathan Muri
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Harold Marcotte
- Department of Biosciences and Nutrition, Karolinska Institutet; Huddinge, Sweden
| | - Antonio Piralla
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo; Pavia, Italy
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Raoul De Gasparo
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Luca Simonelli
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Milos Matkovic
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Chiara Toscano
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Maira Biggiogero
- Clinical Research Unit, Clinica Luganese Moncucco; Lugano, Switzerland
| | | | - Pavel Svoboda
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences; Ceske Budejovice, Czech Republic
- Veterinary Research Institute; Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University; Brno, Czech Republic
- Department of Pharmacology and Pharmacy, Faculty of Veterinary Medicine, University of Veterinary Sciences; Brno, Czech Republic
| | - Tomás Cervantes Rincón
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Tommaso Fava
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Lucie Podešvová
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Akanksha A. Shanbhag
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Andrea Celoria
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Jacopo Sgrignani
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Michal Stefanik
- Veterinary Research Institute; Brno, Czech Republic
- Department of Chemistry and Biochemistry, Mendel University in Brno; Brno, Czech Republic
| | - Vaclav Hönig
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences; Ceske Budejovice, Czech Republic
- Veterinary Research Institute; Brno, Czech Republic
| | - Veronika Pranclova
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences; Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia; Ceske Budejovice, Czech Republic
| | - Tereza Michalcikova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences; Vestec, Czech Republic
| | - Jan Prochazka
- Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences; Vestec, Czech Republic
| | | | - Dora Mehn
- European Commission, Joint Research Centre (JRC); Ispra, Italy
| | - Annalisa Ciabattini
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies; University of Siena, Siena, Italy
| | - Hassan Abolhassani
- Department of Biosciences and Nutrition, Karolinska Institutet; Huddinge, Sweden
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences; Tehran, Iran
| | - David Jarrossay
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Mariagrazia Uguccioni
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Donata Medaglini
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies; University of Siena, Siena, Italy
| | | | - Luigi Calzolai
- European Commission, Joint Research Centre (JRC); Ispra, Italy
| | - Daniel Fernandez
- Sarafan ChEM-H Macromolecular Structure Knowledge Center, Stanford University; Stanford, USA
| | - Fausto Baldanti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo; Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia; Pavia, Italy
| | | | - Christian Garzoni
- Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco; Lugano, Switzerland
| | - Radislav Sedlacek
- Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences; Vestec, Czech Republic
| | - Daniel Ruzek
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences; Ceske Budejovice, Czech Republic
- Veterinary Research Institute; Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University; Brno, Czech Republic
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
- Swiss Institute of Bioinformatics; Lausanne, Switzerland
| | - Christopher O. Barnes
- Department of Biology, Stanford University; Stanford, USA
- Chan Zuckerberg Biohub; San Francisco, USA
| | - Davide F. Robbiani
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
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6
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Bancaro N, Calì B, Troiani M, Elia AR, Arzola RA, Attanasio G, Lai P, Crespo M, Gurel B, Pereira R, Guo C, Mosole S, Brina D, D'Ambrosio M, Pasquini E, Spataro C, Zagato E, Rinaldi A, Pedotti M, Di Lascio S, Meani F, Montopoli M, Ferrari M, Gallina A, Varani L, Pereira Mestre R, Bolis M, Gillessen Sommer S, de Bono J, Calcinotto A, Alimonti A. Apolipoprotein E induces pathogenic senescent-like myeloid cells in prostate cancer. Cancer Cell 2023; 41:602-619.e11. [PMID: 36868226 DOI: 10.1016/j.ccell.2023.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/20/2022] [Accepted: 02/06/2023] [Indexed: 03/05/2023]
Abstract
Tumor cells promote the recruitment of immunosuppressive neutrophils, a subset of myeloid cells driving immune suppression, tumor proliferation, and treatment resistance. Physiologically, neutrophils are known to have a short half-life. Here, we report the identification of a subset of neutrophils that have upregulated expression of cellular senescence markers and persist in the tumor microenvironment. Senescent-like neutrophils express the triggering receptor expressed on myeloid cells 2 (TREM2) and are more immunosuppressive and tumor-promoting than canonical immunosuppressive neutrophils. Genetic and pharmacological elimination of senescent-like neutrophils decreases tumor progression in different mouse models of prostate cancer. Mechanistically, we have found that apolipoprotein E (APOE) secreted by prostate tumor cells binds TREM2 on neutrophils, promoting their senescence. APOE and TREM2 expression increases in prostate cancers and correlates with poor prognosis. Collectively, these results reveal an alternative mechanism of tumor immune evasion and support the development of immune senolytics targeting senescent-like neutrophils for cancer therapy.
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Affiliation(s)
- Nicolò Bancaro
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland; Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland
| | - Bianca Calì
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland; Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland
| | - Martina Troiani
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland; Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland
| | - Angela Rita Elia
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland; Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland
| | - Rydell Alvarez Arzola
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland; Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland
| | - Giuseppe Attanasio
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland; Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland
| | - Ping Lai
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland; Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland
| | - Mateus Crespo
- The Institute of Cancer Research and the Royal Marsden NHS Foundation Trust, London, UK
| | - Bora Gurel
- The Institute of Cancer Research and the Royal Marsden NHS Foundation Trust, London, UK
| | - Rita Pereira
- The Institute of Cancer Research and the Royal Marsden NHS Foundation Trust, London, UK
| | - Christina Guo
- The Institute of Cancer Research and the Royal Marsden NHS Foundation Trust, London, UK
| | - Simone Mosole
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland; Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland
| | - Daniela Brina
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland; Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland
| | - Mariantonietta D'Ambrosio
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland; Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland
| | - Emiliano Pasquini
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland; Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland
| | - Clarissa Spataro
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland; Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland
| | - Elena Zagato
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland; Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland
| | - Andrea Rinaldi
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland; Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland
| | - Mattia Pedotti
- Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland; Institute for Research in Biomedicine (IRB), 6500 Bellinzona, Switzerland
| | - Simona Di Lascio
- Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland; Institute of Oncology of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), Bellinzona, Switzerland
| | - Francesco Meani
- Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland; Institute of Oncology of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), Bellinzona, Switzerland
| | - Monica Montopoli
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy; Veneto Institute of Molecular Medicine, Padova, Italy
| | - Matteo Ferrari
- Department of Urology, Ente Ospedaliero Cantonale, Ospedale Regionale di Lugano - Civico USI - Università della Svizzera Italiana, Lugano, Switzerland
| | - Andrea Gallina
- Department of Urology, Ente Ospedaliero Cantonale, Ospedale Regionale di Lugano - Civico USI - Università della Svizzera Italiana, Lugano, Switzerland
| | - Luca Varani
- Institute for Research in Biomedicine (IRB), 6500 Bellinzona, Switzerland
| | - Ricardo Pereira Mestre
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland; Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland; Institute of Oncology of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), Bellinzona, Switzerland
| | - Marco Bolis
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland; Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland; Computational Oncology Unit, Department of Oncology, IRCCS Istituto di Ricerche Farmacologiche 'Mario Negri', Via Mario Negri 2, 20156 Milano, Italy
| | - Silke Gillessen Sommer
- Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland; Institute of Oncology of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), Bellinzona, Switzerland
| | - Johann de Bono
- The Institute of Cancer Research and the Royal Marsden NHS Foundation Trust, London, UK
| | - Arianna Calcinotto
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland; Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland.
| | - Andrea Alimonti
- Institute of Oncology Research (IOR), 6500 Bellinzona, Switzerland; Università della Svizzera Italiana, Faculty of Biomedical Sciences, 6900 Lugano, Switzerland; Institute of Oncology of Southern Switzerland (IOSI), Ente Ospedaliero Cantonale (EOC), Bellinzona, Switzerland; Veneto Institute of Molecular Medicine, Padova, Italy; Department of Medicine, University of Padova, Padova, Italy; Department of Health Sciences and Technology (D-HEST) ETH Zurich, 8093 Zurich, Switzerland.
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7
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Bianchini F, Crivelli V, Abernathy ME, Guerra C, Palus M, Muri J, Marcotte H, Piralla A, Pedotti M, De Gasparo R, Simonelli L, Matkovic M, Toscano C, Biggiogero M, Calvaruso V, Svoboda P, Rincón TC, Fava T, Podešvová L, Shanbhag AA, Celoria A, Sgrignani J, Stefanik M, Hönig V, Pranclova V, Michalcikova T, Prochazka J, Guerrini G, Mehn D, Ciabattini A, Abolhassani H, Jarrossay D, Uguccioni M, Medaglini D, Pan-Hammarström Q, Calzolai L, Fernandez D, Baldanti F, Franzetti-Pellanda A, Garzoni C, Sedlacek R, Ruzek D, Varani L, Cavalli A, Barnes CO, Robbiani DF. Human neutralizing antibodies to cold linear epitopes and to subdomain 1 of SARS-CoV-2. bioRxiv 2022:2022.11.24.515932. [PMID: 36482967 PMCID: PMC9727766 DOI: 10.1101/2022.11.24.515932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Emergence of SARS-CoV-2 variants diminishes the efficacy of vaccines and antiviral monoclonal antibodies. Continued development of immunotherapies and vaccine immunogens resilient to viral evolution is therefore necessary. Using coldspot-guided antibody discovery, a screening approach that focuses on portions of the virus spike that are both functionally relevant and averse to change, we identified human neutralizing antibodies to highly conserved viral epitopes. Antibody fp.006 binds the fusion peptide and cross-reacts against coronaviruses of the four genera , including the nine human coronaviruses, through recognition of a conserved motif that includes the S2' site of proteolytic cleavage. Antibody hr2.016 targets the stem helix and neutralizes SARS-CoV-2 variants. Antibody sd1.040 binds to subdomain 1, synergizes with antibody rbd.042 for neutralization and, like fp.006 and hr2.016, protects mice when present as bispecific antibody. Thus, coldspot-guided antibody discovery reveals donor-derived neutralizing antibodies that are cross-reactive with Orthocoronavirinae , including SARS-CoV-2 variants. One sentence summary Broadly cross-reactive antibodies that protect from SARS-CoV-2 variants are revealed by virus coldspot-driven discovery.
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Affiliation(s)
- Filippo Bianchini
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Virginia Crivelli
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | | | - Concetta Guerra
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Martin Palus
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences; Ceske Budejovice, Czech Republic
- Veterinary Research Institute; Brno, Czech Republic
| | - Jonathan Muri
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Harold Marcotte
- Department of Biosciences and Nutrition, Karolinska Institutet; Huddinge, Sweden
| | - Antonio Piralla
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo; Pavia, Italy
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Raoul De Gasparo
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Luca Simonelli
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Milos Matkovic
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Chiara Toscano
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Maira Biggiogero
- Clinical Research Unit, Clinica Luganese Moncucco; Lugano, Switzerland
| | | | - Pavel Svoboda
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences; Ceske Budejovice, Czech Republic
- Veterinary Research Institute; Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University; Brno, Czech Republic
- Department of Pharmacology and Pharmacy, Faculty of Veterinary Medicine, University of Veterinary Sciences; Brno, Czech Republic
| | - Tomás Cervantes Rincón
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Tommaso Fava
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Lucie Podešvová
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Akanksha A. Shanbhag
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Andrea Celoria
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Jacopo Sgrignani
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Michal Stefanik
- Veterinary Research Institute; Brno, Czech Republic
- Department of Chemistry and Biochemistry, Mendel University in Brno; Brno, Czech Republic
| | - Vaclav Hönig
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences; Ceske Budejovice, Czech Republic
- Veterinary Research Institute; Brno, Czech Republic
| | - Veronika Pranclova
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences; Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia; Ceske Budejovice, Czech Republic
| | - Tereza Michalcikova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences; Vestec, Czech Republic
| | - Jan Prochazka
- Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences; Vestec, Czech Republic
| | | | - Dora Mehn
- European Commission, Joint Research Centre (JRC); Ispra, Italy
| | - Annalisa Ciabattini
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies; University of Siena, Siena, Italy
| | - Hassan Abolhassani
- Department of Biosciences and Nutrition, Karolinska Institutet; Huddinge, Sweden
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children’s Medical Center, Tehran University of Medical Sciences; Tehran, Iran
| | - David Jarrossay
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Mariagrazia Uguccioni
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Donata Medaglini
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies; University of Siena, Siena, Italy
| | | | - Luigi Calzolai
- European Commission, Joint Research Centre (JRC); Ispra, Italy
| | - Daniel Fernandez
- Sarafan ChEM-H Macromolecular Structure Knowledge Center, Stanford University; Stanford, USA
| | - Fausto Baldanti
- Microbiology and Virology Department, Fondazione IRCCS Policlinico San Matteo; Pavia, Italy
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia; Pavia, Italy
| | | | - Christian Garzoni
- Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco; Lugano, Switzerland
| | - Radislav Sedlacek
- Czech Centre of Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences; Vestec, Czech Republic
| | - Daniel Ruzek
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences; Ceske Budejovice, Czech Republic
- Veterinary Research Institute; Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University; Brno, Czech Republic
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
- Swiss Institute of Bioinformatics; Lausanne, Switzerland
| | - Christopher O. Barnes
- Department of Biology, Stanford University; Stanford, USA
- Chan Zuckerberg Biohub; San Francisco, USA
| | - Davide F. Robbiani
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
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8
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Muri J, Cecchinato V, Cavalli A, Shanbhag AA, Matkovic M, Biggiogero M, Maida PA, Moritz J, Toscano C, Ghovehoud E, Furlan R, Barbic F, Voza A, Nadai GD, Cervia C, Zurbuchen Y, Taeschler P, Murray LA, Danelon-Sargenti G, Moro S, Gong T, Piffaretti P, Bianchini F, Crivelli V, Podešvová L, Pedotti M, Jarrossay D, Sgrignani J, Thelen S, Uhr M, Bernasconi E, Rauch A, Manzo A, Ciurea A, Rocchi MBL, Varani L, Moser B, Bottazzi B, Thelen M, Fallon BA, Boyman O, Mantovani A, Garzoni C, Franzetti-Pellanda A, Uguccioni M, Robbiani DF. Anti-chemokine antibodies after SARS-CoV-2 infection correlate with favorable disease course. bioRxiv 2022:2022.05.23.493121. [PMID: 35664993 PMCID: PMC9164443 DOI: 10.1101/2022.05.23.493121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Infection by SARS-CoV-2 leads to diverse symptoms, which can persist for months. While antiviral antibodies are protective, those targeting interferons and other immune factors are associated with adverse COVID-19 outcomes. Instead, we discovered that antibodies against specific chemokines are omnipresent after COVID-19, associated with favorable disease, and predictive of lack of long COVID symptoms at one year post infection. Anti-chemokine antibodies are present also in HIV-1 infection and autoimmune disorders, but they target different chemokines than those in COVID-19. Monoclonal antibodies derived from COVID- 19 convalescents that bind to the chemokine N-loop impair cell migration. Given the role of chemokines in orchestrating immune cell trafficking, naturally arising anti-chemokine antibodies associated with favorable COVID-19 may be beneficial by modulating the inflammatory response and thus bear therapeutic potential. One-Sentence Summary Naturally arising anti-chemokine antibodies associate with favorable COVID-19 and predict lack of long COVID.
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Affiliation(s)
- Jonathan Muri
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Valentina Cecchinato
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland.,Swiss Institute of Bioinformatics; Lausanne, Switzerland
| | - Akanksha A Shanbhag
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Milos Matkovic
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Maira Biggiogero
- Clinical Research Unit, Clinica Luganese Moncucco; Lugano, Switzerland
| | - Pier Andrea Maida
- Clinical Research Unit, Clinica Luganese Moncucco; Lugano, Switzerland
| | - Jacques Moritz
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Chiara Toscano
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Elaheh Ghovehoud
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Raffaello Furlan
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Milan, Italy.,Internal Medicine, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Franca Barbic
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Milan, Italy.,Internal Medicine, IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Antonio Voza
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Milan, Italy.,Department of Emergency, IRCCS Humanitas Research Hospital, 20089 Rozzano, Milan, Italy
| | - Guendalina De Nadai
- Emergency Medicine Residency School, Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4 - 20090 Pieve Emanuele, Milan, Italy
| | - Carlo Cervia
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Yves Zurbuchen
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Patrick Taeschler
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Lilly A Murray
- Lyme & Tick-Borne Diseases Research Center at Columbia University Irving Medical Center, New York, NY, USA
| | | | - Simone Moro
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Tao Gong
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Pietro Piffaretti
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Filippo Bianchini
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Virginia Crivelli
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Lucie Podešvová
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - David Jarrossay
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Jacopo Sgrignani
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Sylvia Thelen
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | | | - Enos Bernasconi
- Regional Hospital Lugano, Ente Ospedaliero Cantonale; Lugano, Switzerland.,Università della Svizzera italiana; Lugano, Switzerland
| | - Andri Rauch
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern; Bern, Switzerland
| | - Antonio Manzo
- Rheumatology and Translational Immunology Research Laboratories (LaRIT), Division of Rheumatology, IRCCS Policlinico San Matteo Foundation, University of Pavia; Pavia, Italy
| | - Adrian Ciurea
- Department of Rheumatology, Zurich University Hospital, University of Zurich; Zurich, Switzerland
| | - Marco B L Rocchi
- Department of Biomolecular Sciences, Biostatistics Unit, University of Urbino; Urbino, Italy
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Bernhard Moser
- Division of Infection & Immunity, Henry Wellcome Building, Cardiff University School of Medicine; Cardiff, United Kingdom
| | - Barbara Bottazzi
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Marcus Thelen
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
| | - Brian A Fallon
- Lyme & Tick-Borne Diseases Research Center at Columbia University Irving Medical Center, New York, NY, USA.,Lyme Research Program at the New York State Psychiatric Institute, New York, NY, USA
| | - Onur Boyman
- Department of Immunology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.,Faculty of Medicine and Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Alberto Mantovani
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Milan, Italy.,IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy.,The William Harvey Research Institute, Queen Mary University of London, Charterhouse Square, London, UK
| | - Christian Garzoni
- Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco; Lugano, Switzerland
| | | | - Mariagrazia Uguccioni
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland.,Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20090 Pieve Emanuele, Milan, Italy
| | - Davide F Robbiani
- Institute for Research in Biomedicine, Università della Svizzera italiana; Bellinzona, Switzerland
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9
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Stravalaci M, Pagani I, Paraboschi EM, Pedotti M, Doni A, Scavello F, Mapelli SN, Sironi M, Perucchini C, Varani L, Matkovic M, Cavalli A, Cesana D, Gallina P, Pedemonte N, Capurro V, Clementi N, Mancini N, Invernizzi P, Bayarri-Olmos R, Garred P, Rappuoli R, Duga S, Bottazzi B, Uguccioni M, Asselta R, Vicenzi E, Mantovani A, Garlanda C. Recognition and inhibition of SARS-CoV-2 by humoral innate immunity pattern recognition molecules. Nat Immunol 2022; 23:275-286. [DOI: 10.1038/s41590-021-01114-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 12/09/2021] [Indexed: 12/11/2022]
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10
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Sgrignani J, Cecchinato V, Fassi EMA, D'Agostino G, Garofalo M, Danelon G, Pedotti M, Simonelli L, Varani L, Grazioso G, Uguccioni M, Cavalli A. Systematic Development of Peptide Inhibitors Targeting the CXCL12/HMGB1 Interaction. J Med Chem 2021; 64:13439-13450. [PMID: 34510899 DOI: 10.1021/acs.jmedchem.1c00852] [Citation(s) in RCA: 1] [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: 12/15/2022]
Abstract
During inflammatory reactions, the production and release of chemotactic factors guide the recruitment of selective leukocyte subpopulations. The alarmin HMGB1 and the chemokine CXCL12, both released in the microenvironment, can form a heterocomplex, which exclusively acts on the chemokine receptor CXCR4, enhancing cell migration, and in some pathological conditions such as rheumatoid arthritis exacerbates the immune response. An excessive cell influx at the inflammatory site can be diminished by disrupting the heterocomplex. Here, we report the computationally driven identification of the first peptide (HBP08) binding HMGB1 and selectively inhibiting the activity of the CXCL12/HMGB1 heterocomplex. Furthermore, HBP08 binds HMGB1 with the highest affinity reported so far (Kd of 0.8 ± 0.4 μM). The identification of this peptide represents an important step toward the development of innovative pharmacological tools for the treatment of severe chronic inflammatory conditions characterized by an uncontrolled immune response.
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Affiliation(s)
- Jacopo Sgrignani
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Valentina Cecchinato
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Enrico M A Fassi
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland.,Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, 20133 Milan, Italy
| | - Gianluca D'Agostino
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Maura Garofalo
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Gabriela Danelon
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Luca Simonelli
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, 20133 Milan, Italy
| | - Mariagrazia Uguccioni
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland.,Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, 20090 Milan, Italy
| | - Andrea Cavalli
- Institute for Research in Biomedicine, Università della Svizzera italiana, CH-6500 Bellinzona, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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11
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Chiadò A, Bosco F, Bardelli M, Simonelli L, Pedotti M, Marmo L, Varani L. Rational engineering of the lccβ T. versicolor laccase for the mediator-less oxidation of large polycyclic aromatic hydrocarbons. Comput Struct Biotechnol J 2021; 19:2213-2222. [PMID: 33995914 PMCID: PMC8099718 DOI: 10.1016/j.csbj.2021.03.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 03/08/2021] [Accepted: 03/12/2021] [Indexed: 01/10/2023] Open
Abstract
Computational-assisted protein engineering of the binding pocket of laccases. Mutants have activity increased up to ~ 300% in a broader pH range compared to the WT. Enhanced activity towards bulky PAHs in comparison to the WT enzyme. Ability to oxidize harmful PAH model compounds (dyes) that the WT enzyme cannot modify. Higher oxidation levels without mediators compared to the WT laccase with mediators.
Laccases are among the most sought-after biocatalyst for many green applications, from biosensors to pollution remedial, because they simply need oxygen from the air to oxidize and degrade a broad range of substrates. However, natural laccases cannot process large and toxic polycyclic aromatic hydrocarbons (PAHs) except in the presence of small molecules, called mediators, which facilitate the reaction but are inconvenient for practical on-field applications. Here we exploited structure-based protein engineering to generate rationally modified fungal laccases with increased ability to process bulky PAHs even in a mediator-less reaction. Computational simulations were used to estimate the impact of mutations in the enzymatic binding pocket on the ability to bind and oxidize a selected set of organic compounds. The most promising mutants were produced and their activity was evaluated by biochemical assays with phenolic and non-phenolic substrates. Mutant laccases engineered with a larger binding pocket showed enhanced activity (up to ~ 300% at pH 3.0) in a wider range of pH values (3.0–8.0) in comparison to the wild type enzyme. In contrast to the natural laccase, these mutants efficiently degraded bulky and harmful triphenylmethane dyes such as Ethyl Green (up to 91.64% after 24 h), even in the absence of mediators, with positive implications for the use of such modified laccases in many green chemistry processes (e.g. wastewater treatment).
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Affiliation(s)
- Alessandro Chiadò
- Department of Applied Science and Technology, Politecnico di Torino Corso, Duca degli Abruzzi 24, 10129 Torino, Italy
- Corresponding author.
| | - Francesca Bosco
- Department of Applied Science and Technology, Politecnico di Torino Corso, Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Marco Bardelli
- 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
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vincenzo Vela 6, 6500, Bellinzona, Switzerland
| | - Luca Marmo
- Department of Applied Science and Technology, Politecnico di Torino Corso, Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Via Vincenzo Vela 6, 6500, Bellinzona, Switzerland
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12
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Bertoglio F, Meier D, Langreder N, Steinke S, Rand U, Simonelli L, Heine PA, Ballmann R, Schneider KT, Roth KDR, Ruschig M, Riese P, Eschke K, Kim Y, Schäckermann D, Pedotti M, Kuhn P, Zock-Emmenthal S, Wöhrle J, Kilb N, Herz T, Becker M, Grasshoff M, Wenzel EV, Russo G, Kröger A, Brunotte L, Ludwig S, Fühner V, Krämer SD, Dübel S, Varani L, Roth G, Čičin-Šain L, Schubert M, Hust M. SARS-CoV-2 neutralizing human recombinant antibodies selected from pre-pandemic healthy donors binding at RBD-ACE2 interface. Nat Commun 2021; 12:1577. [PMID: 33707427 PMCID: PMC7952403 DOI: 10.1038/s41467-021-21609-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 01/28/2021] [Indexed: 12/20/2022] Open
Abstract
COVID-19 is a severe acute respiratory disease caused by SARS-CoV-2, a new recently emerged sarbecovirus. This virus uses the human ACE2 enzyme as receptor for cell entry, recognizing it with the receptor binding domain (RBD) of the S1 subunit of the viral spike protein. We present the use of phage display to select anti-SARS-CoV-2 spike antibodies from the human naïve antibody gene libraries HAL9/10 and subsequent identification of 309 unique fully human antibodies against S1. 17 antibodies are binding to the RBD, showing inhibition of spike binding to cells expressing ACE2 as scFv-Fc and neutralize active SARS-CoV-2 virus infection of VeroE6 cells. The antibody STE73-2E9 is showing neutralization of active SARS-CoV-2 as IgG and is binding to the ACE2-RBD interface. Thus, universal libraries from healthy human donors offer the advantage that antibodies can be generated quickly and independent from the availability of material from recovering patients in a pandemic situation.
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Affiliation(s)
- Federico Bertoglio
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | - Doris Meier
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | - Nora Langreder
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | - Stephan Steinke
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | - Ulfert Rand
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Luca Simonelli
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Philip Alexander Heine
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | - Rico Ballmann
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | - Kai-Thomas Schneider
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | - Kristian Daniel Ralph Roth
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | - Maximilian Ruschig
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | - Peggy Riese
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Kathrin Eschke
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Yeonsu Kim
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Dorina Schäckermann
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | - Mattia Pedotti
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | | | | | | | | | | | - Marlies Becker
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | - Martina Grasshoff
- Helmholtz Centre for Infection Research, Research Group Innate Immunity and Infection, Braunschweig, Germany
| | - Esther Veronika Wenzel
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | - Giulio Russo
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | - Andrea Kröger
- Helmholtz Centre for Infection Research, Research Group Innate Immunity and Infection, Braunschweig, Germany
| | - Linda Brunotte
- Westfälische Wilhelms-Universität Münster, Institut für Virologie (IVM), Münster, Germany
| | - Stephan Ludwig
- Westfälische Wilhelms-Universität Münster, Institut für Virologie (IVM), Münster, Germany
| | - Viola Fühner
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | | | - Stefan Dübel
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany
| | - Luca Varani
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland.
| | | | - Luka Čičin-Šain
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Braunschweig, Germany.
- Centre for Individualised Infection Medicine (CIIM), a joint venture of Helmholtz Centre for Infection Research and Medical School Hannover, Braunschweig, Germany.
| | - Maren Schubert
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany.
| | - Michael Hust
- Technische Universität Braunschweig, Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Braunschweig, Germany.
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13
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De Gasparo R, Pedotti M, Simonelli L, Nickl P, Muecksch F, Cassaniti I, Percivalle E, Lorenzi JCC, Mazzola F, Magrì D, Michalcikova T, Haviernik J, Honig V, Mrazkova B, Polakova N, Fortova A, Tureckova J, Iatsiuk V, Girolamo SD, Palus M, Zudova D, Bednar P, Bukova I, Bianchini F, Mehn D, Nencka R, Strakova P, Pavlis O, Rozman J, Gioria S, Camilla Sammartino J, Giardina F, Gaiarsa S, Hammarström QP, Barnes CO, Bjorkman PJ, Calzolai L, Piralla A, Baldanti F, Nussenzweig MC, Bieniasz PD, Hatziioannou T, Prochazka J, Sedlacek R, Robbiani DF, Ruzek D, Varani L. Bispecific antibody neutralizes circulating SARS-CoV-2 variants, prevents escape and protects mice from disease. bioRxiv 2021:2021.01.22.427567. [PMID: 33501434 PMCID: PMC7836104 DOI: 10.1101/2021.01.22.427567] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Neutralizing antibodies targeting the receptor binding domain (RBD) of the SARS-CoV-2 Spike (S) are among the most promising approaches against coronavirus disease 2019 (COVID-19) 1,2 . We developed a bispecific, IgG1-like molecule (CoV-X2) based on two antibodies derived from COVID-19 convalescent donors, C121 and C135 3 . CoV-X2 simultaneously binds two independent sites on the RBD and, unlike its parental antibodies, prevents detectable S binding to Angiotensin-Converting Enzyme 2 (ACE2), the virus cellular receptor. Furthermore, CoV-X2 neutralizes SARS-CoV-2 and its variants of concern, as well as the escape mutants generated by the parental monoclonals. In a novel animal model of SARS-CoV-2 infection with lung inflammation, CoV-X2 protects mice from disease and suppresses viral escape. Thus, simultaneous targeting of non-overlapping RBD epitopes by IgG-like bispecific antibodies is feasible and effective, combining into a single molecule the advantages of antibody cocktails.
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14
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Simonelli L, Pedotti M, Bardelli M, Jurt S, Zerbe O, Varani L. Mapping Antibody Epitopes by Solution NMR Spectroscopy: Practical Considerations. Methods Mol Biol 2018; 1785:29-51. [PMID: 29714010 DOI: 10.1007/978-1-4939-7841-0_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Identifying an epitope, the region of the antigen in contact with an antibody, is useful in both basic and pharmaceutical research, as well as in vaccine design. Solution NMR spectroscopy is particularly well suited to the residue level characterization of intermolecular interfaces, including antibody-antigen interactions, and thus to epitope identification. Here, we describe the use of NMR for residue level characterization of protein epitopes, focusing on experimental protocols and practical considerations, highlighting advantages and drawbacks of the approach.
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Affiliation(s)
- Luca Simonelli
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Marco Bardelli
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Simon Jurt
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Luca Varani
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland.
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15
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La Spina R, Ferrero VEV, Aiello V, Pedotti M, Varani L, Lettieri T, Calzolai L, Haasnoot W, Colpo P. Label-Free Biosensor Detection of Endocrine Disrupting Compounds Using Engineered Estrogen Receptors. Biosensors (Basel) 2017; 8:E1. [PMID: 29271936 PMCID: PMC5872049 DOI: 10.3390/bios8010001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 12/15/2017] [Accepted: 12/19/2017] [Indexed: 01/28/2023]
Abstract
Endocrine Disrupting Compounds (EDCs) are chemical substances shown to interfere with endogenous hormones affecting the endocrine, immune and nervous systems of mammals. EDCs are the causative agents of diseases including reproductive disorders and cancers. This highlights the urgency to develop fast and sensitive methods to detect EDCs, which are detrimental even at very low concentrations. In this work, we propose a label-free surface plasmon resonance (SPR) biosensor method to detect specific EDCs (17 β-estradiol (E2), ethinyl-estradiol, 4-nonylphenol, tamoxifen) through their binding to estrogen receptor alpha (ERα). We show that the use of rationally designed ERα (as bio-recognition element) in combination with conformation-sensitive peptides (as amplification agent, resulting in increased responses) enables the detection of low parts per billion (ppb) levels of E2. As a proof of concept, this bioassay was used to detect E2 in (spiked) real water samples from fish farms, rivers and the sea at low ppb levels after concentration by solid phase extraction. In addition, the present SPR assay that combines a conformation-sensitive peptide with an array of ERα mutants is very promising for the assessment of the risk of potential estrogenic activity for chemical substances.
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Affiliation(s)
- Rita La Spina
- European Commission-DG Joint Research Centre, Directorate Health Consumer and Reference Materials, 21027 Ispra, Italy.
| | - Valentina E V Ferrero
- European Commission-DG Joint Research Centre, Directorate Sustainable Resources, 21027 Ispra, Italy.
| | - Venera Aiello
- European Commission-DG Joint Research Centre, Directorate Health Consumer and Reference Materials, 21027 Ispra, Italy.
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500 Bellinzona, Switzerland.
| | - Luca Varani
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500 Bellinzona, Switzerland.
| | - Teresa Lettieri
- European Commission-DG Joint Research Centre, Directorate Sustainable Resources, 21027 Ispra, Italy.
| | - Luigi Calzolai
- European Commission-DG Joint Research Centre, Directorate Health Consumer and Reference Materials, 21027 Ispra, Italy.
| | - Willem Haasnoot
- Authenticity & Bioassays, RIKILT Wageningen University & Research, Wageningen University, 6708 WB Wageningen, The Netherlands.
| | - Pascal Colpo
- European Commission-DG Joint Research Centre, Directorate Health Consumer and Reference Materials, 21027 Ispra, Italy.
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16
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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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17
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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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18
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Simonelli L, Pedotti M, Beltramello M, Livoti E, Calzolai L, Sallusto F, Lanzavecchia A, Varani L. Rational engineering of a human anti-dengue antibody through experimentally validated computational docking. PLoS One 2013; 8:e55561. [PMID: 23405171 PMCID: PMC3566030 DOI: 10.1371/journal.pone.0055561] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [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: 10/17/2012] [Accepted: 12/27/2012] [Indexed: 12/05/2022] Open
Abstract
Antibodies play an increasing pivotal role in both basic research and the biopharmaceutical sector, therefore technology for characterizing and improving their properties through rational engineering is desirable. This is a difficult task thought to require high-resolution x-ray structures, which are not always available. We, instead, use a combination of solution NMR epitope mapping and computational docking to investigate the structure of a human antibody in complex with the four Dengue virus serotypes. Analysis of the resulting models allows us to design several antibody mutants altering its properties in a predictable manner, changing its binding selectivity and ultimately improving its ability to neutralize the virus by up to 40 fold. The successful rational design of antibody mutants is a testament to the accuracy achievable by combining experimental NMR epitope mapping with computational docking and to the possibility of applying it to study antibody/pathogen interactions.
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Affiliation(s)
- Luca Simonelli
- Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Bellinzona, Switzerland
| | | | - Elsa Livoti
- Institute for Research in Biomedicine, Bellinzona, Switzerland
| | - Luigi Calzolai
- Institute for Health and Consumer Protection, Joint Research Centre, Ispra, Italy
| | | | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Bellinzona, Switzerland
- Institute of Microbiology, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Luca Varani
- Institute for Research in Biomedicine, Bellinzona, Switzerland
- * E-mail:
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19
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Schiraldi M, Raucci A, Muñoz LM, Livoti E, Celona B, Venereau E, Apuzzo T, De Marchis F, Pedotti M, Bachi A, Thelen M, Varani L, Mellado M, Proudfoot A, Bianchi ME, Uguccioni M. HMGB1 promotes recruitment of inflammatory cells to damaged tissues by forming a complex with CXCL12 and signaling via CXCR4. ACTA ACUST UNITED AC 2012; 209:551-63. [PMID: 22370717 PMCID: PMC3302219 DOI: 10.1084/jem.20111739] [Citation(s) in RCA: 474] [Impact Index Per Article: 39.5] [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] [Indexed: 02/04/2023]
Abstract
CXCL12 forms a complex with HMGB1 that binds to the chemokine receptor CXCR4 and increases inflammatory cell migration. After tissue damage, inflammatory cells infiltrate the tissue and release proinflammatory cytokines. HMGB1 (high mobility group box 1), a nuclear protein released by necrotic and severely stressed cells, promotes cytokine release via its interaction with the TLR4 (Toll-like receptor 4) receptor and cell migration via an unknown mechanism. We show that HMGB1-induced recruitment of inflammatory cells depends on CXCL12. HMGB1 and CXCL12 form a heterocomplex, which we characterized by nuclear magnetic resonance and surface plasmon resonance, that acts exclusively through CXCR4 and not through other HMGB1 receptors. Fluorescence resonance energy transfer data show that the HMGB1–CXCL12 heterocomplex promotes different conformational rearrangements of CXCR4 from that of CXCL12 alone. Mononuclear cell recruitment in vivo into air pouches and injured muscles depends on the heterocomplex and is inhibited by AMD3100 and glycyrrhizin. Thus, inflammatory cell recruitment and activation both depend on HMGB1 via different mechanisms.
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Affiliation(s)
- Milena Schiraldi
- Institute for Research in Biomedicine, 6500 Bellinzona, Switzerland
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20
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Pedotti M, Rosini E, Molla G, Moschetti T, Savino C, Vallone B, Pollegioni L. Glyphosate resistance by engineering the flavoenzyme glycine oxidase. J Biol Chem 2009; 284:36415-36423. [PMID: 19864430 PMCID: PMC2794757 DOI: 10.1074/jbc.m109.051631] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2009] [Revised: 10/12/2009] [Indexed: 11/06/2022] Open
Abstract
Glycine oxidase from Bacillus subtilis is a homotetrameric flavoprotein of great potential biotechnological use because it catalyzes the oxidative deamination of various amines and d-isomer of amino acids to yield the corresponding alpha-keto acids, ammonia/amine, and hydrogen peroxide. Glyphosate (N-phosphonomethylglycine), a broad spectrum herbicide, is an interesting synthetic amino acid: this compound inhibits 5-enolpyruvylshikimate-3-phosphate synthase in the shikimate pathway, which is essential for the biosynthesis of aromatic amino acids in plants and certain bacteria. In recent years, transgenic crops resistant to glyphosate were mainly generated by overproducing the plant enzyme or by introducing a 5-enolpyruvylshikimate-3-phosphate synthase insensitive to this herbicide. In this work, we propose that the enzymatic oxidation of glyphosate could be an effective alternative to this important biotechnological process. To reach this goal, we used a rational design approach (together with site saturation mutagenesis) to generate a glycine oxidase variant more active on glyphosate than on the physiological substrate glycine. The glycine oxidase containing three point mutations (G51S/A54R/H244A) reaches an up to a 210-fold increase in catalytic efficiency and a 15,000-fold increase in the specificity constant (the k(cat)/K(m) ratio between glyphosate and glycine) as compared with wild-type glycine oxidase. The inspection of its three-dimensional structure shows that the alpha2-alpha3 loop (comprising residues 50-60 and containing two of the mutated residues) assumes a novel conformation and that the newly introduced residue Arg(54) could be the key residue in stabilizing glyphosate binding and destabilizing glycine positioning in the binding site, thus increasing efficiency on the herbicide.
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Affiliation(s)
- Mattia Pedotti
- Dipartimento di Biotecnologie e Scienze Molecolari and the Centro Interuniversitario di Ricerca in Biotecnologie Proteiche "The Protein Factory," Politecnico di Milano, Università degli Studi dell'Insubria, 21100 Varese, Italy
| | - Elena Rosini
- Dipartimento di Biotecnologie e Scienze Molecolari and the Centro Interuniversitario di Ricerca in Biotecnologie Proteiche "The Protein Factory," Politecnico di Milano, Università degli Studi dell'Insubria, 21100 Varese, Italy
| | - Gianluca Molla
- Dipartimento di Biotecnologie e Scienze Molecolari and the Centro Interuniversitario di Ricerca in Biotecnologie Proteiche "The Protein Factory," Politecnico di Milano, Università degli Studi dell'Insubria, 21100 Varese, Italy
| | - Tommaso Moschetti
- Department of Biochemical Sciences, "Sapienza," University of Rome, 00185 Rome, Italy
| | - Carmelinda Savino
- Consiglio Nazionale delle Richerche Institute of Molecular Biology and Pathology, 00185 Rome, Italy
| | - Beatrice Vallone
- Department of Biochemical Sciences, "Sapienza," University of Rome, 00185 Rome, Italy
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze Molecolari and the Centro Interuniversitario di Ricerca in Biotecnologie Proteiche "The Protein Factory," Politecnico di Milano, Università degli Studi dell'Insubria, 21100 Varese, Italy.
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21
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Pedotti M, Rosini E, Molla G, Pollegioni L. Engineering the substrate specificity of glycine oxidase: a new mechanism of glyphosate resistance. N Biotechnol 2009. [DOI: 10.1016/j.nbt.2009.06.899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Pedotti M, Ghisla S, Motteran L, Molla G, Pollegioni L. Catalytic and redox properties of glycine oxidase from Bacillus subtilis. Biochimie 2009; 91:604-12. [DOI: 10.1016/j.biochi.2009.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 02/18/2009] [Indexed: 10/21/2022]
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23
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Piubelli L, Pedotti M, Molla G, Feindler-Boeckh S, Ghisla S, Pilone MS, Pollegioni L. On the oxygen reactivity of flavoprotein oxidases: an oxygen access tunnel and gate in brevibacterium sterolicum cholesterol oxidase. J Biol Chem 2008; 283:24738-47. [PMID: 18614534 DOI: 10.1074/jbc.m802321200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The flavoprotein cholesterol oxidase from Brevibacterium sterolicum (BCO) possesses a narrow channel that links the active center containing the flavin to the outside solvent. This channel has been proposed to serve for the access of dioxygen; it contains at its "bottom" a Glu-Arg pair (Glu-475-Arg-477) that was found by crystallographic studies to exist in two forms named "open" and "closed," which in turn was suggested to constitute a gate functioning in the control of oxygen access. Most mutations of residues that flank the channel have minor effects on the oxygen reactivity. Mutations of Glu-311, however, cause a switch in the basic kinetic mechanism of the reaction of reduced BCO with dioxygen; wild-type BCO and most mutants show a saturation behavior with increasing oxygen concentration, whereas for Glu-311 mutants a linear dependence is found that is assumed to reflect a "simple" second order process. This is taken as support for the assumption that residue Glu-311 finely tunes the Glu-475-Arg-477 pair, forming a gate that functions in modulating the access/reactivity of dioxygen.
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Affiliation(s)
- Luciano Piubelli
- Department of Biotechnology and Molecular Sciences, University of Insubria, 21100 Varese, Italy
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