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Schiffner T, Phung I, Ray R, Irimia A, Tian M, Swanson O, Lee JH, Lee CCD, Marina-Zárate E, Cho SY, Huang J, Ozorowski G, Skog PD, Serra AM, Rantalainen K, Allen JD, Baboo S, Rodriguez OL, Himansu S, Zhou J, Hurtado J, Flynn CT, McKenney K, Havenar-Daughton C, Saha S, Shields K, Schultze S, Smith ML, Liang CH, Toy L, Pecetta S, Lin YC, Willis JR, Sesterhenn F, Kulp DW, Hu X, Cottrell CA, Zhou X, Ruiz J, Wang X, Nair U, Kirsch KH, Cheng HL, Davis J, Kalyuzhniy O, Liguori A, Diedrich JK, Ngo JT, Lewis V, Phelps N, Tingle RD, Spencer S, Georgeson E, Adachi Y, Kubitz M, Eskandarzadeh S, Elsliger MA, Amara RR, Landais E, Briney B, Burton DR, Carnathan DG, Silvestri G, Watson CT, Yates JR, Paulson JC, Crispin M, Grigoryan G, Ward AB, Sok D, Alt FW, Wilson IA, Batista FD, Crotty S, Schief WR. Vaccination induces broadly neutralizing antibody precursors to HIV gp41. Nat Immunol 2024; 25:1073-1082. [PMID: 38816615 PMCID: PMC11147780 DOI: 10.1038/s41590-024-01833-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Accepted: 04/04/2024] [Indexed: 06/01/2024]
Abstract
A key barrier to the development of vaccines that induce broadly neutralizing antibodies (bnAbs) against human immunodeficiency virus (HIV) and other viruses of high antigenic diversity is the design of priming immunogens that induce rare bnAb-precursor B cells. The high neutralization breadth of the HIV bnAb 10E8 makes elicitation of 10E8-class bnAbs desirable; however, the recessed epitope within gp41 makes envelope trimers poor priming immunogens and requires that 10E8-class bnAbs possess a long heavy chain complementarity determining region 3 (HCDR3) with a specific binding motif. We developed germline-targeting epitope scaffolds with affinity for 10E8-class precursors and engineered nanoparticles for multivalent display. Scaffolds exhibited epitope structural mimicry and bound bnAb-precursor human naive B cells in ex vivo screens, protein nanoparticles induced bnAb-precursor responses in stringent mouse models and rhesus macaques, and mRNA-encoded nanoparticles triggered similar responses in mice. Thus, germline-targeting epitope scaffold nanoparticles can elicit rare bnAb-precursor B cells with predefined binding specificities and HCDR3 features.
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Affiliation(s)
- Torben Schiffner
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Institute for Drug Discovery, Leipzig University Medical Faculty, Leipzig, Germany
| | - Ivy Phung
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Rashmi Ray
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Adriana Irimia
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ming Tian
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Olivia Swanson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Jeong Hyun Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Chang-Chun D Lee
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ester Marina-Zárate
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - So Yeon Cho
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jiachen Huang
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gabriel Ozorowski
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Patrick D Skog
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Andreia M Serra
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Kimmo Rantalainen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Joel D Allen
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Sabyasachi Baboo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Oscar L Rodriguez
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | | | - Jianfu Zhou
- Department of Computer Science, Dartmouth College, Hanover, NH, USA
| | - Jonathan Hurtado
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Claudia T Flynn
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Katherine McKenney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Colin Havenar-Daughton
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Swati Saha
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Kaitlyn Shields
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Steven Schultze
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Melissa L Smith
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - Chi-Hui Liang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Laura Toy
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Simone Pecetta
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Ying-Cing Lin
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Jordan R Willis
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Fabian Sesterhenn
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Daniel W Kulp
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Xiaozhen Hu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Christopher A Cottrell
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Xiaoya Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Jennifer Ruiz
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Xuesong Wang
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Usha Nair
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Kathrin H Kirsch
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Hwei-Ling Cheng
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jillian Davis
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Oleksandr Kalyuzhniy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Alessia Liguori
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Julia T Ngo
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Vanessa Lewis
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Nicole Phelps
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Ryan D Tingle
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Skye Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Erik Georgeson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Yumiko Adachi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Michael Kubitz
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Saman Eskandarzadeh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Marc A Elsliger
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rama R Amara
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Microbiology and Immunology, Emory School of Medicine, Atlanta, GA, USA
| | - Elise Landais
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Bryan Briney
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Multi-omics Vaccine Evaluation Consortium, The Scripps Research Institute, La Jolla, CA, USA
- San Diego Center for AIDS Research, The Scripps Research Institute, La Jolla, CA, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA
| | - Diane G Carnathan
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
| | - Guido Silvestri
- Division of Microbiology and Immunology, Emory National Primate Research Center, Emory University, Atlanta, GA, USA
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - James C Paulson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Gevorg Grigoryan
- Department of Computer Science, Dartmouth College, Hanover, NH, USA
- Department of Biological Sciences, Dartmouth College, Hanover, NH, USA
- Generate Biomedicines, Inc., Somerville, MA, USA
| | - Andrew B Ward
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Devin Sok
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Ian A Wilson
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Facundo D Batista
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Shane Crotty
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - William R Schief
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
- IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA.
- Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVD), The Scripps Research Institute, La Jolla, CA, USA.
- The Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA.
- Moderna, Inc., Cambridge, MA, USA.
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Dumonteil E, Tu W, Desale H, Goff K, Marx P, Ortega-Lopez J, Herrera C. Immunoglobulin and T cell receptor repertoire changes induced by a prototype vaccine against Chagas disease in naïve rhesus macaques. J Biomed Sci 2024; 31:58. [PMID: 38824576 PMCID: PMC11143712 DOI: 10.1186/s12929-024-01050-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 05/27/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND A vaccine against Trypanosoma cruzi, the agent of Chagas disease, would be an excellent additional tool for disease control. A recombinant vaccine based on Tc24 and TSA1 parasite antigens was found to be safe and immunogenic in naïve macaques. METHODS We used RNA-sequencing and performed a transcriptomic analysis of PBMC responses to vaccination of naïve macaques after each vaccine dose, to shed light on the immunogenicity of this vaccine and guide the optimization of doses and formulation. We identified differentially expressed genes and pathways and characterized immunoglobulin and T cell receptor repertoires. RESULTS RNA-sequencing analysis indicated a clear transcriptomic response of PBMCs after three vaccine doses, with the up-regulation of several immune cell activation pathways and a broad non-polarized immune profile. Analysis of the IgG repertoire showed that it had a rapid turnover with novel IgGs produced following each vaccine dose, while the TCR repertoire presented several persisting clones that were expanded after each vaccine dose. CONCLUSIONS These data suggest that three vaccine doses may be needed for optimum immunogenicity and support the further evaluation of the protective efficacy of this vaccine.
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Affiliation(s)
- Eric Dumonteil
- Department of Tropical Medicine and Infectious Disease, School of Public Health and Tropical Medicine, and Vector-Borne and Infectious Disease Research Center, Tulane University, 1440 Canal St, New Orleans, Louisiana, 70112, USA.
| | - Weihong Tu
- Department of Tropical Medicine and Infectious Disease, School of Public Health and Tropical Medicine, and Vector-Borne and Infectious Disease Research Center, Tulane University, 1440 Canal St, New Orleans, Louisiana, 70112, USA
| | - Hans Desale
- Department of Tropical Medicine and Infectious Disease, School of Public Health and Tropical Medicine, and Vector-Borne and Infectious Disease Research Center, Tulane University, 1440 Canal St, New Orleans, Louisiana, 70112, USA
| | - Kelly Goff
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA, USA
| | - Preston Marx
- Department of Tropical Medicine and Infectious Disease, School of Public Health and Tropical Medicine, and Vector-Borne and Infectious Disease Research Center, Tulane University, 1440 Canal St, New Orleans, Louisiana, 70112, USA
- Division of Microbiology, Tulane National Primate Research Center, Tulane University, Covington, LA, USA
| | - Jaime Ortega-Lopez
- Departamento de Biotecnología y Bioingeniería, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de Mexico, México
| | - Claudia Herrera
- Department of Tropical Medicine and Infectious Disease, School of Public Health and Tropical Medicine, and Vector-Borne and Infectious Disease Research Center, Tulane University, 1440 Canal St, New Orleans, Louisiana, 70112, USA
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3
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Joshi VR, Claiborne DT, Pack ML, Power KA, Newman RM, Batorsky R, Bean DJ, Goroff MS, Lingwood D, Seaman MS, Rosenberg E, Allen TM. A VRC13-like bNAb response is associated with complex escape pathways in HIV-1 envelope. J Virol 2024; 98:e0172023. [PMID: 38412036 PMCID: PMC10949433 DOI: 10.1128/jvi.01720-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 02/07/2024] [Indexed: 02/29/2024] Open
Abstract
The rational design of HIV-1 immunogens to trigger the development of broadly neutralizing antibodies (bNAbs) requires understanding the viral evolutionary pathways influencing this process. An acute HIV-1-infected individual exhibiting >50% plasma neutralization breadth developed neutralizing antibody specificities against the CD4-binding site (CD4bs) and V1V2 regions of Env gp120. Comparison of pseudoviruses derived from early and late autologous env sequences demonstrated the development of >2 log resistance to VRC13 but not to other CD4bs-specific bNAbs. Mapping studies indicated that the V3 and CD4-binding loops of Env gp120 contributed significantly to developing resistance to the autologous neutralizing response and that the CD4-binding loop (CD4BL) specifically was responsible for the developing resistance to VRC13. Tracking viral evolution during the development of this cross-neutralizing CD4bs response identified amino acid substitutions arising at only 4 of 11 known VRC13 contact sites (K282, T283, K421, and V471). However, each of these mutations was external to the V3 and CD4BL regions conferring resistance to VRC13 and was transient in nature. Rather, complete resistance to VRC13 was achieved through the cooperative expression of a cluster of single amino acid changes within and immediately adjacent to the CD4BL, including a T359I substitution, exchange of a potential N-linked glycosylation (PNLG) site to residue S362 from N363, and a P369L substitution. Collectively, our data characterize complex HIV-1 env evolution in an individual developing resistance to a VRC13-like neutralizing antibody response and identify novel VRC13-associated escape mutations that may be important to inducing VRC13-like bNAbs for lineage-based immunogens.IMPORTANCEThe pursuit of eliciting broadly neutralizing antibodies (bNAbs) through vaccination and their use as therapeutics remains a significant focus in the effort to eradicate HIV-1. Key to our understanding of this approach is a more extensive understanding of bNAb contact sites and susceptible escape mutations in HIV-1 envelope (env). We identified a broad neutralizer exhibiting VRC13-like responses, a non-germline restricted class of CD4-binding site antibody distinct from the well-studied VRC01-class. Through longitudinal envelope sequencing and Env-pseudotyped neutralization assays, we characterized a complex escape pathway requiring the cooperative evolution of four amino acid changes to confer complete resistance to VRC13. This suggests that VRC13-class bNAbs may be refractory to rapid escape and attractive for therapeutic applications. Furthermore, the identification of longitudinal viral changes concomitant with the development of neutralization breadth may help identify the viral intermediates needed for the maturation of VRC13-like responses and the design of lineage-based immunogens.
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Affiliation(s)
- Vinita R. Joshi
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Virology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Virus Immunology, Leibniz Institute of Virology, Hamburg, Germany
| | - Daniel T. Claiborne
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Melissa L. Pack
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Karen A. Power
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ruchi M. Newman
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rebecca Batorsky
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - David J. Bean
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Matthew S. Goroff
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Daniel Lingwood
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael S. Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Eric Rosenberg
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Todd M. Allen
- Ragon Institute of Mass General, MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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4
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Serebrovskaya EO, Bryushkova EA, Lukyanov DK, Mushenkova NV, Chudakov DM, Turchaninova MA. Toolkit for mapping the clonal landscape of tumor-infiltrating B cells. Semin Immunol 2024; 72:101864. [PMID: 38301345 DOI: 10.1016/j.smim.2024.101864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 02/03/2024]
Abstract
Our current understanding of whether B cell involvement in the tumor microenvironment benefits the patient or the tumor - in distinct cancers, subcohorts and individual patients - is quite limited. Both statements are probably true in most cases: certain clonal B cell populations contribute to the antitumor response, while others steer the immune response away from the desired mechanics. To step up to a new level of understanding and managing B cell behaviors in the tumor microenvironment, we need to rationally discern these roles, which are cumulatively defined by B cell clonal functional programs, specificities of their B cell receptors, specificities and isotypes of the antibodies they produce, and their spatial interactions within the tumor environment. Comprehensive analysis of these characteristics of clonal B cell populations is now becoming feasible with the development of a whole arsenal of advanced technical approaches, which include (1) methods of single-cell and spatial transcriptomics, genomics, and proteomics; (2) methods of massive identification of B cell specificities; (3) methods of deep error-free profiling of B cell receptor repertoires. Here we overview existing techniques, summarize their current application for B cells studies and propose promising future directions in advancing B cells exploration.
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Affiliation(s)
- E O Serebrovskaya
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Current position: Miltenyi Biotec B.V. & Co. KG, Bergisch Gladbach, Germany
| | - E A Bryushkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Department of Molecular Biology, Lomonosov Moscow State University, Moscow, Russia
| | - D K Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - N V Mushenkova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Unicorn Capital Partners, 119049, Moscow, Russia
| | - D M Chudakov
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia; Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - M A Turchaninova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
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5
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Raybould MIJ, Turnbull OM, Suter A, Guloglu B, Deane CM. Contextualising the developability risk of antibodies with lambda light chains using enhanced therapeutic antibody profiling. Commun Biol 2024; 7:62. [PMID: 38191620 PMCID: PMC10774428 DOI: 10.1038/s42003-023-05744-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/26/2023] [Indexed: 01/10/2024] Open
Abstract
Antibodies with lambda light chains (λ-antibodies) are generally considered to be less developable than those with kappa light chains (κ-antibodies). Though this hypothesis has not been formally established, it has led to substantial systematic biases in drug discovery pipelines and thus contributed to kappa dominance amongst clinical-stage therapeutics. However, the identification of increasing numbers of epitopes preferentially engaged by λ-antibodies shows there is a functional cost to neglecting to consider them as potential lead candidates. Here, we update our Therapeutic Antibody Profiler (TAP) tool to use the latest data and machine learning-based structure prediction, and apply it to evaluate developability risk profiles for κ-antibodies and λ-antibodies based on their surface physicochemical properties. We find that while human λ-antibodies on average have a higher risk of developability issues than κ-antibodies, a sizeable proportion are assigned lower-risk profiles by TAP and should represent more tractable candidates for therapeutic development. Through a comparative analysis of the low- and high-risk populations, we highlight opportunities for strategic design that TAP suggests would enrich for more developable λ-antibodies. Overall, we provide context to the differing developability of κ- and λ-antibodies, enabling a rational approach to incorporate more diversity into the initial pool of immunotherapeutic candidates.
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Affiliation(s)
- Matthew I J Raybould
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
| | - Oliver M Turnbull
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
| | - Annabel Suter
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
| | - Bora Guloglu
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK
| | - Charlotte M Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, 24-29 St Giles', Oxford, OX1 3LB, UK.
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6
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De Souza Cordeiro LM, Atkinson KC, Aivazian A, Joyce PF, Jia F, Mascioni A. Electrostatic properties of human germlines and biodistribution of small biologics. MAbs 2024; 16:2311991. [PMID: 38334129 PMCID: PMC10860348 DOI: 10.1080/19420862.2024.2311991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/25/2024] [Indexed: 02/10/2024] Open
Abstract
Off-target biodistribution of biologics bears important toxicological consequences. Antibody fragments intended for use as vectors of cytotoxic payloads (e.g. antibody-drug conjugates, radiotherapy) can accumulate at clearance organs like kidneys and liver, where they can cause dose-limiting toxicities. Renal and hepatic uptakes are known to be affected by protein electrostatics, which promote protein internalization through pinocytosis. Using minibodies as a model of an antibody fragment lacking FcRn recycling, we compared the biodistributions of leads with different degrees of accumulation at the kidney and liver. We identified a positive electrostatic patch highly conserved in a germline family very commonly used in the humanization of approved biologics. Neutralization of this patch led to a drastic reduction in the kidney uptake, leading to a biodistribution more favorable to the delivery of highly cytotoxic payloads. Next, we conducted a high throughput study of the electrostatic properties for all combinations of VH and VL germlines. This analysis shows how different VH/VL combinations exhibit varying tendencies to create electrostatic patches, resulting in Fv variants with different isoelectric points. Our work emphasizes the importance of carefully selecting germlines for humanization with optimal electrostatic properties in order to control the unspecific tissue uptake of low molecular weight biologics.
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Affiliation(s)
| | | | - Argin Aivazian
- Preclinical discovery, ImaginAb, Inc, Inglewood, CA, USA
| | | | - Fang Jia
- Preclinical discovery, ImaginAb, Inc, Inglewood, CA, USA
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7
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Thai E, Murugan R, Binter Š, Burn Aschner C, Prieto K, Kassardjian A, Obraztsova AS, Kang RW, Flores-Garcia Y, Mathis-Torres S, Li K, Horn GQ, Huntwork RHC, Bolscher JM, de Bruijni MHC, Sauerwein R, Dennison SM, Tomaras GD, Zavala F, Kellam P, Wardemann H, Julien JP. Molecular determinants of cross-reactivity and potency by VH3-33 antibodies against the Plasmodium falciparum circumsporozoite protein. Cell Rep 2023; 42:113330. [PMID: 38007690 PMCID: PMC10720262 DOI: 10.1016/j.celrep.2023.113330] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 11/27/2023] Open
Abstract
IGHV3-33-encoded antibodies are prevalent in the human humoral response against the Plasmodium falciparum circumsporozoite protein (PfCSP). Among VH3-33 antibodies, cross-reactivity between PfCSP major repeat (NANP), minor (NVDP), and junctional (NPDP) motifs is associated with high affinity and potent parasite inhibition. However, the molecular basis of antibody cross-reactivity and the relationship with efficacy remain unresolved. Here, we perform an extensive structure-function characterization of 12 VH3-33 anti-PfCSP monoclonal antibodies (mAbs) with varying degrees of cross-reactivity induced by immunization of mice expressing a human immunoglobulin gene repertoire. We identify residues in the antibody paratope that mediate cross-reactive binding and delineate four distinct epitope conformations induced by antibody binding, with one consistently associated with high protective efficacy and another that confers comparably potent inhibition of parasite liver invasion. Our data show a link between molecular features of cross-reactive VH3-33 mAb binding to PfCSP and mAb potency, relevant for the development of antibody-based interventions against malaria.
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Affiliation(s)
- Elaine Thai
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Rajagopal Murugan
- B Cell Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Špela Binter
- Kymab Ltd./Sanofi, The Bennet Building (B930), Babraham Research Campus, Cambridge CB22 3AT, UK; RQ Biotechnology Limited, 7th Floor Lynton House, 7-12 Tavistock Square, London WC1H 9LT, UK
| | - Clare Burn Aschner
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Katherine Prieto
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Audrey Kassardjian
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Anna S Obraztsova
- B Cell Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Biosciences Faculty, University of Heidelberg, 69117 Heidelberg, Germany
| | - Ryu Won Kang
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Yevel Flores-Garcia
- Department of Molecular Microbiology and Immunology, Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Shamika Mathis-Torres
- Department of Molecular Microbiology and Immunology, Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Kan Li
- Departments of Surgery, Integrative Immunobiology, Molecular Genetics, and Microbiology, Center for Human Systems Immunology, Duke University, Durham, NC 27710, USA
| | - Gillian Q Horn
- Departments of Surgery, Integrative Immunobiology, Molecular Genetics, and Microbiology, Center for Human Systems Immunology, Duke University, Durham, NC 27710, USA
| | - Richard H C Huntwork
- Departments of Surgery, Integrative Immunobiology, Molecular Genetics, and Microbiology, Center for Human Systems Immunology, Duke University, Durham, NC 27710, USA
| | | | | | | | - S Moses Dennison
- Departments of Surgery, Integrative Immunobiology, Molecular Genetics, and Microbiology, Center for Human Systems Immunology, Duke University, Durham, NC 27710, USA
| | - Georgia D Tomaras
- Departments of Surgery, Integrative Immunobiology, Molecular Genetics, and Microbiology, Center for Human Systems Immunology, Duke University, Durham, NC 27710, USA
| | - Fidel Zavala
- Department of Molecular Microbiology and Immunology, Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Paul Kellam
- Kymab Ltd./Sanofi, The Bennet Building (B930), Babraham Research Campus, Cambridge CB22 3AT, UK; RQ Biotechnology Limited, 7th Floor Lynton House, 7-12 Tavistock Square, London WC1H 9LT, UK; Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London SW7 2BX, UK
| | - Hedda Wardemann
- B Cell Immunology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada; Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada.
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8
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Banach BB, Pletnev S, Olia AS, Xu K, Zhang B, Rawi R, Bylund T, Doria-Rose NA, Nguyen TD, Fahad AS, Lee M, Lin BC, Liu T, Louder MK, Madan B, McKee K, O'Dell S, Sastry M, Schön A, Bui N, Shen CH, Wolfe JR, Chuang GY, Mascola JR, Kwong PD, DeKosky BJ. Antibody-directed evolution reveals a mechanism for enhanced neutralization at the HIV-1 fusion peptide site. Nat Commun 2023; 14:7593. [PMID: 37989731 PMCID: PMC10663459 DOI: 10.1038/s41467-023-42098-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 09/25/2023] [Indexed: 11/23/2023] Open
Abstract
The HIV-1 fusion peptide (FP) represents a promising vaccine target, but global FP sequence diversity among circulating strains has limited anti-FP antibodies to ~60% neutralization breadth. Here we evolve the FP-targeting antibody VRC34.01 in vitro to enhance FP-neutralization using site saturation mutagenesis and yeast display. Successive rounds of directed evolution by iterative selection of antibodies for binding to resistant HIV-1 strains establish a variant, VRC34.01_mm28, as a best-in-class antibody with 10-fold enhanced potency compared to the template antibody and ~80% breadth on a cross-clade 208-strain neutralization panel. Structural analyses demonstrate that the improved paratope expands the FP binding groove to accommodate diverse FP sequences of different lengths while also recognizing the HIV-1 Env backbone. These data reveal critical antibody features for enhanced neutralization breadth and potency against the FP site of vulnerability and accelerate clinical development of broad HIV-1 FP-targeting vaccines and therapeutics.
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Affiliation(s)
- Bailey B Banach
- Bioengineering Graduate Program, The University of Kansas, Lawrence, KS, 66045, USA
| | - Sergei Pletnev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Adam S Olia
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Kai Xu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH, 43210, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Tatsiana Bylund
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Thuy Duong Nguyen
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66045, USA
| | - Ahmed S Fahad
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66045, USA
| | - Myungjin Lee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Bob C Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Tracy Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Bharat Madan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66045, USA
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Mallika Sastry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Arne Schön
- Department of Biology, John Hopkins University, Baltimore, MD, 21218, USA
| | - Natalie Bui
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66045, USA
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Jacy R Wolfe
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66045, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20814, USA.
| | - Brandon J DeKosky
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66045, USA.
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS, 66045, USA.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA.
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9
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Dumonteil E, Tu W, Desale H, Goff K, Marx P, Ortega-Lopez J, Herrera C. Immunoglobin and T cell receptor repertoire changes induced by a prototype vaccine against Chagas disease in naïve rhesus macaques. RESEARCH SQUARE 2023:rs.3.rs-3453582. [PMID: 37961272 PMCID: PMC10635379 DOI: 10.21203/rs.3.rs-3453582/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
A vaccine against Trypanosoma cruzi, the agent of Chagas disease, would be an excellent additional tool for disease control. A recombinant vaccine based on Tc24 and TSA1 parasite antigens was found to be safe and immunogenic in naïve macaques. Here we performed a transcriptomic analysis of PBMC responses to vaccination, to shed light on the immunogenicity of this vaccine and guide the optimization of doses and formulation. RNA-sequencing analysis indicated a clear transcriptomic response of PBMCs from macaques after three vaccine doses, with the up-regulation of several immune cell activation pathways and a broad non-polarized immune profile. Analysis of the IgG repertoire showed that it had a rapid turnover with novel IgGs produced following each vaccine dose, while the TCR repertoire presented several persisting clones that were expanded after each vaccine dose. These data suggest that three vaccine doses may be needed for optimum immunogenecity and support the further evaluation of the protective efficacy of this vaccine.
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10
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Kim DY, Kandalaft H, Lowden MJ, Yang Q, Rossotti MA, Robotham A, Kelly JF, Hussack G, Schrag JD, Henry KA, Tanha J. Sequence tolerance of immunoglobulin variable domain framework regions to noncanonical intradomain disulfide linkages. J Biol Chem 2023; 299:105278. [PMID: 37742917 PMCID: PMC10641266 DOI: 10.1016/j.jbc.2023.105278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023] Open
Abstract
Most immunoglobulin (Ig) domains bear only a single highly conserved canonical intradomain, inter-β-sheet disulfide linkage formed between Cys23-Cys104, and incorporation of rare noncanonical disulfide linkages at other locations can enhance Ig domain stability. Here, we exhaustively surveyed the sequence tolerance of Ig variable (V) domain framework regions (FRs) to noncanonical disulfide linkages. Starting from a destabilized VH domain lacking a Cys23-Cys104 disulfide linkage, we generated and screened phage-displayed libraries of engineered VHs, bearing all possible pairwise combinations of Cys residues in neighboring β-strands of the Ig fold FRs. This approach identified seven novel Cys pairs in VH FRs (Cys4-Cys25, Cys4-Cys118, Cys5-Cys120, Cys6-Cys119, Cys22-Cys88, Cys24-Cys86, and Cys45-Cys100; the international ImMunoGeneTics information system numbering), whose presence rescued domain folding and stability. Introduction of a subset of these noncanonical disulfide linkages (three intra-β-sheet: Cys4-Cys25, Cys22-Cys88, and Cys24-Cys86, and one inter-β-sheet: Cys6-Cys119) into a diverse panel of VH, VL, and VHH domains enhanced their thermostability and protease resistance without significantly impacting expression, solubility, or binding to cognate antigens. None of the noncanonical disulfide linkages identified were present in the natural human VH repertoire. These data reveal an unexpected permissiveness of Ig V domains to noncanonical disulfide linkages at diverse locations in FRs, absent in the human repertoire, whose presence is compatible with antigen recognition and improves domain stability. Our work represents the most complete assessment to date of the role of engineered noncanonical disulfide bonding within FRs in Ig V domain structure and function.
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Affiliation(s)
- Dae Young Kim
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Hiba Kandalaft
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Michael J Lowden
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Qingling Yang
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Martin A Rossotti
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Anna Robotham
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - John F Kelly
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Greg Hussack
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Joseph D Schrag
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Montréal, Quebec, Canada
| | - Kevin A Henry
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Jamshid Tanha
- Life Sciences Division, Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.
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11
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Stamatatos L. 'Immunization during ART and ATI for HIV-1 vaccine discovery/development'. Curr Opin HIV AIDS 2023; 18:309-314. [PMID: 37712859 PMCID: PMC10552831 DOI: 10.1097/coh.0000000000000817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
PURPOSE OF REVIEW Explore whether immunization with germline-targeting Env immunogens during ART, followed by ATI, leads to the identification of viral envelope glycoproteins (Envs) that promote and guide the full maturation of broadly neutralizing antibody responses. RECENT FINDINGS The HIV-1 envelope glycoprotein (Env) does not efficiently engage the germline precursors of broadly neutralizing antibodies (bnAbs). However, Env-derived proteins specifically designed to precisely do that, have been recently developed. These 'germline-targeting' Env immunogens activate naïve B cells that express the germline precursors of bnAbs but by themselves cannot guide their maturation towards their broadly neutralizing forms. This requires sequential immunizations with heterologous sets of Envs. These 'booster' Envs are currently unknown. SUMMARY Combining germline-targeting Env immunization approaches during ART with ATI could lead to the identification of natural Envs that are responsible for the maturation of broadly neutralizing antibody responses during infection. Such Envs could then serve as booster immunogens to guide the maturation of glBCRs that have become activated by germline-targeting immunogens in uninfected subjects.
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Affiliation(s)
- Leonidas Stamatatos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center and University of Washington, Department of Global Health, Seattle, WA, USA
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12
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Math BA, Waibl F, Lamp LM, Fernández‐Quintero ML, Liedl KR. Cross-linking disulfide bonds govern solution structures of diabodies. Proteins 2023; 91:1316-1328. [PMID: 37376973 PMCID: PMC10952579 DOI: 10.1002/prot.26509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/19/2023] [Indexed: 06/29/2023]
Abstract
In the last years, antibodies have emerged as a promising new class of therapeutics, due to their combination of high specificity with long serum half-life and low risk of side-effects. Diabodies are a popular novel antibody format, consisting of two Fv domains connected with short linkers. Like IgG antibodies, they simultaneously bind two target proteins. However, they offer altered properties, given their smaller size and higher rigidity. In this study, we conducted the-to our knowledge-first molecular dynamics (MD) simulations of diabodies and find a surprisingly high conformational flexibility in the relative orientation of the two Fv domains. We observe rigidifying effects through the introduction of disulfide bonds in the Fv -Fv interface and characterize the effect of different disulfide bond locations on the conformation. Additionally, we compare VH -VL orientations and paratope dynamics between diabodies and an antigen binding fragment (Fab) of the same sequence. We find mostly consistent structures and dynamics, indicating similar antigen binding properties. The most significant differences can be found within the CDR-H2 loop dynamics. Of all CDR loops, the CDR-H2 is located closest to the artificial Fv -Fv interface. All examined diabodies show similar VH -VL orientations, Fv -Fv packing and CDR loop conformations. However, the variant with a P14C-K64C disulfide bond differs most from the Fab in our measures, including the CDR-H3 loop conformational ensemble. This suggests altered antigen binding properties and underlines the need for careful validation of the disulfide bond locations in diabodies.
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Affiliation(s)
- Barbara A. Math
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnsbruckAustria
| | - Franz Waibl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnsbruckAustria
| | - Leonida M. Lamp
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnsbruckAustria
| | - Monica L. Fernández‐Quintero
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnsbruckAustria
| | - Klaus R. Liedl
- Institute of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI)University of InnsbruckInnsbruckAustria
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13
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Ramirez Valdez K, Nzau B, Dorey-Robinson D, Jarman M, Nyagwange J, Schwartz JC, Freimanis G, Steyn AW, Warimwe GM, Morrison LJ, Mwangi W, Charleston B, Bonnet-Di Placido M, Hammond JA. A Customizable Suite of Methods to Sequence and Annotate Cattle Antibodies. Vaccines (Basel) 2023; 11:1099. [PMID: 37376488 PMCID: PMC10302312 DOI: 10.3390/vaccines11061099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/07/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Studying the antibody response to infection or vaccination is essential for developing more effective vaccines and therapeutics. Advances in high-throughput antibody sequencing technologies and immunoinformatic tools now allow the fast and comprehensive analysis of antibody repertoires at high resolution in any species. Here, we detail a flexible and customizable suite of methods from flow cytometry, single cell sorting, heavy and light chain amplification to antibody sequencing in cattle. These methods were used successfully, including adaptation to the 10x Genomics platform, to isolate native heavy-light chain pairs. When combined with the Ig-Sequence Multi-Species Annotation Tool, this suite represents a powerful toolkit for studying the cattle antibody response with high resolution and precision. Using three workflows, we processed 84, 96, and 8313 cattle B cells from which we sequenced 24, 31, and 4756 antibody heavy-light chain pairs, respectively. Each method has strengths and limitations in terms of the throughput, timeline, specialist equipment, and cost that are each discussed. Moreover, the principles outlined here can be applied to study antibody responses in other mammalian species.
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Affiliation(s)
| | - Benjamin Nzau
- The Pirbright Institute, Pirbright GU24 0NF, UK
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | | | | | - James Nyagwange
- The Pirbright Institute, Pirbright GU24 0NF, UK
- KEMRI-Wellcome Trust Research Programme CGMRC, Kilifi P.O. Box 230-80108, Kenya
| | | | | | | | - George M Warimwe
- KEMRI-Wellcome Trust Research Programme CGMRC, Kilifi P.O. Box 230-80108, Kenya
| | - Liam J Morrison
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
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14
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Pan X, López Acevedo SN, Cuziol C, De Tavernier E, Fahad AS, Longjam PS, Rao SP, Aguilera-Rodríguez D, Rezé M, Bricault CA, Gutiérrez-González MF, de Souza MO, DiNapoli JM, Vigne E, Shahsavarian MA, DeKosky BJ. Large-scale antibody immune response mapping of splenic B cells and bone marrow plasma cells in a transgenic mouse model. Front Immunol 2023; 14:1137069. [PMID: 37346047 PMCID: PMC10280637 DOI: 10.3389/fimmu.2023.1137069] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/30/2023] [Indexed: 06/23/2023] Open
Abstract
Molecular characterization of antibody immunity and human antibody discovery is mainly carried out using peripheral memory B cells, and occasionally plasmablasts, that express B cell receptors (BCRs) on their cell surface. Despite the importance of plasma cells (PCs) as the dominant source of circulating antibodies in serum, PCs are rarely utilized because they do not express surface BCRs and cannot be analyzed using antigen-based fluorescence-activated cell sorting. Here, we studied the antibodies encoded by the entire mature B cell populations, including PCs, and compared the antibody repertoires of bone marrow and spleen compartments elicited by immunization in a human immunoglobulin transgenic mouse strain. To circumvent prior technical limitations for analysis of plasma cells, we applied single-cell antibody heavy and light chain gene capture from the entire mature B cell repertoires followed by yeast display functional analysis using a cytokine as a model immunogen. We performed affinity-based sorting of antibody yeast display libraries and large-scale next-generation sequencing analyses to follow antibody lineage performance, with experimental validation of 76 monoclonal antibodies against the cytokine antigen that identified three antibodies with exquisite double-digit picomolar binding affinity. We observed that spleen B cell populations generated higher affinity antibodies compared to bone marrow PCs and that antigen-specific splenic B cells had higher average levels of somatic hypermutation. A degree of clonal overlap was also observed between bone marrow and spleen antibody repertoires, indicating common origins of certain clones across lymphoid compartments. These data demonstrate a new capacity to functionally analyze antigen-specific B cell populations of different lymphoid organs, including PCs, for high-affinity antibody discovery and detailed fundamental studies of antibody immunity.
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Affiliation(s)
- Xiaoli Pan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Sheila N. López Acevedo
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
| | - Camille Cuziol
- Large Molecule Research, Sanofi, Vitry sur Seine, France
| | | | - Ahmed S. Fahad
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | | | | | | | - Mathilde Rezé
- Large Molecule Research, Sanofi, Vitry sur Seine, France
| | | | - Matías F. Gutiérrez-González
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Matheus Oliveira de Souza
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | | | | | | | - Brandon J. DeKosky
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS, United States
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15
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Fahad AS, Chung CY, López Acevedo SN, Boyle N, Madan B, Gutiérrez-González MF, Matus-Nicodemos R, Laflin AD, Ladi RR, Zhou J, Wolfe J, Llewellyn-Lacey S, Koup RA, Douek DC, Balfour HH, Price DA, DeKosky BJ. Cell activation-based screening of natively paired human T cell receptor repertoires. Sci Rep 2023; 13:8011. [PMID: 37198258 PMCID: PMC10192375 DOI: 10.1038/s41598-023-31858-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 03/20/2023] [Indexed: 05/19/2023] Open
Abstract
Adoptive immune therapies based on the transfer of antigen-specific T cells have been used successfully to treat various cancers and viral infections, but improved techniques are needed to identify optimally protective human T cell receptors (TCRs). Here we present a high-throughput approach to the identification of natively paired human TCRα and TCRβ (TCRα:β) genes encoding heterodimeric TCRs that recognize specific peptide antigens bound to major histocompatibility complex molecules (pMHCs). We first captured and cloned TCRα:β genes from individual cells, ensuring fidelity using a suppression PCR. We then screened TCRα:β libraries expressed in an immortalized cell line using peptide-pulsed antigen-presenting cells and sequenced activated clones to identify the cognate TCRs. Our results validated an experimental pipeline that allows large-scale repertoire datasets to be annotated with functional specificity information, facilitating the discovery of therapeutically relevant TCRs.
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Affiliation(s)
- Ahmed S Fahad
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Cheng Yu Chung
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Sheila N López Acevedo
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Nicoleen Boyle
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Bharat Madan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | | | - Rodrigo Matus-Nicodemos
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Amy D Laflin
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Rukmini R Ladi
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - John Zhou
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Jacy Wolfe
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA
| | - Sian Llewellyn-Lacey
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, CF14 4XN, UK
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Henry H Balfour
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, CF14 4XN, UK
- Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Cardiff, CF14 4XN, UK
| | - Brandon J DeKosky
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, 66044, USA.
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS, 66044, USA.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139, USA.
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16
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Swanson O, Martin Beem JS, Rhodes B, Wang A, Barr M, Chen H, Parks R, Saunders KO, Haynes BF, Wiehe K, Azoitei ML. Identification of CDRH3 loops in the B cell receptor repertoire that can be engaged by candidate immunogens. PLoS Pathog 2023; 19:e1011401. [PMID: 37196027 PMCID: PMC10228794 DOI: 10.1371/journal.ppat.1011401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 05/30/2023] [Accepted: 05/03/2023] [Indexed: 05/19/2023] Open
Abstract
A major goal for the development of vaccines against rapidly mutating viruses, such as influenza or HIV, is to elicit antibodies with broad neutralization capacity. However, B cell precursors capable of maturing into broadly neutralizing antibodies (bnAbs) can be rare in the immune repertoire. Due to the stochastic nature of B cell receptor (BCR) rearrangement, a limited number of third heavy chain complementary determining region (CDRH3) sequences are identical between different individuals. Thus, in order to successfully engage broadly neutralizing antibody precursors that rely on their CDRH3 loop for antigen recognition, immunogens must be able to tolerate sequence diversity in the B cell receptor repertoire across an entire vaccinated population. Here, we present a combined experimental and computational approach to identify BCRs in the human repertoire with CDRH3 loops predicted to be engaged by a target immunogen. For a given antibody/antigen pair, deep mutational scanning was first used to measure the effect of CDRH3 loop substitution on binding. BCR sequences, isolated experimentally or generated in silico, were subsequently evaluated to identify CDRH3 loops expected to be bound by the candidate immunogen. We applied this method to characterize two HIV-1 germline-targeting immunogens and found differences in the frequencies with which they are expected to engage target B cells, thus illustrating how this approach can be used to evaluate candidate immunogens towards B cell precursors engagement and to inform immunogen optimization strategies for more effective vaccine design.
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Affiliation(s)
- Olivia Swanson
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Joshua S. Martin Beem
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Brianna Rhodes
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Avivah Wang
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Haiyan Chen
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
| | - Kevin O. Saunders
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
- Department of Surgery, Duke University, Durham, North Carolina, United States of America
| | - Barton F. Haynes
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
- Department of Medicine, Duke University, Durham, North Carolina, United States of America
- Department of Immunology, Duke University, Durham, North Carolina, United States of America
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
- Department of Medicine, Duke University, Durham, North Carolina, United States of America
| | - Mihai L. Azoitei
- Duke Human Vaccine Institute, Duke University, Durham, North Carolina, United States of America
- Department of Medicine, Duke University, Durham, North Carolina, United States of America
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17
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Shrock EL, Timms RT, Kula T, Mena EL, West AP, Guo R, Lee IH, Cohen AA, McKay LGA, Bi C, Keerti, Leng Y, Fujimura E, Horns F, Li M, Wesemann DR, Griffiths A, Gewurz BE, Bjorkman PJ, Elledge SJ. Germline-encoded amino acid-binding motifs drive immunodominant public antibody responses. Science 2023; 380:eadc9498. [PMID: 37023193 PMCID: PMC10273302 DOI: 10.1126/science.adc9498] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 03/03/2023] [Indexed: 04/08/2023]
Abstract
Despite the vast diversity of the antibody repertoire, infected individuals often mount antibody responses to precisely the same epitopes within antigens. The immunological mechanisms underpinning this phenomenon remain unknown. By mapping 376 immunodominant "public epitopes" at high resolution and characterizing several of their cognate antibodies, we concluded that germline-encoded sequences in antibodies drive recurrent recognition. Systematic analysis of antibody-antigen structures uncovered 18 human and 21 partially overlapping mouse germline-encoded amino acid-binding (GRAB) motifs within heavy and light V gene segments that in case studies proved critical for public epitope recognition. GRAB motifs represent a fundamental component of the immune system's architecture that promotes recognition of pathogens and leads to species-specific public antibody responses that can exert selective pressure on pathogens.
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Affiliation(s)
- Ellen L. Shrock
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Program in Biological and Biomedical Sciences, Harvard University, Boston, MA 02115, USA
| | - Richard T. Timms
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Tomasz Kula
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Program in Biological and Biomedical Sciences, Harvard University, Boston, MA 02115, USA
- Present address: Society of Fellows, Harvard University, Cambridge, MA 02138, USA
| | - Elijah L. Mena
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Anthony P. West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Rui Guo
- Division of Infectious Disease, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
| | - I-Hsiu Lee
- Center for Systems Biology, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Alexander A. Cohen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lindsay G. A. McKay
- National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Caihong Bi
- Division of Allergy and Immunology, Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Keerti
- Division of Allergy and Immunology, Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
| | - Yumei Leng
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Eric Fujimura
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Felix Horns
- Department of Bioengineering, Department of Applied Physics, Chan Zuckerberg Biohub and Stanford University, Stanford, CA 94305, USA
| | - Mamie Li
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Duane R. Wesemann
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Division of Allergy and Immunology, Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Massachusetts Consortium on Pathogen Readiness, Boston, MA 02115, USA
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, 02139 USA
| | - Anthony Griffiths
- National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston University, Boston, MA 02118, USA
| | - Benjamin E. Gewurz
- Division of Infectious Disease, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Graduate Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Stephen J. Elledge
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
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18
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Hurtado J, Flynn C, Lee JH, Salcedo EC, Cottrell CA, Skog PD, Burton DR, Nemazee D, Schief WR, Landais E, Sok D, Briney B. Efficient isolation of rare B cells using next-generation antigen barcoding. Front Cell Infect Microbiol 2023; 12:962945. [PMID: 36968243 PMCID: PMC10036767 DOI: 10.3389/fcimb.2022.962945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 12/28/2022] [Indexed: 03/12/2023] Open
Abstract
The ability to efficiently isolate antigen-specific B cells in high throughput will greatly accelerate the discovery of therapeutic monoclonal antibodies (mAbs) and catalyze rational vaccine development. Traditional mAb discovery is a costly and labor-intensive process, although recent advances in single-cell genomics using emulsion microfluidics allow simultaneous processing of thousands of individual cells. Here we present a streamlined method for isolation and analysis of large numbers of antigen-specific B cells, including next generation antigen barcoding and an integrated computational framework for B cell multi-omics. We demonstrate the power of this approach by recovering thousands of antigen-specific mAbs, including the efficient isolation of extremely rare precursors of VRC01-class and IOMA-class broadly neutralizing HIV mAbs.
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Affiliation(s)
- Jonathan Hurtado
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, United States
- Center for Viral Systems Biology, Scripps Research, La Jolla, CA, United States
- Consortium for HIV/AIDS Vaccine Development, Scripps Research, La Jolla, CA, United States
| | - Claudia Flynn
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, United States
- Consortium for HIV/AIDS Vaccine Development, Scripps Research, La Jolla, CA, United States
- IAVI Neutralizing Antibody Center, Scripps Research, La Jolla, CA, United States
| | - Jeong Hyun Lee
- Consortium for HIV/AIDS Vaccine Development, Scripps Research, La Jolla, CA, United States
- IAVI Neutralizing Antibody Center, Scripps Research, La Jolla, CA, United States
- International AIDS Vaccine Initiative, New York, NY, United States
| | - Eugenia C. Salcedo
- Consortium for HIV/AIDS Vaccine Development, Scripps Research, La Jolla, CA, United States
- IAVI Neutralizing Antibody Center, Scripps Research, La Jolla, CA, United States
- International AIDS Vaccine Initiative, New York, NY, United States
| | - Christopher A. Cottrell
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, United States
- Consortium for HIV/AIDS Vaccine Development, Scripps Research, La Jolla, CA, United States
- IAVI Neutralizing Antibody Center, Scripps Research, La Jolla, CA, United States
- International AIDS Vaccine Initiative, New York, NY, United States
| | - Patrick D. Skog
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, United States
| | - Dennis R. Burton
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, United States
- Consortium for HIV/AIDS Vaccine Development, Scripps Research, La Jolla, CA, United States
- IAVI Neutralizing Antibody Center, Scripps Research, La Jolla, CA, United States
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, United States
| | - David Nemazee
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, United States
| | - William R. Schief
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, United States
- Consortium for HIV/AIDS Vaccine Development, Scripps Research, La Jolla, CA, United States
- IAVI Neutralizing Antibody Center, Scripps Research, La Jolla, CA, United States
- International AIDS Vaccine Initiative, New York, NY, United States
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT) and Harvard, Cambridge, MA, United States
| | - Elise Landais
- Consortium for HIV/AIDS Vaccine Development, Scripps Research, La Jolla, CA, United States
- IAVI Neutralizing Antibody Center, Scripps Research, La Jolla, CA, United States
- International AIDS Vaccine Initiative, New York, NY, United States
| | - Devin Sok
- Consortium for HIV/AIDS Vaccine Development, Scripps Research, La Jolla, CA, United States
- IAVI Neutralizing Antibody Center, Scripps Research, La Jolla, CA, United States
- International AIDS Vaccine Initiative, New York, NY, United States
| | - Bryan Briney
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, United States
- Center for Viral Systems Biology, Scripps Research, La Jolla, CA, United States
- Consortium for HIV/AIDS Vaccine Development, Scripps Research, La Jolla, CA, United States
- San Diego Center for AIDS Research, Scripps Research, La Jolla, CA, United States
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19
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Characterization of the immunoglobulin lambda chain locus from diverse populations reveals extensive genetic variation. Genes Immun 2023; 24:21-31. [PMID: 36539592 PMCID: PMC10041605 DOI: 10.1038/s41435-022-00188-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/07/2022] [Accepted: 10/13/2022] [Indexed: 12/24/2022]
Abstract
Immunoglobulins (IGs), crucial components of the adaptive immune system, are encoded by three genomic loci. However, the complexity of the IG loci severely limits the effective use of short read sequencing, limiting our knowledge of population diversity in these loci. We leveraged existing long read whole-genome sequencing (WGS) data, fosmid technology, and IG targeted single-molecule, real-time (SMRT) long-read sequencing (IG-Cap) to create haplotype-resolved assemblies of the IG Lambda (IGL) locus from 6 ethnically diverse individuals. In addition, we generated 10 diploid assemblies of IGL from a diverse cohort of individuals utilizing IG-Cap. From these 16 individuals, we identified significant allelic diversity, including 36 novel IGLV alleles. In addition, we observed highly elevated single nucleotide variation (SNV) in IGLV genes relative to IGL intergenic and genomic background SNV density. By comparing SNV calls between our high quality assemblies and existing short read datasets from the same individuals, we show a high propensity for false-positives in the short read datasets. Finally, for the first time, we nucleotide-resolved common 5-10 Kb duplications in the IGLC region that contain functional IGLJ and IGLC genes. Together these data represent a significant advancement in our understanding of genetic variation and population diversity in the IGL locus.
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20
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Dacon C, Peng L, Lin TH, Tucker C, Lee CCD, Cong Y, Wang L, Purser L, Cooper AJR, Williams JK, Pyo CW, Yuan M, Kosik I, Hu Z, Zhao M, Mohan D, Peterson M, Skinner J, Dixit S, Kollins E, Huzella L, Perry D, Byrum R, Lembirik S, Murphy M, Zhang Y, Yang ES, Chen M, Leung K, Weinberg RS, Pegu A, Geraghty DE, Davidson E, Doranz BJ, Douagi I, Moir S, Yewdell JW, Schmaljohn C, Crompton PD, Mascola JR, Holbrook MR, Nemazee D, Wilson IA, Tan J. Rare, convergent antibodies targeting the stem helix broadly neutralize diverse betacoronaviruses. Cell Host Microbe 2023; 31:97-111.e12. [PMID: 36347257 PMCID: PMC9639329 DOI: 10.1016/j.chom.2022.10.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/04/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022]
Abstract
Humanity has faced three recent outbreaks of novel betacoronaviruses, emphasizing the need to develop approaches that broadly target coronaviruses. Here, we identify 55 monoclonal antibodies from COVID-19 convalescent donors that bind diverse betacoronavirus spike proteins. Most antibodies targeted an S2 epitope that included the K814 residue and were non-neutralizing. However, 11 antibodies targeting the stem helix neutralized betacoronaviruses from different lineages. Eight antibodies in this group, including the six broadest and most potent neutralizers, were encoded by IGHV1-46 and IGKV3-20. Crystal structures of three antibodies of this class at 1.5-1.75-Å resolution revealed a conserved mode of binding. COV89-22 neutralized SARS-CoV-2 variants of concern including Omicron BA.4/5 and limited disease in Syrian hamsters. Collectively, these findings identify a class of IGHV1-46/IGKV3-20 antibodies that broadly neutralize betacoronaviruses by targeting the stem helix but indicate these antibodies constitute a small fraction of the broadly reactive antibody response to betacoronaviruses after SARS-CoV-2 infection.
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Affiliation(s)
- Cherrelle Dacon
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Linghang Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ting-Hui Lin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Courtney Tucker
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA; Department of Biology, The Catholic University of America, Washington, DC 20064, USA
| | - Chang-Chun D Lee
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yu Cong
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren Purser
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Andrew J R Cooper
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | | | - Chul-Woo Pyo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Meng Yuan
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ivan Kosik
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhe Hu
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ming Zhao
- Protein Chemistry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Divya Mohan
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Mary Peterson
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Jeff Skinner
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Saurabh Dixit
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Erin Kollins
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Louis Huzella
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Donna Perry
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Russell Byrum
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Sanae Lembirik
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Michael Murphy
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rona S Weinberg
- New York Blood Center, Lindsley F. Kimball Research Institute, New York, NY 10065, USA
| | - Amarendra Pegu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | | | - Iyadh Douagi
- Flow Cytometry Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Susan Moir
- B Cell Immunology Section, Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan W Yewdell
- Cellular Biology Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Connie Schmaljohn
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - Peter D Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Michael R Holbrook
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD 21702, USA
| | - David Nemazee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ian A Wilson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joshua Tan
- Antibody Biology Unit, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA.
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21
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Fahad AS, Madan B, DeKosky BJ. Bioinformatic Analysis of Natively Paired VH:VL Antibody Repertoires for Antibody Discovery. Methods Mol Biol 2023; 2552:447-463. [PMID: 36346608 DOI: 10.1007/978-1-0716-2609-2_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Next-generation DNA sequencing (NGS) of human antibody repertoires has been extensively implemented to discover novel antibody drugs, to analyze B-cell developmental features, and to investigate antibody responses to infectious diseases and vaccination. Because the antibody repertoire encoded by human B cells is highly diverse, NGS analyses of antibody genes have provided a new window into understanding antibody responses for basic immunology, biopharmaceutical drug discovery, and immunotherapy. However, many antibody discovery protocols analyze the heavy and light chains separately due to the short-read nature of most NGS technologies, whereas paired heavy and light chain data are required for complete antibody characterization. Here, we describe a computational workflow to process millions of paired antibody heavy and light chain DNA sequence reads using the Illumina MiSeq 2x300 NGS platform. In this workflow, we describe raw NGS read processing and initial quality filtering, the annotation and assembly of antibody clonotypes relating to paired heavy and light chain antibody lineages, and the generation of complete heavy+light consensus sequences for the downstream cloning and expression of human antibody proteins.
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Affiliation(s)
- Ahmed S Fahad
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, USA
| | - Bharat Madan
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, USA
| | - Brandon J DeKosky
- The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, USA.
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS, USA.
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22
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Mejias-Gomez O, Madsen AV, Skovgaard K, Pedersen LE, Morth JP, Jenkins TP, Kristensen P, Goletz S. A window into the human immune system: comprehensive characterization of the complexity of antibody complementary-determining regions in functional antibodies. MAbs 2023; 15:2268255. [PMID: 37876265 PMCID: PMC10601506 DOI: 10.1080/19420862.2023.2268255] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023] Open
Abstract
The human immune system uses antibodies to neutralize foreign antigens. They are composed of heavy and light chains, both with constant and variable regions. The variable region has six hypervariable loops, also known as complementary-determining regions (CDRs) that determine antibody diversity and antigen specificity. Knowledge of their significance, and certain residues present in these areas, is vital for antibody therapeutics development. This study includes an analysis of more than 11,000 human antibody sequences from the International Immunogenetics information system (IMGT). The analysis included parameters such as length distribution, overall amino acid diversity, amino acid frequency per CDR and residue position within antibody chains. Overall, our findings confirm existing knowledge, such as CDRH3's high length diversity and amino acid variability, increased aromatic residue usage, particularly tyrosine, charged and polar residues like aspartic acid, serine, and the flexible residue glycine. Specific residue positions within each CDR influence these occurrences, implying a unique amino acid type distribution pattern. We compared amino acid type usage in CDRs and non-CDR regions, both in globular and transmembrane proteins, which revealed distinguishing features, such as increased frequency of tyrosine, serine, aspartic acid, and arginine. These findings should prove useful for future optimization, improvement of affinity, synthetic antibody library design, or the creation of antibodies de-novo in silico.
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Affiliation(s)
- Oscar Mejias-Gomez
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Andreas V. Madsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Lasse E. Pedersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - J. Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Timothy P. Jenkins
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Peter Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Steffen Goletz
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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23
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Ralph DK, Matsen FA. Inference of B cell clonal families using heavy/light chain pairing information. PLoS Comput Biol 2022; 18:e1010723. [PMID: 36441808 PMCID: PMC9731466 DOI: 10.1371/journal.pcbi.1010723] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 12/08/2022] [Accepted: 11/09/2022] [Indexed: 11/29/2022] Open
Abstract
Next generation sequencing of B cell receptor (BCR) repertoires has become a ubiquitous tool for understanding the antibody-mediated immune response: it is now common to have large volumes of sequence data coding for both the heavy and light chain subunits of the BCR. However, until the recent development of high throughput methods of preserving heavy/light chain pairing information, these samples contained no explicit information on which heavy chain sequence pairs with which light chain sequence. One of the first steps in analyzing such BCR repertoire samples is grouping sequences into clonally related families, where each stems from a single rearrangement event. Many methods of accomplishing this have been developed, however, none so far has taken full advantage of the newly-available pairing information. This information can dramatically improve clustering performance, especially for the light chain. The light chain has traditionally been challenging for clonal family inference because of its low diversity and consequent abundance of non-clonal families with indistinguishable naive rearrangements. Here we present a method of incorporating this pairing information into the clustering process in order to arrive at a more accurate partition of the data into clonally related families. We also demonstrate two methods of fixing imperfect pairing information, which may allow for simplified sample preparation and increased sequencing depth. Finally, we describe several other improvements to the partis software package.
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Affiliation(s)
- Duncan K. Ralph
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail:
| | - Frederick A. Matsen
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Statistics, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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24
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de Souza MO, Madan B, Teng IT, Huang A, Liu L, Fahad AS, Lopez Acevedo SN, Pan X, Sastry M, Gutierrez-Gonzalez M, Yin MT, Zhou T, Ho DD, Kwong PD, DeKosky BJ. Mapping monoclonal anti-SARS-CoV-2 antibody repertoires against diverse coronavirus antigens. Front Immunol 2022; 13:977064. [PMID: 36119018 PMCID: PMC9478573 DOI: 10.3389/fimmu.2022.977064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged continuously, challenging the effectiveness of vaccines, diagnostics, and treatments. Moreover, the possibility of the appearance of a new betacoronavirus with high transmissibility and high fatality is reason for concern. In this study, we used a natively paired yeast display technology, combined with next-generation sequencing (NGS) and massive bioinformatic analysis to perform a comprehensive study of subdomain specificity of natural human antibodies from two convalescent donors. Using this screening technology, we mapped the cross-reactive responses of antibodies generated by the two donors against SARS-CoV-2 variants and other betacoronaviruses. We tested the neutralization potency of a set of the cross-reactive antibodies generated in this study and observed that most of the antibodies produced by these patients were non-neutralizing. We performed a comparison of the specific and non-specific antibodies by somatic hypermutation in a repertoire-scale for the two individuals and observed that the degree of somatic hypermutation was unique for each patient. The data from this study provide functional insights into cross-reactive antibodies that can assist in the development of strategies against emerging SARS-CoV-2 variants and divergent betacoronaviruses.
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Affiliation(s)
- Matheus Oliveira de Souza
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
| | - Bharat Madan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Aric Huang
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
| | - Lihong Liu
- Aaron Diamond acquired immunodeficiency syndrome (AIDS) Research Center, Columbia University Irving Medical Center, New York, NY, United States
| | - Ahmed S. Fahad
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
| | - Sheila N. Lopez Acevedo
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
| | - Xiaoli Pan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
| | - Mallika Sastry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Matias Gutierrez-Gonzalez
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
| | - Michael T. Yin
- Department of Medicine , Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY, United States
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - David D. Ho
- Aaron Diamond acquired immunodeficiency syndrome (AIDS) Research Center, Columbia University Irving Medical Center, New York, NY, United States
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, United States
| | - Brandon J. DeKosky
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS, United States
- Ragon Institute of Massachusetts General Hospital (MGH), Massachusetts Institute of Technology (MIT), and Harvard, Cambridge, MA, United States
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
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25
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Claireaux M, Caniels TG, de Gast M, Han J, Guerra D, Kerster G, van Schaik BDC, Jongejan A, Schriek AI, Grobben M, Brouwer PJM, van der Straten K, Aldon Y, Capella-Pujol J, Snitselaar JL, Olijhoek W, Aartse A, Brinkkemper M, Bontjer I, Burger JA, Poniman M, Bijl TPL, Torres JL, Copps J, Martin IC, de Taeye SW, de Bree GJ, Ward AB, Sliepen K, van Kampen AHC, Moerland PD, Sanders RW, van Gils MJ. A public antibody class recognizes an S2 epitope exposed on open conformations of SARS-CoV-2 spike. Nat Commun 2022; 13:4539. [PMID: 35927266 PMCID: PMC9352689 DOI: 10.1038/s41467-022-32232-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 07/22/2022] [Indexed: 12/21/2022] Open
Abstract
Delineating the origins and properties of antibodies elicited by SARS-CoV-2 infection and vaccination is critical for understanding their benefits and potential shortcomings. Therefore, we investigate the SARS-CoV-2 spike (S)-reactive B cell repertoire in unexposed individuals by flow cytometry and single-cell sequencing. We show that ∼82% of SARS-CoV-2 S-reactive B cells harbor a naive phenotype, which represents an unusually high fraction of total human naive B cells (∼0.1%). Approximately 10% of these naive S-reactive B cells share an IGHV1-69/IGKV3-11 B cell receptor pairing, an enrichment of 18-fold compared to the complete naive repertoire. Following SARS-CoV-2 infection, we report an average 37-fold enrichment of IGHV1-69/IGKV3-11 B cell receptor pairing in the S-reactive memory B cells compared to the unselected memory repertoire. This class of B cells targets a previously undefined non-neutralizing epitope on the S2 subunit that becomes exposed on S proteins used in approved vaccines when they transition away from the native pre-fusion state because of instability. These findings can help guide the improvement of SARS-CoV-2 vaccines.
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Affiliation(s)
- Mathieu Claireaux
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Tom G Caniels
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Marlon de Gast
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Denise Guerra
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Gius Kerster
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Barbera D C van Schaik
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Public Health, Amsterdam, the Netherlands
| | - Aldo Jongejan
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Public Health, Amsterdam, the Netherlands
| | - Angela I Schriek
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Marloes Grobben
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Philip J M Brouwer
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Karlijn van der Straten
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
| | - Yoann Aldon
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Joan Capella-Pujol
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Jonne L Snitselaar
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Wouter Olijhoek
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Aafke Aartse
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
- Department of Virology, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - Mitch Brinkkemper
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Ilja Bontjer
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Judith A Burger
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Meliawati Poniman
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Tom P L Bijl
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Isabel Cuella Martin
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Steven W de Taeye
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Godelieve J de Bree
- Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Kwinten Sliepen
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands
| | - Antoine H C van Kampen
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Public Health, Amsterdam, the Netherlands
| | - Perry D Moerland
- Bioinformatics Laboratory, Department of Epidemiology and Data Science, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam Institute for Public Health, Amsterdam, the Netherlands
| | - Rogier W Sanders
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands.
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands.
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, USA.
| | - Marit J van Gils
- Amsterdam UMC, University of Amsterdam, Department of Medical Microbiology and Infection prevention, Laboratory of Experimental Virology, Amsterdam, the Netherlands.
- Amsterdam institute for Infection and Immunity, Infectious diseases, Amsterdam, the Netherlands.
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26
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Banach BB, Tripathi P, Da Silva Pereira L, Gorman J, Nguyen TD, Dillon M, Fahad AS, Kiyuka PK, Madan B, Wolfe JR, Bonilla B, Flynn B, Francica JR, Hurlburt NK, Kisalu NK, Liu T, Ou L, Rawi R, Schön A, Shen CH, Teng IT, Zhang B, Pancera M, Idris AH, Seder RA, Kwong PD, DeKosky BJ. Highly protective antimalarial antibodies via precision library generation and yeast display screening. J Exp Med 2022; 219:e20220323. [PMID: 35736810 PMCID: PMC9242090 DOI: 10.1084/jem.20220323] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 02/03/2023] Open
Abstract
The monoclonal antibody CIS43 targets the Plasmodium falciparum circumsporozoite protein (PfCSP) and prevents malaria infection in humans for up to 9 mo following a single intravenous administration. To enhance the potency and clinical utility of CIS43, we used iterative site-saturation mutagenesis and DNA shuffling to screen precise gene-variant yeast display libraries for improved PfCSP antigen recognition. We identified several mutations that improved recognition, predominately in framework regions, and combined these to produce a panel of antibody variants. The most improved antibody, CIS43_Var10, had three mutations and showed approximately sixfold enhanced protective potency in vivo compared to CIS43. Co-crystal and cryo-electron microscopy structures of CIS43_Var10 with the peptide epitope or with PfCSP, respectively, revealed functional roles for each of these mutations. The unbiased site-directed mutagenesis and screening pipeline described here represent a powerful approach to enhance protective potency and to enable broader clinical use of antimalarial antibodies.
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Affiliation(s)
- Bailey B. Banach
- Bioengineering Graduate Program, The University of Kansas, Lawrence, KS
| | - Prabhanshu Tripathi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Lais Da Silva Pereira
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Thuy Duong Nguyen
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS
| | - Marlon Dillon
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Ahmed S. Fahad
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS
| | - Patience K. Kiyuka
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Bharat Madan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS
| | - Jacy R. Wolfe
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS
| | - Brian Bonilla
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Barbara Flynn
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Joseph R. Francica
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Nicholas K. Hurlburt
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA
| | - Neville K. Kisalu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Tracy Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Li Ou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Arne Schön
- Department of Biology, Johns Hopkins University, Baltimore, MD
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Marie Pancera
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA
| | - Azza H. Idris
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Robert A. Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD
| | - Brandon J. DeKosky
- Bioengineering Graduate Program, The University of Kansas, Lawrence, KS
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA
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27
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Collins AM, Watson CT, Breden F. Immunoglobulin genes, reproductive isolation and vertebrate speciation. Immunol Cell Biol 2022; 100:497-506. [PMID: 35781330 PMCID: PMC9545137 DOI: 10.1111/imcb.12567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/19/2022] [Accepted: 06/21/2022] [Indexed: 12/15/2022]
Abstract
Reproductive isolation drives the formation of new species, and many genes contribute to this through Dobzhansky–Muller incompatibilities (DMIs). These incompatibilities occur when gene divergence affects loci encoding interacting products such as receptors and their ligands. We suggest here that the nature of vertebrate immunoglobulin (IG) genes must make them prone to DMIs. The genes of these complex loci form functional genes through the process of recombination, giving rise to a repertoire of heterodimeric receptors of incredible diversity. This repertoire, within individuals and within species, must defend against pathogens but must also avoid pathogenic self‐reactivity. We suggest that this avoidance of autoimmunity is only achieved through a coordination of evolution between heavy‐ and light‐chain genes, and between these genes and the rest of the genome. Without coordinated evolution, the hybrid offspring of two diverging populations will carry a heavy burden of DMIs, resulting in a loss of fitness. Critical incompatibilities could manifest as incompatibilities between a mother and her divergent offspring. During fetal development, biochemical differences between the parents of hybrid offspring could make their offspring a target of the maternal immune system. This hypothesis was conceived in the light of recent insights into the population genetics of IG genes. This has suggested that antibody genes are probably as susceptible to evolutionary forces as other parts of the genome. Further repertoire studies in human and nonhuman species should now help determine whether antibody genes have been part of the evolutionary forces that drive the development of species.
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Affiliation(s)
- Andrew M Collins
- School of Biotechnology and Biomolecular Sciences University of New South Wales Sydney NSW Australia
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics University of Louisville School of Medicine Louisville KY USA
| | - Felix Breden
- Department of Biological Sciences Simon Fraser University Burnaby BC Canada
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28
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Designing antibodies as therapeutics. Cell 2022; 185:2789-2805. [PMID: 35868279 DOI: 10.1016/j.cell.2022.05.029] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/18/2022] [Accepted: 05/31/2022] [Indexed: 12/25/2022]
Abstract
Antibody therapeutics are a large and rapidly expanding drug class providing major health benefits. We provide a snapshot of current antibody therapeutics including their formats, common targets, therapeutic areas, and routes of administration. Our focus is on selected emerging directions in antibody design where progress may provide a broad benefit. These topics include enhancing antibodies for cancer, antibody delivery to organs such as the brain, gastrointestinal tract, and lungs, plus antibody developability challenges including immunogenicity risk assessment and mitigation and subcutaneous delivery. Machine learning has the potential, albeit as yet largely unrealized, for a transformative future impact on antibody discovery and engineering.
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29
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Cullen JN, Martin J, Vilella AJ, Treeful A, Sargan D, Bradley A, Friedenberg SG. Development and application of a next-generation sequencing protocol and bioinformatics pipeline for the comprehensive analysis of the canine immunoglobulin repertoire. PLoS One 2022; 17:e0270710. [PMID: 35802654 PMCID: PMC9269486 DOI: 10.1371/journal.pone.0270710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 06/15/2022] [Indexed: 11/18/2022] Open
Abstract
Profiling the adaptive immune repertoire using next generation sequencing (NGS) has become common in human medicine, showing promise in characterizing clonal expansion of B cell clones through analysis of B cell receptors (BCRs) in patients with lymphoid malignancies. In contrast, most work evaluating BCR repertoires in dogs has employed traditional PCR-based approaches analyzing the IGH locus only. The objectives of this study were to: (1) describe a novel NGS protocol to evaluate canine BCRs; (2) develop a bioinformatics pipeline for processing canine BCR sequencing data; and (3) apply these methods to derive insights into BCR repertoires of healthy dogs and dogs undergoing treatment for B-cell lymphoma. RNA from peripheral blood mononuclear cells of healthy dogs (n = 25) and dogs newly diagnosed with intermediate-to-large B-cell lymphoma (n = 18) with intent to pursue chemotherapy was isolated, converted into cDNA and sequenced by NGS. The BCR repertoires were identified and quantified using a novel analysis pipeline. The IGK repertoires of the healthy dogs were far less diverse compared to IGL which, as with IGH, was highly diverse. Strong biases at key positions within the CDR3 sequence were identified within the healthy dog BCR repertoire. For a subset of the dogs with B-cell lymphoma, clonal expansion of specific IGH sequences pre-treatment and reduction post-treatment was observed. The degree of expansion and reduction correlated with the clinical outcome in this subset. Future studies employing these techniques may improve disease monitoring, provide earlier recognition of disease progression, and ultimately lead to more targeted therapeutics.
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Affiliation(s)
- Jonah N. Cullen
- Department of Veterinary Clinical Sciences, University of Minnesota College of Veterinary Medicine, St. Paul, Minnesota, United States of America
| | - Jolyon Martin
- Wellcome Trust Genome Campus, Hinxton, Saffron Walden, United Kingdom
- PetMedix Ltd, Glenn Berge Building, Babraham Research Campus, Cambridge, United Kingdom
| | - Albert J. Vilella
- PetMedix Ltd, Glenn Berge Building, Babraham Research Campus, Cambridge, United Kingdom
| | - Amy Treeful
- Department of Veterinary Clinical Sciences, University of Minnesota College of Veterinary Medicine, St. Paul, Minnesota, United States of America
| | - David Sargan
- Department of Veterinary Medicine, Madingley Road, Cambridge, United Kingdom
| | - Allan Bradley
- Wellcome Trust Genome Campus, Hinxton, Saffron Walden, United Kingdom
- PetMedix Ltd, Glenn Berge Building, Babraham Research Campus, Cambridge, United Kingdom
- Department of Medicine, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
| | - Steven G. Friedenberg
- Department of Veterinary Clinical Sciences, University of Minnesota College of Veterinary Medicine, St. Paul, Minnesota, United States of America
- * E-mail:
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30
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Clonal structure, stability and dynamics of human memory B cells and circulating plasmablasts. Nat Immunol 2022; 23:1076-1085. [PMID: 35761085 PMCID: PMC9276532 DOI: 10.1038/s41590-022-01230-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/26/2022] [Indexed: 12/22/2022]
Abstract
Memory B cells persist for a lifetime and rapidly differentiate into antibody-producing plasmablasts and plasma cells upon antigen re-encounter. The clonal relationship and evolution of memory B cells and circulating plasmablasts is not well understood. Using single-cell sequencing combined with isolation of specific antibodies, we found that in two healthy donors, the memory B cell repertoire was dominated by large IgM, IgA and IgG2 clonal families, whereas IgG1 families, including those specific for recall antigens, were of small size. Analysis of multiyear samples demonstrated stability of memory B cell clonal families and revealed that a large fraction of recently generated plasmablasts was derived from long-term memory B cell families and was found recurrently. Collectively, this study provides a systematic description of the structure, stability and dynamics of the human memory B cell pool and suggests that memory B cells may be active at any time point in the generation of plasmablasts.
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31
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Abstract
High-throughput sequencing for B cell receptor (BCR) repertoire provides useful insights for the adaptive immune system. With the continuous development of the BCR-seq technology, many efforts have been made to develop methods for analyzing the ever-increasing BCR repertoire data. In this review, we comprehensively outline different BCR repertoire library preparation protocols and summarize three major steps of BCR-seq data analysis, i. e., V(D)J sequence annotation, clonal phylogenetic inference, and BCR repertoire profiling and mining. Different from other reviews in this field, we emphasize background intuition and the statistical principle of each method to help biologists better understand it. Finally, we discuss data mining problems for BCR-seq data and with a highlight on recently emerging multiple-sample analysis.
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32
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Koers J, Pollastro S, Tol S, Pico-Knijnenburg I, Derksen NIL, van Schouwenburg PA, van der Burg M, van Ham SM, Rispens T. CD45RB Glycosylation and Ig Isotype Define Maturation of Functionally Distinct B Cell Subsets in Human Peripheral Blood. Front Immunol 2022; 13:891316. [PMID: 35572548 PMCID: PMC9095956 DOI: 10.3389/fimmu.2022.891316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Glycosylation of CD45RB (RB+) has recently been identified to mark antigen-experienced B cells, independent of their CD27 expression. By using a novel combination of markers including CD45RB glycosylation, CD27 and IgM/IgD isotype expression we segregated human peripheral blood B cell subsets and investigated their IGHV repertoire and in vitro functionality. We observed distinct maturation stages for CD27-RB+ cells, defined by differential expression of non-switched Ig isotypes. CD27-RB+ cells, which only express IgM, were more matured in terms of Ig gene mutation levels and function as compared to CD27-RB+ cells that express both IgM and IgD or cells that were CD27-RB-. Moreover, CD27-RB+IgM+ cells already showed remarkable rigidity in IgM isotype commitment, different from CD27-RB+IgMD+ and CD27-RB- cells that still demonstrated great plasticity in B cell fate decision. Thus, glycosylation of CD45RB is indicative for antigen-primed B cells, which are, dependent on the Ig isotype, functionally distinct.
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Affiliation(s)
- Jana Koers
- Landsteiner Laboratory, Sanquin Research, Department of Immunopathology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Sabrina Pollastro
- Landsteiner Laboratory, Sanquin Research, Department of Immunopathology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Simon Tol
- Landsteiner Laboratory, Sanquin Research, Department of Research Facilities, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
| | - Ingrid Pico-Knijnenburg
- Laboratory for Pediatric Immunology, Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
| | - Ninotska I L Derksen
- Landsteiner Laboratory, Sanquin Research, Department of Immunopathology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Pauline A van Schouwenburg
- Laboratory for Pediatric Immunology, Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
| | - Mirjam van der Burg
- Laboratory for Pediatric Immunology, Department of Pediatrics, Leiden University Medical Center, Leiden, Netherlands
| | - S Marieke van Ham
- Landsteiner Laboratory, Sanquin Research, Department of Immunopathology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Theo Rispens
- Landsteiner Laboratory, Sanquin Research, Department of Immunopathology, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
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33
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Pashova S, Balabanski L, Elmadjian G, Savov A, Stoyanova E, Shivarov V, Petrov P, Pashov A. Restriction of the Global IgM Repertoire in Antiphospholipid Syndrome. Front Immunol 2022; 13:865232. [PMID: 35493489 PMCID: PMC9043687 DOI: 10.3389/fimmu.2022.865232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/21/2022] [Indexed: 11/22/2022] Open
Abstract
The typical anti-phospholipid antibodies (APLA) in the anti-phospholipid syndrome (APS) are reactive with the phospholipid-binding protein β2GPI as well as a growing list of other protein targets. The relation of APLA to natural antibodies and the fuzzy set of autoantigens involved provoked us to study the changes in the IgM repertoire in APS. To this end, peptides selected by serum IgM from a 7-residue linear peptide phage display library (PDL) were deep sequenced. The analysis was aided by a novel formal representation of the Igome (the mimotope set reflecting the IgM specificities) in the form of a sequence graph. The study involved women with APLA and habitual abortions (n=24) compared to age-matched clinically healthy pregnant women (n=20). Their pooled Igomes (297 028 mimotope sequences) were compared also to the global public repertoire Igome of pooled donor plasma IgM (n=2 796 484) and a set of 7-mer sequences found in the J regions of human immunoglobulins (n=4 433 252). The pooled Igome was represented as a graph connecting the sequences as similar as the mimotopes of the same monoclonal antibody. The criterion was based on previously published data. In the resulting graph, identifiable clusters of vertices were considered related to the footprints of overlapping antibody cross-reactivities. A subgraph based on the clusters with a significant differential expression of APS patients’ mimotopes contained predominantly specificities underrepresented in APS. The differentially expressed IgM footprints showed also an increased cross-reactivity with immunoglobulin J regions. The specificities underexpressed in APS had a higher correlation with public specificities than those overexpressed. The APS associated specificities were strongly related also to the human peptidome with 1 072 mimotope sequences found in 7 519 human proteins. These regions were characterized by low complexity. Thus, the IgM repertoire of the APS patients was found to be characterized by a significant reduction of certain public specificities found in the healthy controls with targets representing low complexity linear self-epitopes homologous to human antibody J regions.
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Affiliation(s)
- Shina Pashova
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Lubomir Balabanski
- Department of Medical Genetics, Medical University-Sofia, Sofia, Bulgaria.,Genomics Laboratory, Hospital "Malinov", Sofia, Bulgaria
| | - Gabriel Elmadjian
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Alexey Savov
- Department of Medical Genetics, Medical University-Sofia, Sofia, Bulgaria
| | - Elena Stoyanova
- Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | - Peter Petrov
- Institute Mathematics and Informatics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Anastas Pashov
- Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
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34
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Phenotypic determinism and stochasticity in antibody repertoires of clonally expanded plasma cells. Proc Natl Acad Sci U S A 2022; 119:e2113766119. [PMID: 35486691 PMCID: PMC9170022 DOI: 10.1073/pnas.2113766119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
B cell clonal selection and expansion from a genetically diverse antibody repertoire guides the immune response to a target antigen. It remains unclear if clonal selection and expansion follow any deterministic rules or are stochastic with regards to phenotypic antibody properties such as antigen-binding, affinity, and epitope specificity. We perform the in-depth genotypic and phenotypic characterization of antibody repertoires following immunization in mice. We identify the degree to which clonal expansion is driven by antibody binding, affinity, and epitope specificity and as such may provide greater insight into vaccine-induced immunity. The capacity of humoral B cell-mediated immunity to effectively respond to and protect against pathogenic infections is largely driven by the presence of a diverse repertoire of polyclonal antibodies in the serum, which are produced by plasma cells (PCs). Recent studies have started to reveal the balance between deterministic mechanisms and stochasticity of antibody repertoires on a genotypic level (i.e., clonal diversity, somatic hypermutation, and germline gene usage). However, it remains unclear if clonal selection and expansion of PCs follow any deterministic rules or are stochastic with regards to phenotypic antibody properties (i.e., antigen-binding, affinity, and epitope specificity). Here, we report on the in-depth genotypic and phenotypic characterization of clonally expanded PC antibody repertoires following protein immunization. We find that clonal expansion drives antigen specificity of the most expanded clones (top ∼10), whereas among the rest of the clonal repertoire antigen specificity is stochastic. Furthermore, we report both on a polyclonal repertoire and clonal lineage level that antibody-antigen binding affinity does not correlate with clonal expansion or somatic hypermutation. Last, we provide evidence for convergence toward targeting dominant epitopes despite clonal sequence diversity among the most expanded clones. Our results highlight the extent to which clonal expansion can be ascribed to antigen binding, affinity, and epitope specificity, and they have implications for the assessment of effective vaccines.
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35
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Li D, Brackenridge S, Walters LC, Swanson O, Harlos K, Rozbesky D, Cain DW, Wiehe K, Scearce RM, Barr M, Mu Z, Parks R, Quastel M, Edwards RJ, Wang Y, Rountree W, Saunders KO, Ferrari G, Borrow P, Jones EY, Alam SM, Azoitei ML, Gillespie GM, McMichael AJ, Haynes BF. Mouse and human antibodies bind HLA-E-leader peptide complexes and enhance NK cell cytotoxicity. Commun Biol 2022; 5:271. [PMID: 35347236 PMCID: PMC8960791 DOI: 10.1038/s42003-022-03183-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/17/2022] [Indexed: 12/16/2022] Open
Abstract
The non-classical class Ib molecule human leukocyte antigen E (HLA-E) has limited polymorphism and can bind HLA class Ia leader peptides (VL9). HLA-E-VL9 complexes interact with the natural killer (NK) cell receptors NKG2A-C/CD94 and regulate NK cell-mediated cytotoxicity. Here we report the isolation of 3H4, a murine HLA-E-VL9-specific IgM antibody that enhances killing of HLA-E-VL9-expressing cells by an NKG2A+ NK cell line. Structural analysis reveal that 3H4 acts by preventing CD94/NKG2A docking on HLA-E-VL9. Upon in vitro maturation, an affinity-optimized IgG form of 3H4 showes enhanced NK killing of HLA-E-VL9-expressing cells. HLA-E-VL9-specific IgM antibodies similar in function to 3H4 are also isolated from naïve B cells of cytomegalovirus (CMV)-negative, healthy humans. Thus, HLA-E-VL9-targeting mouse and human antibodies isolated from the naïve B cell antibody pool have the capacity to enhance NK cell cytotoxicity.
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Affiliation(s)
- Dapeng Li
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Simon Brackenridge
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Lucy C Walters
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Olivia Swanson
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Karl Harlos
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Daniel Rozbesky
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- Department of Cell Biology, Charles University, Prague, 12800, Czech Republic
| | - Derek W Cain
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kevin Wiehe
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Richard M Scearce
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Zekun Mu
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Max Quastel
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Robert J Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Yunfei Wang
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Wes Rountree
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Guido Ferrari
- Department of Surgery, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Persephone Borrow
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - E Yvonne Jones
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - S Munir Alam
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Mihai L Azoitei
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Medicine, Duke University School of Medicine, Durham, NC, 27710, USA.
| | - Geraldine M Gillespie
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
| | - Andrew J McMichael
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, OX3 7FZ, UK.
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Immunology, Duke University School of Medicine, Durham, NC, 27710, USA.
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36
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Fahad AS, Chung CY, Lopez Acevedo SN, Boyle N, Madan B, Gutiérrez-González MF, Matus-Nicodemos R, Laflin AD, Ladi RR, Zhou J, Wolfe J, Llewellyn-Lacey S, Koup RA, Douek DC, Balfour Jr HH, Price DA, DeKosky BJ. Immortalization and functional screening of natively paired human T cell receptor repertoires. Protein Eng Des Sel 2022; 35:gzab034. [PMID: 35174859 PMCID: PMC9005053 DOI: 10.1093/protein/gzab034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/16/2021] [Accepted: 12/29/2021] [Indexed: 11/13/2022] Open
Abstract
Functional analyses of the T cell receptor (TCR) landscape can reveal critical information about protection from disease and molecular responses to vaccines. However, it has proven difficult to combine advanced next-generation sequencing technologies with methods to decode the peptide-major histocompatibility complex (pMHC) specificity of individual TCRs. We developed a new high-throughput approach to enable repertoire-scale functional evaluations of natively paired TCRs. In particular, we leveraged the immortalized nature of physically linked TCRα:β amplicon libraries to analyze binding against multiple recombinant pMHCs on a repertoire scale, and to exemplify the utility of this approach, we also performed affinity-based functional mapping in conjunction with quantitative next-generation sequencing to track antigen-specific TCRs. These data successfully validated a new immortalization and screening platform to facilitate detailed molecular analyses of disease-relevant antigen interactions with human TCRs.
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Affiliation(s)
- Ahmed S Fahad
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Cheng-Yu Chung
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Sheila N Lopez Acevedo
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Nicoleen Boyle
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Bharat Madan
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | | | - Rodrigo Matus-Nicodemos
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy D Laflin
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Rukmini R Ladi
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - John Zhou
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Jacy Wolfe
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
| | - Sian Llewellyn-Lacey
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, UK
| | - Richard A Koup
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Henry H Balfour Jr
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN 55455, USA
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - David A Price
- Division of Infection and Immunity, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, UK
- Systems Immunity Research Institute, Cardiff University School of Medicine, University Hospital of Wales, Cardiff CF14 4XN, UK
| | - Brandon J DeKosky
- Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66044, USA
- Department of Chemical Engineering, The University of Kansas, Lawrence, KS 66044, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- The Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
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37
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Khetan R, Curtis R, Deane CM, Hadsund JT, Kar U, Krawczyk K, Kuroda D, Robinson SA, Sormanni P, Tsumoto K, Warwicker J, Martin ACR. Current advances in biopharmaceutical informatics: guidelines, impact and challenges in the computational developability assessment of antibody therapeutics. MAbs 2022; 14:2020082. [PMID: 35104168 PMCID: PMC8812776 DOI: 10.1080/19420862.2021.2020082] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Therapeutic monoclonal antibodies and their derivatives are key components of clinical pipelines in the global biopharmaceutical industry. The availability of large datasets of antibody sequences, structures, and biophysical properties is increasingly enabling the development of predictive models and computational tools for the "developability assessment" of antibody drug candidates. Here, we provide an overview of the antibody informatics tools applicable to the prediction of developability issues such as stability, aggregation, immunogenicity, and chemical degradation. We further evaluate the opportunities and challenges of using biopharmaceutical informatics for drug discovery and optimization. Finally, we discuss the potential of developability guidelines based on in silico metrics that can be used for the assessment of antibody stability and manufacturability.
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Affiliation(s)
- Rahul Khetan
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Robin Curtis
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | | | | | - Uddipan Kar
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | | | - Daisuke Kuroda
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.,Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan
| | | | - Pietro Sormanni
- Chemistry of Health, Yusuf Hamied Department of Chemistry, University of Cambridge
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, Japan.,Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo, Japan.,Department of Chemistry and Biotechnology, School of Engineering, The University of Tokyo, Tokyo, Japan.,The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jim Warwicker
- Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
| | - Andrew C R Martin
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
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38
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Lindeman I, Polak J, Qiao S, Holmøy T, Høglund RA, Vartdal F, Berg‐Hansen P, Sollid LM, Lossius A. Stereotyped B‐cell responses are linked to IgG constant region polymorphisms in multiple sclerosis. Eur J Immunol 2022; 52:550-565. [DOI: 10.1002/eji.202149576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/19/2021] [Accepted: 01/10/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Ida Lindeman
- Department of Immunology Oslo University Hospital Oslo Norway
- Department of Immunology Institute of Clinical Medicine University of Oslo Norway
- K.G. Jebsen Coeliac Disease Research Centre University of Oslo Norway
| | - Justyna Polak
- Department of Immunology Institute of Clinical Medicine University of Oslo Norway
- K.G. Jebsen Coeliac Disease Research Centre University of Oslo Norway
| | - Shuo‐Wang Qiao
- Department of Immunology Oslo University Hospital Oslo Norway
- Department of Immunology Institute of Clinical Medicine University of Oslo Norway
- K.G. Jebsen Coeliac Disease Research Centre University of Oslo Norway
| | - Trygve Holmøy
- Department of Neurology Akershus University Hospital Lørenskog Norway
- Department of Neurology Institute of Clinical Medicine University of Oslo Norway
| | - Rune A. Høglund
- Department of Neurology Akershus University Hospital Lørenskog Norway
- Department of Neurology Institute of Clinical Medicine University of Oslo Norway
| | - Frode Vartdal
- Department of Immunology Institute of Clinical Medicine University of Oslo Norway
- K.G. Jebsen Coeliac Disease Research Centre University of Oslo Norway
| | - Pål Berg‐Hansen
- Department of Neurology Oslo University Hospital Oslo Norway
| | - Ludvig M. Sollid
- Department of Immunology Oslo University Hospital Oslo Norway
- Department of Immunology Institute of Clinical Medicine University of Oslo Norway
- K.G. Jebsen Coeliac Disease Research Centre University of Oslo Norway
| | - Andreas Lossius
- K.G. Jebsen Coeliac Disease Research Centre University of Oslo Norway
- Department of Neurology Akershus University Hospital Lørenskog Norway
- Department of Molecular Medicine Institute of Basic Medical Sciences University of Oslo Norway
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39
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Ehling RA, Weber CR, Mason DM, Friedensohn S, Wagner B, Bieberich F, Kapetanovic E, Vazquez-Lombardi R, Di Roberto RB, Hong KL, Wagner C, Pataia M, Overath MD, Sheward DJ, Murrell B, Yermanos A, Cuny AP, Savic M, Rudolf F, Reddy ST. SARS-CoV-2 reactive and neutralizing antibodies discovered by single-cell sequencing of plasma cells and mammalian display. Cell Rep 2022; 38:110242. [PMID: 34998467 PMCID: PMC8692065 DOI: 10.1016/j.celrep.2021.110242] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 09/22/2021] [Accepted: 12/20/2021] [Indexed: 01/05/2023] Open
Abstract
Characterization of COVID-19 antibodies has largely focused on memory B cells; however, it is the antibody-secreting plasma cells that are directly responsible for the production of serum antibodies, which play a critical role in resolving SARS-CoV-2 infection. Little is known about the specificity of plasma cells, largely because plasma cells lack surface antibody expression, thereby complicating their screening. Here, we describe a technology pipeline that integrates single-cell antibody repertoire sequencing and mammalian display to interrogate the specificity of plasma cells from 16 convalescent patients. Single-cell sequencing allows us to profile antibody repertoire features and identify expanded clonal lineages. Mammalian display screening is used to reveal that 43 antibodies (of 132 candidates) derived from expanded plasma cell lineages are specific to SARS-CoV-2 antigens, including antibodies with high affinity to the SARS-CoV-2 receptor-binding domain (RBD) that exhibit potent neutralization and broad binding to the RBD of SARS-CoV-2 variants (of concern/interest).
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Affiliation(s)
- Roy A Ehling
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Cédric R Weber
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; deepCDR Biologics AG, Basel, Switzerland
| | - Derek M Mason
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; deepCDR Biologics AG, Basel, Switzerland
| | - Simon Friedensohn
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; deepCDR Biologics AG, Basel, Switzerland
| | - Bastian Wagner
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Florian Bieberich
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Edo Kapetanovic
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Raphaël B Di Roberto
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Kai-Lin Hong
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Botnar Research Centre for Child Health, Basel, Switzerland
| | | | - Michele Pataia
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; deepCDR Biologics AG, Basel, Switzerland
| | - Max D Overath
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Daniel J Sheward
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Botnar Research Centre for Child Health, Basel, Switzerland; Institute of Microbiology and Immunology, Department of Biology, ETH Zurich, Zurich, Switzerland; Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | - Andreas P Cuny
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstr. 26, 4058 Basel, Switzerland
| | - Miodrag Savic
- Department of Biomedical Engineering, University of Basel, Allschwil, Switzerland; Department of Surgery, Oral and Cranio-Maxillofacial Surgery, University Hospital Basel, Basel, Switzerland; Department of Health, Economics and Health Directorate, Canton Basel-Landschaft, Switzerland
| | - Fabian Rudolf
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Swiss Institute of Bioinformatics, Mattenstr. 26, 4058 Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; Botnar Research Centre for Child Health, Basel, Switzerland.
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40
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Madan B, Reddem ER, Wang P, Casner RG, Nair MS, Huang Y, Fahad AS, de Souza MO, Banach BB, López Acevedo SN, Pan X, Nimrania R, Teng I, Bahna F, Zhou T, Zhang B, Yin MT, Ho DD, Kwong PD, Shapiro L, DeKosky BJ. Antibody screening at reduced pH enables preferential selection of potently neutralizing antibodies targeting SARS-CoV-2. AIChE J 2021; 67:e17440. [PMID: 34898670 PMCID: PMC8646896 DOI: 10.1002/aic.17440] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/28/2021] [Accepted: 08/19/2021] [Indexed: 12/28/2022]
Abstract
Antiviral monoclonal antibody (mAb) discovery enables the development of antibody-based antiviral therapeutics. Traditional antiviral mAb discovery relies on affinity between antibody and a viral antigen to discover potent neutralizing antibodies, but these approaches are inefficient because many high affinity mAbs have no neutralizing activity. We sought to determine whether screening for anti-SARS-CoV-2 mAbs at reduced pH could provide more efficient neutralizing antibody discovery. We mined the antibody response of a convalescent COVID-19 patient at both physiological pH (7.4) and reduced pH (4.5), revealing that SARS-CoV-2 neutralizing antibodies were preferentially enriched in pH 4.5 yeast display sorts. Structural analysis revealed that a potent new antibody called LP5 targets the SARS-CoV-2 N-terminal domain supersite via a unique binding recognition mode. Our data combine with evidence from prior studies to support antibody screening at pH 4.5 to accelerate antiviral neutralizing antibody discovery.
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Affiliation(s)
- Bharat Madan
- Department of Pharmaceutical ChemistryThe University of KansasLawrenceKansasUSA
| | - Eswar R. Reddem
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
- Zuckerman Mind Brain Behavior InstituteColumbia UniversityNew YorkNew YorkUSA
| | - Pengfei Wang
- Aaron Diamond AIDS Research CenterColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Ryan G. Casner
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
- Zuckerman Mind Brain Behavior InstituteColumbia UniversityNew YorkNew YorkUSA
| | - Manoj S. Nair
- Aaron Diamond AIDS Research CenterColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research CenterColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Ahmed S. Fahad
- Department of Pharmaceutical ChemistryThe University of KansasLawrenceKansasUSA
| | | | - Bailey B. Banach
- Department of Pharmaceutical ChemistryThe University of KansasLawrenceKansasUSA
| | | | - Xiaoli Pan
- Department of Pharmaceutical ChemistryThe University of KansasLawrenceKansasUSA
| | - Rajani Nimrania
- Department of Pharmaceutical ChemistryThe University of KansasLawrenceKansasUSA
| | - I‐Ting Teng
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesBethesdaMarylandUSA
| | - Fabiana Bahna
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
- Zuckerman Mind Brain Behavior InstituteColumbia UniversityNew YorkNew YorkUSA
| | - Tongqing Zhou
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesBethesdaMarylandUSA
| | - Baoshan Zhang
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesBethesdaMarylandUSA
| | - Michael T. Yin
- Department of Medicine, Division of Infectious DiseasesColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - David D. Ho
- Aaron Diamond AIDS Research CenterColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Peter D. Kwong
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
- Vaccine Research CenterNational Institute of Allergy and Infectious DiseasesBethesdaMarylandUSA
| | - Lawrence Shapiro
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
- Zuckerman Mind Brain Behavior InstituteColumbia UniversityNew YorkNew YorkUSA
- Aaron Diamond AIDS Research CenterColumbia University Irving Medical CenterNew YorkNew YorkUSA
| | - Brandon J. DeKosky
- Department of Pharmaceutical ChemistryThe University of KansasLawrenceKansasUSA
- Department of Chemical EngineeringThe University of KansasLawrenceKansasUSA
- The Ragon Institute of MGHMIT, and Harvard, Cambridge, MA
- Department of Chemical EngineeringMassachusetts Institute of Technology, Cambridge, MA
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41
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Griffith SA, McCoy LE. To bnAb or Not to bnAb: Defining Broadly Neutralising Antibodies Against HIV-1. Front Immunol 2021; 12:708227. [PMID: 34737737 PMCID: PMC8560739 DOI: 10.3389/fimmu.2021.708227] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/30/2021] [Indexed: 12/13/2022] Open
Abstract
Since their discovery, antibodies capable of broad neutralisation have been at the forefront of HIV-1 research and are of particular interest due to in vivo passive transfer studies demonstrating their potential to provide protection. Currently an exact definition of what is required for a monoclonal antibody to be classed as a broadly neutralising antibody (bnAb) has not yet been established. This has led to hundreds of antibodies with varying neutralisation breadth being studied and has given insight into antibody maturation pathways and epitopes targeted. However, even with this knowledge, immunisation studies and vaccination trials to date have had limited success in eliciting antibodies with neutralisation breadth. For this reason there is a growing need to identify factors specifically associated with bnAb development, yet to do this a set of criteria is necessary to distinguish bnAbs from non-bnAbs. This review aims to define what it means to be a HIV-1 bnAb by comparing neutralisation breadth, genetic features and epitopes of bnAbs, and in the process highlights the challenges of comparing the array of antibodies that have been isolated over the years.
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Affiliation(s)
- Sarah A Griffith
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, United Kingdom
| | - Laura E McCoy
- Division of Infection and Immunity, Institute of Immunity and Transplantation, University College London, London, United Kingdom
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42
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Anumukonda K, Francis M, Currie P, Tulenko F, Hsu E. Heavy chain-only antibody genes in fish evolved to generate unique CDR3 repertoire. Eur J Immunol 2021; 52:247-260. [PMID: 34708869 DOI: 10.1002/eji.202149588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/08/2021] [Accepted: 10/26/2021] [Indexed: 11/11/2022]
Abstract
In addition to conventional immunoglobulin, camelids and cartilaginous fish express a special class of antibody that consists only of heavy (H) chain (HCAbs). In the holocephalan elephantfish, there are two HCAb classes, one of which has evolved surprising features. The H-chain genes in cartilaginous fish are organized as 20-200 minigenes, or clusters, each consisting of VH, 1-3 DH, JH gene segments with one set of constant region exons. We report that HHC2 (holocephalan H-chain antibody 2) evolved from IgM H-chain clusters, but its DH gene segments have diverged considerably. The three DH in HHC2 clusters are A-rich, so that one to three potential reading frames for each DH encode lysine and arginine. All three are incorporated into the rearranged VDJ, ensuring that the ligand-binding site carries multiple basic residues, as cDNA sequences demonstrate. The electropositive character in HHC2 CDR3 is accompanied by a paucity of aromatic amino acids, the latter feature at variance to the established, interactive role of tyrosine not only in ligand-binding but generally at interfaces of protein complexes. The selection for these divergent HHC2 features challenges currently accepted ideas on what determines antibody reactivity and molecular recognition.
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Affiliation(s)
- Kamala Anumukonda
- Department of Physiology and Pharmacology, State University of New York Downstate Health Sciences University, Brooklyn, NY, 11203, USA
| | - Malcolm Francis
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Peter Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Frank Tulenko
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, 3800, Australia
| | - Ellen Hsu
- Department of Physiology and Pharmacology, State University of New York Downstate Health Sciences University, Brooklyn, NY, 11203, USA
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43
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Rodríguez-Caballero A, Fuentes Herrero B, Oliva Ariza G, Criado I, Alcoceba M, Prieto C, Pérez Caro M, García-Montero AC, González Díaz M, Forconi F, Sarmento-Ribeiro AB, Almeida J, Orfao A. The Hydropathy Index of the HCDR3 Region of the B-Cell Receptor Identifies Two Subgroups of IGHV-Mutated Chronic Lymphocytic Leukemia Patients With Distinct Outcome. Front Oncol 2021; 11:723722. [PMID: 34765543 PMCID: PMC8577851 DOI: 10.3389/fonc.2021.723722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
The HCDR3 sequences of the B-cell receptor (BCR) undergo constraints in length, amino acid use, and charge during maturation of B-cell precursors and after antigen encounter, leading to BCR and antibodies with high affinity to specific antigens. Chronic lymphocytic leukemia consists of an expansion of B-cells with a mixed immature and "antigen-experienced" phenotype, with either a mutated (M-CLL) or unmutated (U-CLL) tumor BCR, associated with distinct patient outcomes. Here, we investigated the hydropathy index of the BCR of 138 CLL patients and its association with the IGHV mutational status and patient outcome. Overall, two clearly distinct subgroups of M-CLL patients emerged, based on a neutral (mean hydropathy index of -0.1) vs. negatively charged BCR (mean hydropathy index of -1.1) with molecular features closer to those of B-cell precursors and peripheral/mature B-cells, respectively. Despite that M-CLL with neutral HCDR3 did not show traits associated with a mature B-cell repertoire, important differences in IGHV gene usage of tumor cells and patient outcome were observed in this subgroup of patients once compared to both U-CLL and M-CLL with negatively charged HCDR3 sequences. Compared to M-CLL with negatively charged HCDR3 sequences, M-CLL with neutral HCDR3 sequences showed predominance of men, more advanced stages of the disease, and a greater frequency of genetic alterations-e.g., del(17p)-together with a higher rate of disease progression and shorter time to therapy (TTT), independently of other prognostic factors. Our data suggest that the hydropathy index of the HCDR3 sequences of CLL cells allows the identification of a subgroup of M-CLL with intermediate prognostic features between U-CLL and the more favorable subgroup of M-CLL with a negatively charged BCR.
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Affiliation(s)
- Arancha Rodríguez-Caballero
- Translational and Clinical Research Program, Cancer Research Center Institute of Cancer Molecular and Cellular Biology (IBMCC), University of Salamanca-The Spanish National Research Council (USAL-CSIC), Department of Medicine and Cytometry Service, Nucleus Research Support Platform from University of Salamanca (NUCLEUS), University of Salamanca, Salamanca, Spain
- CIBERONC Program of Liquid Biopsy, Hematologic Tumors, Centro de Investigación Biomédica en Red de Cáncer CB16/12/00400 and CB16/12/00233 (CIBERONC), Madrid, Spain
- Molecular and Cellular Biology of Hematologic Tumors, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain
| | - Blanca Fuentes Herrero
- Translational and Clinical Research Program, Cancer Research Center Institute of Cancer Molecular and Cellular Biology (IBMCC), University of Salamanca-The Spanish National Research Council (USAL-CSIC), Department of Medicine and Cytometry Service, Nucleus Research Support Platform from University of Salamanca (NUCLEUS), University of Salamanca, Salamanca, Spain
- CIBERONC Program of Liquid Biopsy, Hematologic Tumors, Centro de Investigación Biomédica en Red de Cáncer CB16/12/00400 and CB16/12/00233 (CIBERONC), Madrid, Spain
- Molecular and Cellular Biology of Hematologic Tumors, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain
| | - Guillermo Oliva Ariza
- Translational and Clinical Research Program, Cancer Research Center Institute of Cancer Molecular and Cellular Biology (IBMCC), University of Salamanca-The Spanish National Research Council (USAL-CSIC), Department of Medicine and Cytometry Service, Nucleus Research Support Platform from University of Salamanca (NUCLEUS), University of Salamanca, Salamanca, Spain
- CIBERONC Program of Liquid Biopsy, Hematologic Tumors, Centro de Investigación Biomédica en Red de Cáncer CB16/12/00400 and CB16/12/00233 (CIBERONC), Madrid, Spain
- Molecular and Cellular Biology of Hematologic Tumors, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain
| | - Ignacio Criado
- Translational and Clinical Research Program, Cancer Research Center Institute of Cancer Molecular and Cellular Biology (IBMCC), University of Salamanca-The Spanish National Research Council (USAL-CSIC), Department of Medicine and Cytometry Service, Nucleus Research Support Platform from University of Salamanca (NUCLEUS), University of Salamanca, Salamanca, Spain
- CIBERONC Program of Liquid Biopsy, Hematologic Tumors, Centro de Investigación Biomédica en Red de Cáncer CB16/12/00400 and CB16/12/00233 (CIBERONC), Madrid, Spain
- Molecular and Cellular Biology of Hematologic Tumors, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain
| | - Miguel Alcoceba
- CIBERONC Program of Liquid Biopsy, Hematologic Tumors, Centro de Investigación Biomédica en Red de Cáncer CB16/12/00400 and CB16/12/00233 (CIBERONC), Madrid, Spain
- Molecular and Cellular Biology of Hematologic Tumors, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca/Biomedical Research Institute of Salamanca (HUS/IBSAL), Salamanca, Spain
| | - Carlos Prieto
- Bioinformatics Service, Nucleus Research Support Platform from University of Salamanca (NUCLEUS), University of Salamanca, Salamanca, Spain
| | - María Pérez Caro
- Spanish National DNA Bank Carlos III, University of Salamanca, Salamanca, Spain
| | - Andrés C. García-Montero
- Translational and Clinical Research Program, Cancer Research Center Institute of Cancer Molecular and Cellular Biology (IBMCC), University of Salamanca-The Spanish National Research Council (USAL-CSIC), Department of Medicine and Cytometry Service, Nucleus Research Support Platform from University of Salamanca (NUCLEUS), University of Salamanca, Salamanca, Spain
- CIBERONC Program of Liquid Biopsy, Hematologic Tumors, Centro de Investigación Biomédica en Red de Cáncer CB16/12/00400 and CB16/12/00233 (CIBERONC), Madrid, Spain
- Molecular and Cellular Biology of Hematologic Tumors, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain
| | - Marcos González Díaz
- CIBERONC Program of Liquid Biopsy, Hematologic Tumors, Centro de Investigación Biomédica en Red de Cáncer CB16/12/00400 and CB16/12/00233 (CIBERONC), Madrid, Spain
- Molecular and Cellular Biology of Hematologic Tumors, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca/Biomedical Research Institute of Salamanca (HUS/IBSAL), Salamanca, Spain
| | - Francesco Forconi
- Haematology Oncology Group, School of Cancer Sciences, Cancer Research UK Centre and National Institute for Health Research Experimental Cancer Medicine, University of Southampton, Faculty of Medicine, Southampton, United Kingdom
| | - Ana Bela Sarmento-Ribeiro
- Faculty of Medicine, University of Coimbra (FMUC), Coimbra, Portugal
- Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
| | - Julia Almeida
- Translational and Clinical Research Program, Cancer Research Center Institute of Cancer Molecular and Cellular Biology (IBMCC), University of Salamanca-The Spanish National Research Council (USAL-CSIC), Department of Medicine and Cytometry Service, Nucleus Research Support Platform from University of Salamanca (NUCLEUS), University of Salamanca, Salamanca, Spain
- CIBERONC Program of Liquid Biopsy, Hematologic Tumors, Centro de Investigación Biomédica en Red de Cáncer CB16/12/00400 and CB16/12/00233 (CIBERONC), Madrid, Spain
- Molecular and Cellular Biology of Hematologic Tumors, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain
| | - Alberto Orfao
- Translational and Clinical Research Program, Cancer Research Center Institute of Cancer Molecular and Cellular Biology (IBMCC), University of Salamanca-The Spanish National Research Council (USAL-CSIC), Department of Medicine and Cytometry Service, Nucleus Research Support Platform from University of Salamanca (NUCLEUS), University of Salamanca, Salamanca, Spain
- CIBERONC Program of Liquid Biopsy, Hematologic Tumors, Centro de Investigación Biomédica en Red de Cáncer CB16/12/00400 and CB16/12/00233 (CIBERONC), Madrid, Spain
- Molecular and Cellular Biology of Hematologic Tumors, Biomedical Research Institute of Salamanca (IBSAL), Salamanca, Spain
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44
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Burman L, Chong YE, Duncan S, Klaus A, Rauch K, Hamel K, Hervé K, Pfaffen S, Collins DW, Heyries K, Nangle L, Hansen C, King DJ. Isolation of monoclonal antibodies from anti-synthetase syndrome patients and affinity maturation by recombination of independent somatic variants. MAbs 2021; 12:1836718. [PMID: 33131414 PMCID: PMC7646482 DOI: 10.1080/19420862.2020.1836718] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The autoimmune disease known as Jo-1 positive anti-synthetase syndrome (ASS) is characterized by circulating antibody titers to histidyl-tRNA synthetase (HARS), which may play a role in modulating the non-canonical functions of HARS. Monoclonal antibodies to HARS were isolated by single-cell screening and sequencing from three Jo-1 positive ASS patients and shown to be of high affinity, covering diverse epitope space. The immune response was further characterized by repertoire sequencing from the most productive of the donor samples. In line with previous studies of autoimmune repertoires, these antibodies tended to have long complementarity-determining region H3 sequences with more positive-charged residues than average. Clones of interest were clustered into groups with related sequences, allowing us to observe different somatic mutations in related clones. We postulated that these had found alternate structural solutions for high affinity binding, but that mutations might be transferable between clones to further enhance binding affinity. Transfer of somatic mutations between antibodies within the same clonal group was able to enhance binding affinity in a number of cases, including beneficial transfer of a mutation from a lower affinity clone into one of higher affinity. Affinity enhancement was seen with mutation transfer both between related single-cell clones, and directly from related repertoire sequences. To our knowledge, this is the first demonstration of somatic hypermutation transfer from repertoire sequences to further mature in vivo derived antibodies, and represents an additional tool to aid in affinity maturation for the development of antibodies.
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Affiliation(s)
- Luke Burman
- Discovery Biology, aTyr Pharma , San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | - Carl Hansen
- AbCellera Biologics Inc ., Vancouver, BC, USA
| | - David J King
- Discovery Biology, aTyr Pharma , San Diego, CA, USA
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45
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Machine learning analyses of antibody somatic mutations predict immunoglobulin light chain toxicity. Nat Commun 2021; 12:3532. [PMID: 34112780 PMCID: PMC8192768 DOI: 10.1038/s41467-021-23880-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/23/2021] [Indexed: 02/05/2023] Open
Abstract
In systemic light chain amyloidosis (AL), pathogenic monoclonal immunoglobulin light chains (LC) form toxic aggregates and amyloid fibrils in target organs. Prompt diagnosis is crucial to avoid permanent organ damage, but delayed diagnosis is common because symptoms usually appear only after strong organ involvement. Here we present LICTOR, a machine learning approach predicting LC toxicity in AL, based on the distribution of somatic mutations acquired during clonal selection. LICTOR achieves a specificity and a sensitivity of 0.82 and 0.76, respectively, with an area under the receiver operating characteristic curve (AUC) of 0.87. Tested on an independent set of 12 LCs sequences with known clinical phenotypes, LICTOR achieves a prediction accuracy of 83%. Furthermore, we are able to abolish the toxic phenotype of an LC by in silico reverting two germline-specific somatic mutations identified by LICTOR, and by experimentally assessing the loss of in vivo toxicity in a Caenorhabditis elegans model. Therefore, LICTOR represents a promising strategy for AL diagnosis and reducing high mortality rates in AL.
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A conditionally replication-defective cytomegalovirus vaccine elicits potent and diverse functional monoclonal antibodies in a phase I clinical trial. NPJ Vaccines 2021; 6:79. [PMID: 34078915 PMCID: PMC8172929 DOI: 10.1038/s41541-021-00342-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/24/2021] [Indexed: 02/03/2023] Open
Abstract
A conditionally replication-defective human cytomegalovirus (HCMV) vaccine, V160, was shown to be safe and immunogenic in a two-part, double-blind, randomized, placebo-controlled phase I clinical trial (NCT01986010). However, the specificities and functional properties of V160-elicited antibodies remain undefined. Here, we characterized 272 monoclonal antibodies (mAbs) isolated from single memory B cells of six V160-vaccinated subjects. The mAbs bind to diverse HCMV antigens, including multiple components of the pentamer, gB, and tegument proteins. The most-potent neutralizing antibodies target the pentamer-UL subunits. The binding sites of the antibodies overlap with those of antibodies responding to natural HCMV infection. The majority of the neutralizing antibodies target the gHgL subunit. The non-neutralizing antibodies predominantly target the gB and pp65 proteins. Sequence analysis indicated that V160 induced a class of gHgL antibodies expressing the HV1-18/KV1-5 germline genes in multiple subjects. This study provides valuable insights into primary targets for anti-HCMV antibodies induced by V160 vaccination.
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Chuang GY, Shen CH, Cheung CSF, Gorman J, Creanga A, Joyce MG, Leung K, Rawi R, Wang L, Yang ES, Yang Y, Zhang B, Zhang Y, Kanekiyo M, Zhou T, DeKosky BJ, Graham BS, Mascola JR, Kwong PD. Sequence-Signature Optimization Enables Improved Identification of Human HV6-1-Derived Class Antibodies That Neutralize Diverse Influenza A Viruses. Front Immunol 2021; 12:662909. [PMID: 34135892 PMCID: PMC8201785 DOI: 10.3389/fimmu.2021.662909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/26/2021] [Indexed: 11/13/2022] Open
Abstract
Sequence signatures of multidonor broadly neutralizing influenza antibodies can be used to quantify the prevalence of B cells with virus-neutralizing potential to accelerate development of broadly protective vaccine strategies. Antibodies of the same class share similar recognition modes and developmental pathways, and several antibody classes have been identified that neutralize diverse group 1- and group 2-influenza A viruses and have been observed in multiple human donors. One such multidonor antibody class, the HV6-1-derived class, targets the stem region of hemagglutinin with extraordinary neutralization breadth. Here, we use an iterative process to combine informatics, biochemical, and structural analyses to delineate an improved sequence signature for HV6-1-class antibodies. Based on sequence and structure analyses of known HV6-1 class antibodies, we derived a more inclusive signature (version 1), which we used to search for matching B-cell transcripts from published next-generation sequencing datasets of influenza vaccination studies. We expressed selected antibodies, evaluated their function, and identified amino acid-level requirements from which to refine the sequence signature (version 2). The cryo-electron microscopy structure for one of the signature-identified antibodies in complex with hemagglutinin confirmed motif recognition to be similar to known HV6-1-class members, MEDI8852 and 56.a.09, despite differences in recognition-loop length. Threading indicated the refined signature to have increased accuracy, and signature-identified heavy chains, when paired with the light chain of MEDI8852, showed neutralization comparable to the most potent members of the class. Incorporating sequences of additional class members thus enables an improved sequence signature for HV6-1-class antibodies, which can identify class members with increased accuracy.
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Affiliation(s)
- Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Crystal Sao-Fong Cheung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Jason Gorman
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Adrian Creanga
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - M Gordon Joyce
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Kwanyee Leung
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Yi Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Masaru Kanekiyo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Brandon J DeKosky
- Department of Pharmaceutical Chemistry and Department of Chemical Engineering, University of Kansas, Lawrence, KS, United States
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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Marrero Diaz de Villegas R, Seki C, Mattion NM, König GA. Functional and in silico Characterization of Neutralizing Interactions Between Antibodies and the Foot-and-Mouth Disease Virus Immunodominant Antigenic Site. Front Vet Sci 2021; 8:554383. [PMID: 34026880 PMCID: PMC8137985 DOI: 10.3389/fvets.2021.554383] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 02/19/2021] [Indexed: 12/04/2022] Open
Abstract
Molecular knowledge of virus–antibody interactions is essential for the development of better vaccines and for a timely assessment of the spread and severity of epidemics. For foot-and-mouth disease virus (FMDV) research, in particular, computational methods for antigen–antibody (Ag–Ab) interaction, and cross-antigenicity characterization and prediction are critical to design engineered vaccines with robust, long-lasting, and wider response against different strains. We integrated existing structural modeling and prediction algorithms to study the surface properties of FMDV Ags and Abs and their interaction. First, we explored four modeling and two Ag–Ab docking methods and implemented a computational pipeline based on a reference Ag–Ab structure for FMDV of serotype C, to be used as a source protocol for the study of unknown interaction pairs of Ag–Ab. Next, we obtained the variable region sequence of two monoclonal IgM and IgG antibodies that recognize and neutralize antigenic site A (AgSA) epitopes from South America serotype A FMDV and developed two peptide ELISAs for their fine epitope mapping. Then, we applied the previous Ag–Ab molecular structure modeling and docking protocol further scored by functional peptide ELISA data. This work highlights a possible different behavior in the immune response of IgG and IgM Ab isotypes. The present method yielded reliable Ab models with differential paratopes and Ag interaction topologies in concordance with their isotype classes. Moreover, it demonstrates the applicability of computational prediction techniques to the interaction phenomena between the FMDV immunodominant AgSA and Abs, and points out their potential utility as a metric for virus-related, massive Ab repertoire analysis or as a starting point for recombinant vaccine design.
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Affiliation(s)
- Ruben Marrero Diaz de Villegas
- Instituto de Agrobiotecnología y Biología Molecular, Instituto Nacional de Tecnología Agropecuaria, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
| | - Cristina Seki
- Centro de Virología Animal, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Universidad Abierta Interamericana, Buenos Aires, Argentina
| | - Nora M Mattion
- Centro de Virología Animal, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Universidad Abierta Interamericana, Buenos Aires, Argentina
| | - Guido A König
- Instituto de Agrobiotecnología y Biología Molecular, Instituto Nacional de Tecnología Agropecuaria, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Buenos Aires, Argentina
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Prabakaran P, Rao SP, Wendt M. Animal immunization merges with innovative technologies: A new paradigm shift in antibody discovery. MAbs 2021; 13:1924347. [PMID: 33947305 PMCID: PMC8118498 DOI: 10.1080/19420862.2021.1924347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Animal-derived antibody sources, particularly, transgenic mice that are engineered with human immunoglobulin loci, along with advanced antibody generation technology platforms have facilitated the discoveries of human antibody therapeutics. For example, isolation of antigen-specific B cells, microfluidics, and next-generation sequencing have emerged as powerful tools for identifying and developing monoclonal antibodies (mAbs). These technologies enable not only antibody drug discovery but also lead to the understanding of B cell biology, immune mechanisms and immunogenetics of antibodies. In this perspective article, we discuss the scientific merits of animal immunization combined with advanced methods for antibody generation as compared to animal-free alternatives through in-vitro-generated antibody libraries. The knowledge gained from animal-derived antibodies concerning the recombinational diversity, somatic hypermutation patterns, and physiochemical properties is found more valuable and prerequisite for developing in vitro libraries, as well as artificial intelligence/machine learning methods to discover safe and effective mAbs.
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Affiliation(s)
- Ponraj Prabakaran
- Biologics Research US, Global Large Molecules Research, Sanofi, Framingham, MA, USA
| | - Sambasiva P Rao
- Biologics Research US, Global Large Molecules Research, Sanofi, Framingham, MA, USA
| | - Maria Wendt
- Biologics Research US, Global Large Molecules Research, Sanofi, Framingham, MA, USA
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50
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Seydoux E, Wan YH, Feng J, Wall A, Aljedani S, Homad LJ, MacCamy AJ, Weidle C, Gray MD, Brumage L, Taylor JJ, Pancera M, Stamatatos L, McGuire AT. Development of a VRC01-class germline targeting immunogen derived from anti-idiotypic antibodies. Cell Rep 2021; 35:109084. [PMID: 33951425 PMCID: PMC8127986 DOI: 10.1016/j.celrep.2021.109084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/08/2021] [Accepted: 04/13/2021] [Indexed: 10/27/2022] Open
Abstract
An effective HIV-1 vaccine will likely need to elicit broadly neutralizing antibodies (bNAbs). Broad and potent VRC01-class bNAbs have been isolated from multiple infected individuals, suggesting that they could be reproducibly elicited by vaccination. Several HIV-1 envelope-derived germline-targeting immunogens have been designed to engage naive VRC01-class precursor B cells. However, they also present off-target epitopes that could hinder development of VRC01-class bNAbs. We characterize a panel of anti-idiotypic monoclonal antibodies (ai-mAbs) raised against inferred-germline (iGL) VRC01-class antibodies. By leveraging binding, structural, and B cell sorting data, we engineered a bispecific molecule derived from two ai-mAbs; one specific for VRC01-class heavy chains and one specific for VRC01-class light chains. The bispecific molecule preferentially activates iGL-VRC01 B cells in vitro and induces specific antibody responses in a murine adoptive transfer model with a diverse polyclonal B cell repertoire. This molecule represents an alternative non-envelope-derived germline-targeting immunogen that can selectively activate VRC01-class precursors in vivo.
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Affiliation(s)
- Emilie Seydoux
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Yu-Hsin Wan
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Junli Feng
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Abigail Wall
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Safia Aljedani
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Leah J Homad
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Anna J MacCamy
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Connor Weidle
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Matthew D Gray
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Lauren Brumage
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Justin J Taylor
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA; University of Washington, Department of Global Health, Seattle, WA 98195, USA; University of Washington, Department of Immunology, Seattle, WA 98109, USA
| | - Marie Pancera
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA
| | - Leonidas Stamatatos
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA; University of Washington, Department of Global Health, Seattle, WA 98195, USA.
| | - Andrew T McGuire
- Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA; University of Washington, Department of Global Health, Seattle, WA 98195, USA.
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