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Chen JS, Chow RD, Song E, Mao T, Israelow B, Kamath K, Bozekowski J, Haynes WA, Filler RB, Menasche BL, Wei J, Alfajaro MM, Song W, Peng L, Carter L, Weinstein JS, Gowthaman U, Chen S, Craft J, Shon JC, Iwasaki A, Wilen CB, Eisenbarth SC. High-affinity, neutralizing antibodies to SARS-CoV-2 can be made without T follicular helper cells. Sci Immunol 2022; 7:eabl5652. [PMID: 34914544 PMCID: PMC8977051 DOI: 10.1126/sciimmunol.abl5652] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
T follicular helper (TFH) cells are the conventional drivers of protective, germinal center (GC)–based antiviral antibody responses. However, loss of TFH cells and GCs has been observed in patients with severe COVID-19. As T cell–B cell interactions and immunoglobulin class switching still occur in these patients, noncanonical pathways of antibody production may be operative during SARS-CoV-2 infection. We found that both TFH-dependent and -independent antibodies were induced against SARS-CoV-2 infection, SARS-CoV-2 vaccination, and influenza A virus infection. Although TFH-independent antibodies to SARS-CoV-2 had evidence of reduced somatic hypermutation, they were still high affinity, durable, and reactive against diverse spike-derived epitopes and were capable of neutralizing both homologous SARS-CoV-2 and the B.1.351 (beta) variant of concern. We found by epitope mapping and B cell receptor sequencing that TFH cells focused the B cell response, and therefore, in the absence of TFH cells, a more diverse clonal repertoire was maintained. These data support an alternative pathway for the induction of B cell responses during viral infection that enables effective, neutralizing antibody production to complement traditional GC-derived antibodies that might compensate for GCs damaged by viral inflammation.
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Affiliation(s)
- Jennifer S. Chen
- Department of Laboratory Medicine, Yale University School of Medicine; New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine; New Haven, CT, USA
| | - Ryan D. Chow
- Department of Genetics, Yale University School of Medicine; New Haven, CT, USA
- Systems Biology Institute, Yale University; West Haven, CT, USA
| | - Eric Song
- Department of Immunobiology, Yale University School of Medicine; New Haven, CT, USA
| | - Tianyang Mao
- Department of Immunobiology, Yale University School of Medicine; New Haven, CT, USA
| | - Benjamin Israelow
- Department of Immunobiology, Yale University School of Medicine; New Haven, CT, USA
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine; New Haven, CT, USA
| | | | | | | | - Renata B. Filler
- Department of Laboratory Medicine, Yale University School of Medicine; New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine; New Haven, CT, USA
| | - Bridget L. Menasche
- Department of Laboratory Medicine, Yale University School of Medicine; New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine; New Haven, CT, USA
| | - Jin Wei
- Department of Laboratory Medicine, Yale University School of Medicine; New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine; New Haven, CT, USA
| | - Mia Madel Alfajaro
- Department of Laboratory Medicine, Yale University School of Medicine; New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine; New Haven, CT, USA
| | - Wenzhi Song
- Department of Immunobiology, Yale University School of Medicine; New Haven, CT, USA
| | - Lei Peng
- Department of Genetics, Yale University School of Medicine; New Haven, CT, USA
- Systems Biology Institute, Yale University; West Haven, CT, USA
| | - Lauren Carter
- Institute for Protein Design, University of Washington; Seattle, WA, USA
| | - Jason S. Weinstein
- Center for Immunity and Inflammation, Rutgers New Jersey Medical School; Newark, NJ, USA
| | - Uthaman Gowthaman
- Deparment of Pathology, University of Massachusetts Medical School; Worcester, MA, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine; New Haven, CT, USA
- Systems Biology Institute, Yale University; West Haven, CT, USA
| | - Joe Craft
- Department of Immunobiology, Yale University School of Medicine; New Haven, CT, USA
| | | | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine; New Haven, CT, USA
- Howard Hughes Medical Institute; Chevy Chase, MD, USA
| | - Craig B. Wilen
- Department of Laboratory Medicine, Yale University School of Medicine; New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine; New Haven, CT, USA
| | - Stephanie C. Eisenbarth
- Department of Laboratory Medicine, Yale University School of Medicine; New Haven, CT, USA
- Department of Immunobiology, Yale University School of Medicine; New Haven, CT, USA
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Haynes WA, Kamath K, Bozekowski J, Baum-Jones E, Campbell M, Casanovas-Massana A, Daugherty PS, Dela Cruz CS, Dhal A, Farhadian SF, Fitzgibbons L, Fournier J, Jhatro M, Jordan G, Klein J, Lucas C, Kessler D, Luchsinger LL, Martinez B, Catherine Muenker M, Pischel L, Reifert J, Sawyer JR, Waitz R, Wunder EA, Zhang M, Iwasaki A, Ko A, Shon JC. High-resolution epitope mapping and characterization of SARS-CoV-2 antibodies in large cohorts of subjects with COVID-19. Commun Biol 2021; 4:1317. [PMID: 34811480 PMCID: PMC8608966 DOI: 10.1038/s42003-021-02835-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
As Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to spread, characterization of its antibody epitopes, emerging strains, related coronaviruses, and even the human proteome in naturally infected patients can guide the development of effective vaccines and therapies. Since traditional epitope identification tools are dependent upon pre-defined peptide sequences, they are not readily adaptable to diverse viral proteomes. The Serum Epitope Repertoire Analysis (SERA) platform leverages a high diversity random bacterial display library to identify proteome-independent epitope binding specificities which are then analyzed in the context of organisms of interest. When evaluating immune response in the context of SARS-CoV-2, we identify dominant epitope regions and motifs which demonstrate potential to classify mild from severe disease and relate to neutralization activity. We highlight SARS-CoV-2 epitopes that are cross-reactive with other coronaviruses and demonstrate decreased epitope signal for mutant SARS-CoV-2 strains. Collectively, the evolution of SARS-CoV-2 mutants towards reduced antibody response highlight the importance of data-driven development of the vaccines and therapies to treat COVID-19. Using a high throughput, random bacterial peptide display approach applied to patient serum samples, Haynes, Kamath, Bozekowski et al identify the antigens and epitopes that elicit a SARS-CoV-2 humoral response. They identify differences depending on disease severity and further in silico analysis suggests decreased epitope signal for Q677P but not for D614G mutant SARSCoV-2 strains.
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Affiliation(s)
| | | | | | | | - Melissa Campbell
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Charles S Dela Cruz
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, Yale University School of Medicine, New Haven, CT, USA
| | | | - Shelli F Farhadian
- Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | | | - John Fournier
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | | | - Jon Klein
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Carolina Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | | | | | | | - M Catherine Muenker
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Lauren Pischel
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.,Department of Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT, USA
| | | | | | | | - Elsio A Wunder
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | | | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Albert Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
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Wang K, Dropulic L, Bozekowski J, Pietz HL, Jegaskanda S, Dowdell K, Vogel JS, Garabedian D, Oestreich M, Nguyen H, Ali MA, Lumbard K, Hunsberger S, Reifert J, Haynes WA, Sawyer JR, Shon JC, Daugherty PS, Cohen JI. Serum and Cervicovaginal Fluid Antibody Profiling in Herpes Simplex Virus (HSV) Seronegative Recipients of the HSV529 Vaccine. J Infect Dis 2021; 224:1509-1519. [PMID: 33718970 DOI: 10.1093/infdis/jiab139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 03/12/2021] [Indexed: 11/14/2022] Open
Abstract
Previous HSV2 vaccines have not prevented genital herpes. Concerns have been raised about the choice of antigen, the type of antibody induced by the vaccine, and whether antibody is present in the genital tract where infection occurs. We reported results of a trial of an HSV2 replication-defective vaccine, HSV529, that induced serum neutralizing antibody responses in 78% of HSV1 -/HSV2 - vaccine recipients. Here we show that HSV1 -/HSV2 - vaccine recipients developed antibodies to epitopes of several viral proteins; however, fewer antibody epitopes were detected in vaccine recipients compared with naturally infected persons. HSV529 induced antibodies that mediated HSV2-specific NK cell activation. Depletion of gD-binding antibody from sera reduced neutralizing titers by 62% and NK cell activation by 81%. HSV2 gD antibody was detected in cervicovaginal fluid at about one-third the level of that in serum. A vaccine that induces potent serum antibodies transported to the genital tract might reduce HSV genital infection.
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Affiliation(s)
- Kening Wang
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lesia Dropulic
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Harlan L Pietz
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sinthujan Jegaskanda
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Kennichi Dowdell
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Joshua S Vogel
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Doreen Garabedian
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Makinna Oestreich
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Hanh Nguyen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mir A Ali
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Keith Lumbard
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sally Hunsberger
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | | - Jeffrey I Cohen
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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Reifert J, Kamath K, Bozekowski J, Lis E, Horn EJ, Granger D, Theel ES, Shon J, Sawyer JR, Daugherty PS. Serum Epitope Repertoire Analysis Enables Early Detection of Lyme Disease with Improved Sensitivity in an Expandable Multiplex Format. J Clin Microbiol 2021; 59:e01836-20. [PMID: 33148704 PMCID: PMC8111119 DOI: 10.1128/jcm.01836-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/27/2020] [Indexed: 12/25/2022] Open
Abstract
Widely employed diagnostic antibody serology for Lyme disease, known as standard two-tier testing (STTT), exhibits insufficient sensitivity in early Lyme disease, yielding many thousands of false-negative test results each year. Given this problem, we applied serum antibody repertoire analysis (SERA), or next-generation sequencing (NGS)-based serology, to discover IgG and IgM antibody epitope motifs capable of detecting Lyme disease-specific antibodies with high sensitivity and specificity. Iterative motif discovery and bioinformatic analysis of epitope repertoires from subjects with Lyme disease (n = 264) and controls (n = 391) yielded a set of 28 epitope motifs representing 20 distinct IgG antibody epitopes and a set of 38 epitope motifs representing 21 distinct IgM epitopes, which performed equivalently in a large validation cohort of STTT-positive samples. In a second validation set from subjects with clinically defined early Lyme disease (n = 119) and controls (n = 257), the SERA Lyme IgG and IgM assay exhibited significantly improved sensitivity relative to STTT (77% versus 62%; Z-test; P = 0.013) and improved specificity (99% versus 97%). Early Lyme disease subjects exhibited significantly fewer reactive epitopes (Mann-Whitney U test; P < 0.0001) relative to subjects with Lyme arthritis. Thus, SERA Lyme IgG and M panels provided increased accuracy in early Lyme disease in a readily expandable multiplex assay format.
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Affiliation(s)
| | | | | | - Ewa Lis
- Serimmune Inc., Goleta, California, USA
| | | | - Dane Granger
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester Minnesota, USA
| | - Elitza S Theel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester Minnesota, USA
| | - John Shon
- Serimmune Inc., Goleta, California, USA
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5
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Pantazes RJ, Reifert J, Bozekowski J, Ibsen KN, Murray JA, Daugherty PS. Identification of disease-specific motifs in the antibody specificity repertoire via next-generation sequencing. Sci Rep 2016; 6:30312. [PMID: 27481573 PMCID: PMC4969583 DOI: 10.1038/srep30312] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 07/04/2016] [Indexed: 12/12/2022] Open
Abstract
Disease-specific antibodies can serve as highly effective biomarkers but have been identified for only a relatively small number of autoimmune diseases. A method was developed to identify disease-specific binding motifs through integration of bacterial display peptide library screening, next-generation sequencing (NGS) and computational analysis. Antibody specificity repertoires were determined by identifying bound peptide library members for each specimen using cell sorting and performing NGS. A computational algorithm, termed Identifying Motifs Using Next- generation sequencing Experiments (IMUNE), was developed and applied to discover disease- and healthy control-specific motifs. IMUNE performs comprehensive pattern searches, identifies patterns statistically enriched in the disease or control groups and clusters the patterns to generate motifs. Using celiac disease sera as a discovery set, IMUNE identified a consensus motif (QPEQPF[PS]E) with high diagnostic sensitivity and specificity in a validation sera set, in addition to novel motifs. Peptide display and sequencing (Display-Seq) coupled with IMUNE analysis may thus be useful to characterize antibody repertoires and identify disease-specific antibody epitopes and biomarkers.
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Affiliation(s)
- Robert J Pantazes
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.,Serimmune, Inc, Santa Barbara, CA 93105, USA
| | - Jack Reifert
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.,Serimmune, Inc, Santa Barbara, CA 93105, USA
| | - Joel Bozekowski
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Kelly N Ibsen
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Joseph A Murray
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota 55905, USA
| | - Patrick S Daugherty
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.,Serimmune, Inc, Santa Barbara, CA 93105, USA
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