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Fiala J, Schuster D, Ollivier S, Pengelley S, Lubeck M, Busch F, Jankevics A, Raether O, Greisch JF, Heck AJR. Protein-Centric Analysis of Personalized Antibody Repertoires Using LC-MS-Based Fab-Profiling on a timsTOF. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1292-1300. [PMID: 38662593 PMCID: PMC11157643 DOI: 10.1021/jasms.4c00076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 06/06/2024]
Abstract
Endogenous antibodies, or immunoglobulins (Igs), abundantly present in body fluids, represent some of the most challenging samples to analyze, largely due to the immense variability in their sequences and concentrations. It has been estimated that our body can produce billions of different Ig proteins with different isotypes, making their individual analysis seemingly impossible. However, recent advances in protein-centric proteomics using LC-MS coupled to Orbitrap mass analyzers to profile intact Fab fragments formed by selective cleavage at the IgG-hinge revealed that IgG repertoires may be less diverse, albeit unique for each donor. Serum repertoires seem to be dominated by a few hundred clones that cumulatively make up 50-95% of the total IgG content. Enabling such analyses required careful optimization of the chromatography and mass analysis, as all Fab analytes are highly alike in mass (46-51 kDa) and sequence. To extend the opportunities of this mass-spectrometry-based profiling of antibody repertoires, we here report the optimization and evaluation of an alternative MS platform, namely, the timsTOF, for antibody repertoire profiling. The timsTOF mass analyzer has gained traction in recent years for peptide-centric proteomics and found wide applicability in plasma proteomics, affinity proteomics, and HLA peptidomics, to name a few. However, for protein-centric analysis, this platform has been less explored. Here, we demonstrate that the timsTOF platform can be adapted to perform protein-centric LC-MS-based profiling of antibody repertoires. In a side-by-side comparison of the timsTOF and the Orbitrap we demonstrate that the extracted serum antibody repertoires are alike qualitatively and quantitatively, whereby in particular the sensitivity of the timsTOF platform excels. Future incorporation of advanced top-down capabilities on the timsTOF may make this platform a very valuable alternative for protein-centric proteomics and top-down proteomics and thus also for personalized antibody repertoire profiling.
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Affiliation(s)
- Jan Fiala
- Biomolecular
Mass Spectrometry & Proteomics, Bijvoet Center for Biomolecular
Research & Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The
Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Dina Schuster
- Biomolecular
Mass Spectrometry & Proteomics, Bijvoet Center for Biomolecular
Research & Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The
Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Simon Ollivier
- Biomolecular
Mass Spectrometry & Proteomics, Bijvoet Center for Biomolecular
Research & Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The
Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Stuart Pengelley
- Bruker
Daltonics GmbH & Co. KG, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Markus Lubeck
- Bruker
Daltonics GmbH & Co. KG, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | - Florian Busch
- Bruker
Switzerland AG, 8117 Fällanden, Zurich Switzerland
| | - Andris Jankevics
- Biomolecular
Mass Spectrometry & Proteomics, Bijvoet Center for Biomolecular
Research & Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The
Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Oliver Raether
- Bruker
Daltonics GmbH & Co. KG, Fahrenheitstrasse 4, 28359 Bremen, Germany
| | | | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry & Proteomics, Bijvoet Center for Biomolecular
Research & Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584
CH Utrecht, The
Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
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2
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Hsiao MH, Miao Y, Liu Z, Schütze K, Limjunyawong N, Chien DCC, Monteiro WD, Chu LS, Morgenlander W, Jayaraman S, Jang SE, Gray JJ, Zhu H, Dong X, Steinegger M, Larman HB. Molecular Display of the Animal Meta-Venome for Discovery of Novel Therapeutic Peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.27.595990. [PMID: 38854075 PMCID: PMC11160688 DOI: 10.1101/2024.05.27.595990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Animal venoms, distinguished by their unique structural features and potent bioactivities, represent a vast and relatively untapped reservoir of therapeutic molecules. However, limitations associated with extracting or expressing large numbers of individual venoms and venom-like molecules have precluded their therapeutic evaluation via high throughput screening. Here, we developed an innovative computational approach to design a highly diverse library of animal venoms and "metavenoms". We employed programmable M13 hyperphage display to preserve critical disulfide-bonded structures for highly parallelized single-round biopanning with quantitation via high-throughput DNA sequencing. Our approach led to the discovery of Kunitz type domain containing proteins that target the human itch receptor Mas-related G protein-coupled receptor X4 (MRGPRX4), which plays a crucial role in itch perception. Deep learning-based structural homology mining identified two endogenous human homologs, tissue factor pathway inhibitor (TFPI) and serine peptidase inhibitor, Kunitz type 2 (SPINT2), which exhibit agonist-dependent potentiation of MRGPRX4. Highly multiplexed screening of animal venoms and metavenoms is therefore a promising approach to uncover new drug candidates.
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Affiliation(s)
- Meng-Hsuan Hsiao
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- These authors contributed equally to this work
| | - Yang Miao
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- These authors contributed equally to this work
| | - Zixing Liu
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biology, Zanvyl Krieger School of Arts and Sciences, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Konstantin Schütze
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Nathachit Limjunyawong
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center of Research Excellence in Allergy and Immunology, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand
| | - Daphne Chun-Che Chien
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Wayne Denis Monteiro
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Lee-Shin Chu
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - William Morgenlander
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sahana Jayaraman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sung-eun Jang
- School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Viral Oncology Program, Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Xinzhong Dong
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Martin Steinegger
- School of Biological Sciences, Seoul National University, Seoul, South Korea
- Artificial Intelligence Institute, Seoul National University, Seoul, South Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, South Korea
| | - H. Benjamin Larman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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3
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Dong J, Zhang Q, Yang J, Zhao Y, Miao Z, Pei S, Qin H, Jing C, Wen G, Zhang A, Tao P. BacScan: a novel genome-wide strategy for uncovering broadly immunogenic proteins in bacteria. Front Immunol 2024; 15:1392456. [PMID: 38779673 PMCID: PMC11109440 DOI: 10.3389/fimmu.2024.1392456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 04/15/2024] [Indexed: 05/25/2024] Open
Abstract
In response to the global threat posed by bacterial pathogens, which are the second leading cause of death worldwide, vaccine development is challenged by the diversity of bacterial serotypes and the lack of immunoprotection across serotypes. To address this, we introduce BacScan, a novel genome-wide technology for the rapid discovery of conserved highly immunogenic proteins (HIPs) across serotypes. Using bacterial-specific serum, BacScan combines phage display, immunoprecipitation, and next-generation sequencing to comprehensively identify all the HIPs in a single assay, thereby paving the way for the development of universally protective vaccines. Our validation of this technique with Streptococcus suis, a major pathogenic threat, led to the identification of 19 HIPs, eight of which conferred 20-100% protection against S. suis challenge in animal models. Remarkably, HIP 8455 induced complete immunity, making it an exemplary vaccine target. BacScan's adaptability to any bacterial pathogen positions it as a revolutionary tool that can expedite the development of vaccines with broad efficacy, thus playing a critical role in curbing bacterial transmission and slowing the march of antimicrobial resistance.
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Affiliation(s)
- Junhua Dong
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Qian Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Jinyue Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Yacan Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Zhuangxia Miao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Siyang Pei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Huan Qin
- College of Life Science, Wuhan University, Wuhan, Hubei, China
| | - Changwei Jing
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Guoyuan Wen
- Institute of Animal Husbandry and Veterinary Sciences, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Anding Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
| | - Pan Tao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Prevention & Control for African Swine Fever and Other Major Pig Diseases, Ministry of Agriculture and Rural Affairs, Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, China
- Hubei Hongshan Lab, Wuhan, Hubei, China
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4
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Lidenge SJ, Yalcin D, Bennett SJ, Ngalamika O, Kweyamba BB, Mwita CJ, Tso FY, Mwaiselage J, West JT, Wood C. Viral Epitope Scanning Reveals Correlation between Seasonal HCoVs and SARS-CoV-2 Antibody Responses among Cancer and Non-Cancer Patients. Viruses 2024; 16:448. [PMID: 38543814 PMCID: PMC10975915 DOI: 10.3390/v16030448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 02/23/2024] [Accepted: 03/09/2024] [Indexed: 04/01/2024] Open
Abstract
Seasonal coronaviruses (HCoVs) are known to contribute to cross-reactive antibody (Ab) responses against SARS-CoV-2. While these responses are predictable due to the high homology between SARS-CoV-2 and other CoVs, the impact of these responses on susceptibility to SARS-CoV-2 infection in cancer patients is unclear. To investigate the influence of prior HCoV infection on anti-SARS-CoV-2 Ab responses among COVID-19 asymptomatic individuals with cancer and controls without cancers, we utilized the VirScan technology in which phage immunoprecipitation and sequencing (PhIP-seq) of longitudinal plasma samples was performed to investigate high-resolution (i.e., epitope level) humoral CoV responses. Despite testing positive for anti-SARS-CoV-2 Ab in the plasma, a majority of the participants were asymptomatic for COVID-19 with no prior history of COVID-19 diagnosis. Although the magnitudes of the anti-SARS-CoV-2 Ab responses were lower in individuals with Kaposi sarcoma (KS) compared to non-KS cancer individuals and those without cancer, the HCoV Ab repertoire was similar between individuals with and without cancer independent of age, sex, HIV status, and chemotherapy. The magnitudes of the anti-spike HCoV responses showed a strong positive association with those of the anti-SARS-CoV-2 spike in cancer patients, and only a weak association in non-cancer patients, suggesting that prior infection with HCoVs might play a role in limiting SARS-CoV-2 infection and COVID-19 disease severity.
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Affiliation(s)
- Salum J. Lidenge
- Department of Clinical Research, Training, and Consultancy, Ocean Road Cancer Institute, Dar es Salaam P.O. Box 3592, Tanzania; (S.J.L.); (B.B.K.); (J.M.)
- Department of Clinical Oncology, Muhimbili University of Health and Allied Sciences, Dar es Salaam P.O. Box 65001, Tanzania
| | - Dicle Yalcin
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (D.Y.); (S.J.B.); (F.Y.T.); (J.T.W.)
| | - Sydney J. Bennett
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (D.Y.); (S.J.B.); (F.Y.T.); (J.T.W.)
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68516, USA
| | - Owen Ngalamika
- Dermatology and Venereology Division, University Teaching Hospital, University of Zambia School of Medicine, Lusaka P.O. Box 50001, Zambia;
| | - Brenda B. Kweyamba
- Department of Clinical Research, Training, and Consultancy, Ocean Road Cancer Institute, Dar es Salaam P.O. Box 3592, Tanzania; (S.J.L.); (B.B.K.); (J.M.)
| | - Chacha J. Mwita
- Department of Clinical Research, Training, and Consultancy, Ocean Road Cancer Institute, Dar es Salaam P.O. Box 3592, Tanzania; (S.J.L.); (B.B.K.); (J.M.)
| | - For Yue Tso
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (D.Y.); (S.J.B.); (F.Y.T.); (J.T.W.)
| | - Julius Mwaiselage
- Department of Clinical Research, Training, and Consultancy, Ocean Road Cancer Institute, Dar es Salaam P.O. Box 3592, Tanzania; (S.J.L.); (B.B.K.); (J.M.)
- Department of Clinical Oncology, Muhimbili University of Health and Allied Sciences, Dar es Salaam P.O. Box 65001, Tanzania
| | - John T. West
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (D.Y.); (S.J.B.); (F.Y.T.); (J.T.W.)
| | - Charles Wood
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; (D.Y.); (S.J.B.); (F.Y.T.); (J.T.W.)
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68516, USA
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5
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Fleischer S, Nash TR, Tamargo MA, Lock RI, Venturini G, Morsink M, Li V, Lamberti MJ, Graney PL, Liberman M, Kim Y, Zhuang RZ, Whitehead J, Friedman RA, Soni RK, Seidman JG, Seidman CE, Geraldino-Pardilla L, Winchester R, Vunjak-Novakovic G. An engineered human cardiac tissue model reveals contributions of systemic lupus erythematosus autoantibodies to myocardial injury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583787. [PMID: 38559188 PMCID: PMC10979865 DOI: 10.1101/2024.03.07.583787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Systemic lupus erythematosus (SLE) is a highly heterogenous autoimmune disease that affects multiple organs, including the heart. The mechanisms by which myocardial injury develops in SLE, however, remain poorly understood. Here we engineered human cardiac tissues and cultured them with IgG fractions containing autoantibodies from SLE patients with and without myocardial involvement. We observed unique binding patterns of IgG from two patient subgroups: (i) patients with severe myocardial inflammation exhibited enhanced binding to apoptotic cells within cardiac tissues subjected to stress, and (ii) patients with systolic dysfunction exhibited enhanced binding to the surfaces of viable cardiomyocytes. Functional assays and RNA sequencing (RNA-seq) revealed that IgGs from patients with systolic dysfunction exerted direct effects on engineered tissues in the absence of immune cells, altering tissue cellular composition, respiration and calcium handling. Autoantibody target characterization by phage immunoprecipitation sequencing (PhIP-seq) confirmed distinctive IgG profiles between patient subgroups. By coupling IgG profiling with cell surface protein analyses, we identified four pathogenic autoantibody candidates that may directly alter the function of cells within the myocardium. Taken together, these observations provide insights into the cellular processes of myocardial injury in SLE that have the potential to improve patient risk stratification and inform the development of novel therapeutic strategies.
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Affiliation(s)
- Sharon Fleischer
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Trevor R Nash
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Manuel A Tamargo
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Roberta I Lock
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | | | - Margaretha Morsink
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Vanessa Li
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Morgan J Lamberti
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Pamela L Graney
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Martin Liberman
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Youngbin Kim
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Richard Z Zhuang
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Jaron Whitehead
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Richard A Friedman
- Biomedical Informatics Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
- Department of Biomedical Informatics, Columbia University, New York, NY, USA
| | - Rajesh K Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Cardiovascular Medicine, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - Robert Winchester
- Department of Medicine, Columbia University, New York, NY, USA
- Columbia Center for Translational Immunology, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Gordana Vunjak-Novakovic
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Department of Medicine, Columbia University, New York, NY, USA
- College of Dental Medicine, Columbia University, New York, NY, USA
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6
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Liebhoff AM, Venkataraman T, Morgenlander WR, Na M, Kula T, Waugh K, Morrison C, Rewers M, Longman R, Round J, Elledge S, Ruczinski I, Langmead B, Larman HB. Efficient encoding of large antigenic spaces by epitope prioritization with Dolphyn. Nat Commun 2024; 15:1577. [PMID: 38383452 PMCID: PMC10881494 DOI: 10.1038/s41467-024-45601-8] [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: 07/14/2023] [Accepted: 01/26/2024] [Indexed: 02/23/2024] Open
Abstract
We investigate a relatively underexplored component of the gut-immune axis by profiling the antibody response to gut phages using Phage Immunoprecipitation Sequencing (PhIP-Seq). To cover large antigenic spaces, we develop Dolphyn, a method that uses machine learning to select peptides from protein sets and compresses the proteome through epitope-stitching. Dolphyn compresses the size of a peptide library by 78% compared to traditional tiling, increasing the antibody-reactive peptides from 10% to 31%. We find that the immune system develops antibodies to human gut bacteria-infecting viruses, particularly E.coli-infecting Myoviridae. Cost-effective PhIP-Seq libraries designed with Dolphyn enable the assessment of a wider range of proteins in a single experiment, thus facilitating the study of the gut-immune axis.
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Affiliation(s)
- Anna-Maria Liebhoff
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Thiagarajan Venkataraman
- Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - William R Morgenlander
- Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Miso Na
- Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Tomasz Kula
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA
| | - Kathleen Waugh
- Barbara Davis Center for Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - Charles Morrison
- Behavioral, Clinical and Epidemiologic Sciences, FHI 360, Durham, NC, USA
| | - Marian Rewers
- Barbara Davis Center for Diabetes, University of Colorado Denver, Aurora, CO, USA
| | - Randy Longman
- Jill Roberts Institute for Research in IBD, Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - June Round
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Stephen Elledge
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA
| | - Ben Langmead
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - H Benjamin Larman
- Institute of Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA.
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7
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Bennett SJ, Yalcin D, Privatt SR, Ngalamika O, Lidenge SJ, West JT, Wood C. Antibody profiling and predictive modeling discriminate between Kaposi sarcoma and asymptomatic KSHV infection. PLoS Pathog 2024; 20:e1012023. [PMID: 38381773 PMCID: PMC10911871 DOI: 10.1371/journal.ppat.1012023] [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: 11/13/2023] [Revised: 03/04/2024] [Accepted: 02/02/2024] [Indexed: 02/23/2024] Open
Abstract
Protein-level immunodominance patterns against Kaposi sarcoma-associated herpesvirus (KSHV), the aetiologic agent of Kaposi sarcoma (KS), have been revealed from serological probing of whole protein arrays, however, the epitopes that underlie these patterns have not been defined. We recently demonstrated the utility of phage display in high-resolution linear epitope mapping of the KSHV latency-associated nuclear antigen (LANA/ORF73). Here, a VirScan phage immunoprecipitation and sequencing approach, employing a library of 1,988 KSHV proteome-derived peptides, was used to quantify the breadth and magnitude of responses of 59 sub-Saharan African KS patients and 22 KSHV-infected asymptomatic individuals (ASY), and ultimately to support an application of machine-learning-based predictive modeling using the peptide-level responses. Comparing anti-KSHV antibody repertoire revealed that magnitude, not breadth, increased in KS. The most targeted epitopes in both KS and ASY were in the immunodominant proteins, notably, K8.129-56 and ORF65140-168, in addition to LANA. Finally, using unbiased machine-learning-based predictive models, reactivity to a subset of 25 discriminative peptides was demonstrated to successfully classify KS patients from asymptomatic individuals. Our study provides the highest resolution mapping of antigenicity across the entire KSHV proteome to date, which is vital to discern mechanisms of viral pathogenesis, to define prognostic biomarkers, and to design effective vaccine and therapeutic strategies. Future studies will investigate the diagnostic, prognostic, and therapeutic potential of the 25 discriminative peptides.
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Affiliation(s)
- Sydney J. Bennett
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Dicle Yalcin
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Sara R. Privatt
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Owen Ngalamika
- Dermatology and Venereology Section, University Teaching Hospital, University of Zambia School of Medicine, Lusaka, Zambia
| | - Salum J. Lidenge
- Ocean Road Cancer Institute, Dar es Salaam, Tanzania
- Department of Clinical Oncology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - John T. West
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Charles Wood
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
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8
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Pardo CA. Clinical Approach to Myelopathy Diagnosis. Continuum (Minneap Minn) 2024; 30:14-52. [PMID: 38330471 DOI: 10.1212/con.0000000000001390] [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] [Indexed: 02/10/2024]
Abstract
OBJECTIVE This article describes an integrative strategy to evaluate patients with suspected myelopathy, provides advice on diagnostic approach, and outlines the framework for the etiologic diagnosis of myelopathies. LATEST DEVELOPMENTS Advances in diagnostic neuroimaging techniques of the spinal cord and improved understanding of the immune pathogenic mechanisms associated with spinal cord disorders have expanded the knowledge of inflammatory and noninflammatory myelopathies. The discovery of biomarkers of disease, such as anti-aquaporin 4 and anti-myelin oligodendrocyte glycoprotein antibodies involved in myelitis and other immune-related mechanisms, the emergence and identification of infectious disorders that target the spinal cord, and better recognition of myelopathies associated with vascular pathologies have expanded our knowledge about the broad clinical spectrum of myelopathies. ESSENTIAL POINTS Myelopathies include a group of inflammatory and noninflammatory disorders of the spinal cord that exhibit a wide variety of motor, sensory, gait, and sensory disturbances and produce major neurologic disability. Both inflammatory and noninflammatory myelopathies comprise a broad spectrum of pathophysiologic mechanisms and etiologic factors that lead to specific clinical features and presentations. Knowledge of the clinical variety of myelopathies and understanding of strategies for the precise diagnosis, identification of etiologic factors, and implementation of therapies can help improve outcomes.
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9
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Lastwika KJ, Lampe PD. Breaking tolerance: autoantibodies can target protein posttranslational modifications. Curr Opin Biotechnol 2024; 85:103056. [PMID: 38141322 PMCID: PMC10922400 DOI: 10.1016/j.copbio.2023.103056] [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: 04/04/2023] [Revised: 11/28/2023] [Accepted: 12/03/2023] [Indexed: 12/25/2023]
Abstract
Autoantibodies (AAb) are an immunological resource ripe for exploitation in cancer detection and treatment. Key to this translation is a better understanding of the self-epitope that AAb target in tumor tissue, but do not bind to in normal tissue. Posttranslational modifications (PTMs) on self-proteins are known to break tolerance in many autoimmune diseases and have also recently been described in cancer. This scope of possible autoantigens is quite broad and new high-dimensional and -throughput technologies to probe this repertoire will be necessary to fully exploit their potential. Here, we discuss the strengths and weaknesses of existing high-throughput platforms to detect AAb, review the current methods for characterizing immunogenic PTMs, describe the main challenges to identifying disease-relevant antigens and suggest the properties of future technologies that may be able to address these challenges. We conclude that exploiting the evolutionary power of the immune system to distinguish between self and nonself has great potential to be translated into antibody-based clinical applications.
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Affiliation(s)
- Kristin J Lastwika
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Paul D Lampe
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA.
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10
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Woellner-Santos D, Tahira AC, Malvezzi JVM, Mesel V, Morales-Vicente DA, Trentini MM, Marques-Neto LM, Matos IA, Kanno AI, Pereira ASA, Teixeira AAR, Giordano RJ, Leite LCC, Pereira CAB, DeMarco R, Amaral MS, Verjovski-Almeida S. Schistosoma mansoni vaccine candidates identified by unbiased phage display screening in self-cured rhesus macaques. NPJ Vaccines 2024; 9:5. [PMID: 38177171 PMCID: PMC10767053 DOI: 10.1038/s41541-023-00803-x] [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: 08/03/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Schistosomiasis, a challenging neglected tropical disease, affects millions of people worldwide. Developing a prophylactic vaccine against Schistosoma mansoni has been hindered by the parasite's biological complexity. In this study, we utilized the innovative phage-display immunoprecipitation followed by a sequencing approach (PhIP-Seq) to screen the immune response of 10 infected rhesus macaques during self-cure and challenge-resistant phases, identifying vaccine candidates. Our high-throughput S. mansoni synthetic DNA phage-display library encoded 99.6% of 119,747 58-mer peptides, providing comprehensive coverage of the parasite's proteome. Library screening with rhesus macaques' antibodies, from the early phase of establishment of parasite infection, identified significantly enriched epitopes of parasite extracellular proteins known to be expressed in the digestive tract, shifting towards intracellular proteins during the late phase of parasite clearance. Immunization of mice with a selected pool of PhIP-Seq-enriched phage-displayed peptides from MEG proteins, cathepsins B, and asparaginyl endopeptidase significantly reduced worm burden in a vaccination assay. These findings enhance our understanding of parasite-host immune responses and provide promising prospects for developing an effective schistosomiasis vaccine.
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Affiliation(s)
- Daisy Woellner-Santos
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ana C Tahira
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
| | - João V M Malvezzi
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
- Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Vinicius Mesel
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
| | - David A Morales-Vicente
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Monalisa M Trentini
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, SP, Brazil
| | - Lázaro M Marques-Neto
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, SP, Brazil
| | - Isaac A Matos
- Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Alex I Kanno
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, SP, Brazil
| | - Adriana S A Pereira
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
| | - André A R Teixeira
- Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil
- Institute for Protein Innovation, Boston, MA, USA
| | | | - Luciana C C Leite
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, São Paulo, SP, Brazil
| | - Carlos A B Pereira
- Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ricardo DeMarco
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Murilo S Amaral
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
| | - Sergio Verjovski-Almeida
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil.
- Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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11
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Filimonova I, Innocenti G, Vogl T. Phage Immunoprecipitation Sequencing (PhIP-Seq) for Analyzing Antibody Epitope Repertoires Against Food Antigens. Methods Mol Biol 2024; 2717:101-122. [PMID: 37737980 DOI: 10.1007/978-1-0716-3453-0_7] [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: 09/23/2023]
Abstract
While thousands of food and environmental allergens have been reported, conventional methods for allergy testing typically rely on measuring immunoglobulin E (IgE) binding against panels of dozens to hundreds of antigens. Beyond IgE, also the specificity of other Ig (sub-)classes such as IgG4, has gained interest because of a potential protective role toward allergy.Phage immunoprecipitation sequencing (PhIP-Seq) allows to study hundreds of thousands of rationally selected peptide antigens and to resolve binding specificities of different Ig classes. This technology combines synthetic DNA libraries encoding antigens, with the display on the surface of T7 bacteriophages and next-generation sequencing (NGS) for quantitative readouts. Thereby binding of entire Ig repertoires can be measured to detect the exact epitopes of food allergens and to study potential cross-reactivity.In this chapter, we provide a summary of both the key experimental steps and various strategies for analyzing PhIP-Seq datasets, as well as comparing the advantages and disadvantages of this methodology for measuring antibody responses against food antigens.
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Affiliation(s)
- Ioanna Filimonova
- Medical University of Vienna, Center for Cancer Research, Vienna, Austria
| | - Gabriel Innocenti
- Medical University of Vienna, Center for Cancer Research, Vienna, Austria
| | - Thomas Vogl
- Medical University of Vienna, Center for Cancer Research, Vienna, Austria.
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12
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Linnoila JJ. Paraneoplastic antibodies targeting intracellular antigens. HANDBOOK OF CLINICAL NEUROLOGY 2024; 200:335-346. [PMID: 38494288 DOI: 10.1016/b978-0-12-823912-4.00021-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Although they are relatively rare, the diagnosis of paraneoplastic neurologic syndromes (PNS) can be aided by the identification of neural autoantibodies in patients' serum and cerebrospinal fluid (CSF). They often clinically manifest as characteristic syndromes, including limbic encephalitis, opsoclonus-myoclonus syndrome, paraneoplastic cerebellar degeneration, and paraneoplastic encephalomyelitis. The antibodies are directed either toward intracellular targets, or epitopes on the cell surface. As compared to cell surface antibodies, intracellular paraneoplastic autoantibodies are more classically associated with cancer, most often lung, breast, thymoma, gynecologic, testicular, and/or neuroendocrine cancers. The malignancies themselves tend to be small and regionally contained, attesting to the strength of the immune system in cancer immunosurveillance. Typically, the intracellular antibodies are not directly pathogenic and tend to be associated with PNS that are poorly responsive to treatment. With some notable exceptions, including patients with PNS associated with testicular cancer, patients with intracellular antibodies are typically older individuals, in their 7th decade of life and beyond. Many of them are current or former smokers. Treatment strategies include tumor removal as well as immunotherapy to treat the concomitant PNS. Newer technologies and the ever-broadening use of cancer immunotherapies are contributing to the continued identification of novel intracellularly targeted autoantibodies.
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Affiliation(s)
- Jenny J Linnoila
- Department of Neurology, Massachusetts General Hospital, Boston, MA, United States.
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13
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Rackaityte E, Proekt I, Miller HS, Ramesh A, Brooks JF, Kung AF, Mandel-Brehm C, Yu D, Zamecnik CR, Bair R, Vazquez SE, Sunshine S, Abram CL, Lowell CA, Rizzuto G, Wilson MR, Zikherman J, Anderson MS, DeRisi JL. Validation of a murine proteome-wide phage display library for identification of autoantibody specificities. JCI Insight 2023; 8:e174976. [PMID: 37934865 PMCID: PMC10795829 DOI: 10.1172/jci.insight.174976] [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: 08/21/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023] Open
Abstract
Autoimmunity is characterized by loss of tolerance to tissue-specific as well as systemic antigens, resulting in complex autoantibody landscapes. Here, we introduce and extensively validate the performance characteristics of a murine proteome-wide library for phage display immunoprecipitation and sequencing (PhIP-seq) in profiling mouse autoantibodies. This library was validated using 7 genetically distinct mouse lines across a spectrum of autoreactivity. Mice deficient in antibody production (Rag2-/- and μMT) were used to model nonspecific peptide enrichments, while cross-reactivity was evaluated using anti-ovalbumin B cell receptor-restricted OB1 mice as a proof of principle. The PhIP-seq approach was then utilized to interrogate 3 distinct autoimmune disease models. First, serum from Lyn-/- IgD+/- mice with lupus-like disease was used to identify nuclear and apoptotic bleb reactivities. Second, serum from nonobese diabetic (NOD) mice, a polygenic model of pancreas-specific autoimmunity, was enriched in peptides derived from both insulin and predicted pancreatic proteins. Lastly, Aire-/- mouse sera were used to identify numerous autoantigens, many of which were also observed in previous studies of humans with autoimmune polyendocrinopathy syndrome type 1 carrying recessive mutations in AIRE. These experiments support the use of murine proteome-wide PhIP-seq for antigenic profiling and autoantibody discovery, which may be employed to study a range of immune perturbations in mouse models of autoimmunity profiling.
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Affiliation(s)
| | | | - Haleigh S. Miller
- Department of Biochemistry and Biophysics
- Biological and Medical Informatics Program
| | - Akshaya Ramesh
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine
| | - Jeremy F. Brooks
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, and
| | - Andrew F. Kung
- Department of Biochemistry and Biophysics
- Biological and Medical Informatics Program
| | | | - David Yu
- Diabetes Center, School of Medicine
| | - Colin R. Zamecnik
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine
| | - Rebecca Bair
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine
| | - Sara E. Vazquez
- Department of Biochemistry and Biophysics
- Diabetes Center, School of Medicine
| | | | - Clare L. Abram
- Department of Laboratory Medicine, UCSF, San Francisco, California, USA
| | | | - Gabrielle Rizzuto
- Human Oncology & Pathogenesis Program and Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael R. Wilson
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine
| | - Julie Zikherman
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, and
| | | | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics
- Chan Zuckerberg Biohub, San Francisco, California, USA
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14
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Naigeon M, Roulleaux Dugage M, Danlos FX, Boselli L, Jouniaux JM, de Oliveira C, Ferrara R, Duchemann B, Berthot C, Girard L, Flippot R, Albiges L, Farhane S, Saulnier P, Lacroix L, Griscelli F, Roman G, Hulett T, Marabelle A, Cassard L, Besse B, Chaput N. Human virome profiling identified CMV as the major viral driver of a high accumulation of senescent CD8 + T cells in patients with advanced NSCLC. SCIENCE ADVANCES 2023; 9:eadh0708. [PMID: 37939189 PMCID: PMC10631735 DOI: 10.1126/sciadv.adh0708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 10/05/2023] [Indexed: 11/10/2023]
Abstract
Circulating senescent CD8+ T (T8sen) cells are characterized by a lack of proliferative capacities but retain cytotoxic activity and have been associated to resistance to immunotherapy in patients with advanced non-small cell lung cancer (aNSCLC). We aimed to better characterize T8sen and to determine which factors were associated with their accumulation in patients with aNSCLC. Circulating T8sen cells were characterized by a higher expression of SA-βgal and the transcription factor T-bet, confirming their senescent status. Using whole virome profiling, cytomegalovirus (CMV) was the only virus associated with T8sen. CMV was necessary but not sufficient to explain high accumulation of T8sen (T8senhigh status). In CMV+ patients, the proportion of T8sen cells increased with cancer progression. Last, CMV-induced T8senhigh phenotype but not CMV seropositivity itself was associated with worse progression-free and overall survival in patients treated with anti-PD-(L)1 therapy but not with chemotherapy. Overall, CMV is the unique viral driver of T8sen-driven resistance to anti-PD-(L)1 antibodies in patients with aNSCLC.
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Affiliation(s)
- Marie Naigeon
- Laboratoire d'Immunomonitoring en Oncologie, INSERM US23, CNRS UMS 3655, Gustave Roussy, Villejuif, France
- Faculté de Médecine, Université Paris-Saclay, Le Kremlin-Bicêtre, France
- Faculté de Pharmacie, Université Paris-Saclay, Orsay, France
| | - Matthieu Roulleaux Dugage
- Laboratoire d'Immunomonitoring en Oncologie, INSERM US23, CNRS UMS 3655, Gustave Roussy, Villejuif, France
- Service d’Oncologie Médicale, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
- Département d’Innovation Thérapeutique et d’Essais Précoces (DITEP), Gustave Roussy, Villejuif, France
| | - François-Xavier Danlos
- Faculté de Médecine, Université Paris-Saclay, Le Kremlin-Bicêtre, France
- Département d’Innovation Thérapeutique et d’Essais Précoces (DITEP), Gustave Roussy, Villejuif, France
- Laboratoire de Recherche Translationnelle en Immunothérapie (LRTI), INSERM U1015 and Centre d’Investigation Clinique BIOTHERIS, INSERM CIC1428, Gustave Roussy, Villejuif, France
| | - Lisa Boselli
- Laboratoire d'Immunomonitoring en Oncologie, INSERM US23, CNRS UMS 3655, Gustave Roussy, Villejuif, France
| | - Jean-Mehdi Jouniaux
- Laboratoire d'Immunomonitoring en Oncologie, INSERM US23, CNRS UMS 3655, Gustave Roussy, Villejuif, France
| | - Caroline de Oliveira
- Laboratoire d'Immunomonitoring en Oncologie, INSERM US23, CNRS UMS 3655, Gustave Roussy, Villejuif, France
| | - Roberto Ferrara
- Laboratoire d'Immunomonitoring en Oncologie, INSERM US23, CNRS UMS 3655, Gustave Roussy, Villejuif, France
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Boris Duchemann
- Laboratoire d'Immunomonitoring en Oncologie, INSERM US23, CNRS UMS 3655, Gustave Roussy, Villejuif, France
- Département d’oncologie thoracique et médicale, Hôpitaux Universitaires Paris Seine-Saint-Denis, Hôpital Avicenne, AP-HP, Bobigny, France
| | - Caroline Berthot
- Laboratoire d'Immunomonitoring en Oncologie, INSERM US23, CNRS UMS 3655, Gustave Roussy, Villejuif, France
| | - Lou Girard
- Laboratoire d'Immunomonitoring en Oncologie, INSERM US23, CNRS UMS 3655, Gustave Roussy, Villejuif, France
- Faculté de Pharmacie, Université Paris-Saclay, Orsay, France
| | - Ronan Flippot
- Laboratoire d'Immunomonitoring en Oncologie, INSERM US23, CNRS UMS 3655, Gustave Roussy, Villejuif, France
- Faculté de Médecine, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Laurence Albiges
- Faculté de Médecine, Université Paris-Saclay, Le Kremlin-Bicêtre, France
- Département de Médecine Oncologique, Gustave Roussy, Villejuif, France
| | - Siham Farhane
- Département d’Innovation Thérapeutique et d’Essais Précoces (DITEP), Gustave Roussy, Villejuif, France
- Laboratoire de Recherche Translationnelle en Immunothérapie (LRTI), INSERM U1015 and Centre d’Investigation Clinique BIOTHERIS, INSERM CIC1428, Gustave Roussy, Villejuif, France
| | | | - Ludovic Lacroix
- AMMICa, UAR 3655/US23, Gustave Roussy, Villejuif, France
- Département de Biologie Médicale et Pathologie Médicales, Gustave Roussy, Villejuif, France
| | - Frank Griscelli
- Département de Biologie Médicale et Pathologie Médicales, Gustave Roussy, Villejuif, France
| | - Gabriel Roman
- CDI Laboratories Inc., 1 N. Haven Street, Suite B001, Baltimore, MD 21224, USA
| | - Tyler Hulett
- CDI Laboratories Inc., 1 N. Haven Street, Suite B001, Baltimore, MD 21224, USA
| | - Aurélien Marabelle
- Département d’Innovation Thérapeutique et d’Essais Précoces (DITEP), Gustave Roussy, Villejuif, France
- Laboratoire de Recherche Translationnelle en Immunothérapie (LRTI), INSERM U1015 and Centre d’Investigation Clinique BIOTHERIS, INSERM CIC1428, Gustave Roussy, Villejuif, France
| | - Lydie Cassard
- Laboratoire d'Immunomonitoring en Oncologie, INSERM US23, CNRS UMS 3655, Gustave Roussy, Villejuif, France
| | - Benjamin Besse
- Faculté de Médecine, Université Paris-Saclay, Le Kremlin-Bicêtre, France
- Département de Médecine Oncologique, Gustave Roussy, Villejuif, France
| | - Nathalie Chaput
- Laboratoire d'Immunomonitoring en Oncologie, INSERM US23, CNRS UMS 3655, Gustave Roussy, Villejuif, France
- Faculté de Pharmacie, Université Paris-Saclay, Orsay, France
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15
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Galloway JG, Sung K, Minot SS, Garrett ME, Stoddard CI, Willcox AC, Yaffe ZA, Yucha R, Overbaugh J, Matsen FA. phippery: a software suite for PhIP-Seq data analysis. Bioinformatics 2023; 39:btad583. [PMID: 37740324 PMCID: PMC10547927 DOI: 10.1093/bioinformatics/btad583] [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: 09/28/2022] [Revised: 08/14/2023] [Accepted: 09/20/2023] [Indexed: 09/24/2023] Open
Abstract
SUMMARY We present the phippery software suite for analyzing data from phage display methods that use immunoprecipitation and deep sequencing to capture antibody binding to peptides, often referred to as PhIP-Seq. It has three main components that can be used separately or in conjunction: (i) a Nextflow pipeline, phip-flow, to process raw sequencing data into a compact, multidimensional dataset format and allows for end-to-end automation of reproducible workflows. (ii) a Python API, phippery, which provides interfaces for tasks such as count normalization, enrichment calculation, multidimensional scaling, and more, and (iii) a Streamlit application, phip-viz, as an interactive interface for visualizing the data as a heatmap in a flexible manner. AVAILABILITY AND IMPLEMENTATION All software packages are publicly available under the MIT License. The phip-flow pipeline: https://github.com/matsengrp/phip-flow. The phippery library: https://github.com/matsengrp/phippery. The phip-viz Streamlit application: https://github.com/matsengrp/phip-viz.
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Affiliation(s)
- Jared G Galloway
- Computational Biology, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Kevin Sung
- Computational Biology, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Samuel S Minot
- Data Core, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Meghan E Garrett
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Caitlin I Stoddard
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Alexandra C Willcox
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Zak A Yaffe
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Ryan Yucha
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Julie Overbaugh
- Computational Biology, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Frederick A Matsen
- Computational Biology, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Seattle, WA, 98109, USA
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16
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Ciocan D, Turpin W. New insights into an old paradigm: why IgA accumulates in alcoholic liver disease and what could be its role. Gut 2023; 72:1812-1814. [PMID: 36898829 DOI: 10.1136/gutjnl-2022-329415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 02/24/2023] [Indexed: 03/12/2023]
Affiliation(s)
- Dragos Ciocan
- Systems Immunology Department, Weizmann Institute of Science, Rehovot, Israel
| | - Williams Turpin
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario, Canada
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17
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Hu D, Irving AT. Massively-multiplexed epitope mapping techniques for viral antigen discovery. Front Immunol 2023; 14:1192385. [PMID: 37818363 PMCID: PMC10561112 DOI: 10.3389/fimmu.2023.1192385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/04/2023] [Indexed: 10/12/2023] Open
Abstract
Following viral infection, viral antigens bind specifically to receptors on the surface of lymphocytes thereby activating adaptive immunity in the host. An epitope, the smallest structural and functional unit of an antigen, binds specifically to an antibody or antigen receptor, to serve as key sites for the activation of adaptive immunity. The complexity and diverse range of epitopes are essential to study and map for the diagnosis of disease, the design of vaccines and for immunotherapy. Mapping the location of these specific epitopes has become a hot topic in immunology and immune therapy. Recently, epitope mapping techniques have evolved to become multiplexed, with the advent of high-throughput sequencing and techniques such as bacteriophage-display libraries and deep mutational scanning. Here, we briefly introduce the principles, advantages, and disadvantages of the latest epitope mapping techniques with examples for viral antigen discovery.
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Affiliation(s)
- Diya Hu
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Aaron T. Irving
- Department of Clinical Laboratory Studies, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Centre for Infection, Immunity & Cancer, Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
- Biomedical and Health Translational Research Centre of Zhejiang Province (BIMET), Haining, China
- College of Medicine & Veterinary Medicine, The University of Edinburgh, Edinburgh, United Kingdom
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18
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Ruhs EC, Chia WN, Foo R, Peel AJ, Li Y, Larman HB, Irving AT, Wang L, Brook CE. Applications of VirScan to broad serological profiling of bat reservoirs for emerging zoonoses. Front Public Health 2023; 11:1212018. [PMID: 37808979 PMCID: PMC10559906 DOI: 10.3389/fpubh.2023.1212018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Bats are important providers of ecosystem services such as pollination, seed dispersal, and insect control but also act as natural reservoirs for virulent zoonotic viruses. Bats host multiple viruses that cause life-threatening pathology in other animals and humans but, themselves, experience limited pathological disease from infection. Despite bats' importance as reservoirs for several zoonotic viruses, we know little about the broader viral diversity that they host. Bat virus surveillance efforts are challenged by difficulties of field capture and the limited scope of targeted PCR- or ELISA-based molecular and serological detection. Additionally, virus shedding is often transient, thus also limiting insights gained from nucleic acid testing of field specimens. Phage ImmunoPrecipitation Sequencing (PhIP-Seq), a broad serological tool used previously to comprehensively profile viral exposure history in humans, offers an exciting prospect for viral surveillance efforts in wildlife, including bats. Methods Here, for the first time, we apply PhIP-Seq technology to bat serum, using a viral peptide library originally designed to simultaneously assay exposures to the entire human virome. Results Using VirScan, we identified past exposures to 57 viral genera-including betacoronaviruses, henipaviruses, lyssaviruses, and filoviruses-in semi-captive Pteropus alecto and to nine viral genera in captive Eonycteris spelaea. Consistent with results from humans, we find that both total peptide hits (the number of enriched viral peptides in our library) and the corresponding number of inferred past virus exposures in bat hosts were correlated with poor bat body condition scores and increased with age. High and low body condition scores were associated with either seropositive or seronegative status for different viruses, though in general, virus-specific age-seroprevalence curves defied assumptions of lifelong immunizing infection, suggesting that many bat viruses may circulate via complex transmission dynamics. Discussion Overall, our work emphasizes the utility of applying biomedical tools, like PhIP-Seq, first developed for humans to viral surveillance efforts in wildlife, while highlighting opportunities for taxon-specific improvements.
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Affiliation(s)
- Emily Cornelius Ruhs
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
- Grainger Bioinformatics Center, Field Museum of Natural History, Chicago, IL, United States
| | - Wan Ni Chia
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- CoV Biotechnology Pte Ltd., Singapore, Singapore
| | - Randy Foo
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Alison J. Peel
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Brisband, QLD, Australia
| | - Yimei Li
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
- Quantitative and Computational Biology, Princeton University, Princeton, NJ, United States
| | - H. Benjamin Larman
- HBL – Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, United States
| | - Aaron T. Irving
- Second Affiliated Hospital of Zhejiang University, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Zhejiang University-University of Edinburgh Institute, Haining, Zhejiang, China
- BIMET - Biomedical and Translational Research Centre of Zhejiang Province, Zhejiang Province, China
| | - Linfa Wang
- Program in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
- SingHealth Duke-NUS Global Health Institute, Singapore, Singapore
| | - Cara E. Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
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19
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Longobardi S, Lopez-Davis C, Khatri B, Georgescu C, Pritchett-Frazee C, Lawrence C, Rasmussen A, Radfar L, Scofield RH, Baer AN, Robinson SA, Darrah E, Axtell RC, Pardo G, Wren JD, Koelsch KA, Guthridge JM, James JA, Lessard CJ, Farris AD. Autoantibodies identify primary Sjögren's syndrome in patients lacking serum IgG specific for Ro/SS-A and La/SS-B. Ann Rheum Dis 2023; 82:1181-1190. [PMID: 37147113 PMCID: PMC10546962 DOI: 10.1136/ard-2022-223105] [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: 07/18/2022] [Accepted: 04/21/2023] [Indexed: 05/07/2023]
Abstract
OBJECTIVE Identify autoantibodies in anti-Ro/SS-A negative primary Sjögren's syndrome (SS). METHODS This is a proof-of-concept, case-control study of SS, healthy (HC) and other disease (OD) controls. A discovery dataset of plasma samples (n=30 SS, n=15 HC) was tested on human proteome arrays containing 19 500 proteins. A validation dataset of plasma and stimulated parotid saliva from additional SS cases (n=46 anti-Ro+, n=50 anti-Ro-), HC (n=42) and OD (n=54) was tested on custom arrays containing 74 proteins. For each protein, the mean+3 SD of the HC value defined the positivity threshold. Differences from HC were determined by Fisher's exact test and random forest machine learning using 2/3 of the validation dataset for training and 1/3 for testing. Applicability of the results was explored in an independent rheumatology practice cohort (n=38 Ro+, n=36 Ro-, n=10 HC). Relationships among antigens were explored using Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) interactome analysis. RESULTS Ro+ SS parotid saliva contained autoantibodies binding to Ro60, Ro52, La/SS-B and muscarinic receptor 5. SS plasma contained 12 novel autoantibody specificities, 11 of which were detected in both the discovery and validation datasets. Binding to ≥1 of the novel antigens identified 54% of Ro- SS and 37% of Ro+ SS cases, with 100% specificity in both groups. Machine learning identified 30 novel specificities showing receiver operating characteristic area under the curve of 0.79 (95% CI 0.64 to 0.93) for identifying Ro- SS. Sera from Ro- cases of an independent cohort bound 17 of the non-canonical antigens. Antigenic targets in both Ro+ and Ro- SS were part of leukaemia cell, ubiquitin conjugation and antiviral defence pathways. CONCLUSION We identified antigenic targets of the autoantibody response in SS that may be useful for identifying up to half of Ro seronegative SS cases.
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Affiliation(s)
- Sherri Longobardi
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Charmaine Lopez-Davis
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Bhuwan Khatri
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Constantin Georgescu
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Cherilyn Pritchett-Frazee
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Christina Lawrence
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Astrid Rasmussen
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Lida Radfar
- College of Dentistry, Department of Oral Diagnosis and Radiology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Robert Hal Scofield
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Department of Medicine, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Alan N Baer
- Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Susan A Robinson
- Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Erika Darrah
- Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert C Axtell
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Gabriel Pardo
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Jonathan D Wren
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Kristi A Koelsch
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Department of Medicine, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Joel M Guthridge
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Judith A James
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Department of Medicine, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Christopher J Lessard
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
| | - Amy Darise Farris
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA
- Department of Microbiology and Immunology, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
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20
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Lingasamy P, Modhukur V, Mändar R, Salumets A. Exploring Immunome and Microbiome Interplay in Reproductive Health: Current Knowledge, Challenges, and Novel Diagnostic Tools. Semin Reprod Med 2023; 41:172-189. [PMID: 38262441 PMCID: PMC10846929 DOI: 10.1055/s-0043-1778017] [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: 01/25/2024]
Abstract
The dynamic interplay between the immunome and microbiome in reproductive health is a complex and rapidly advancing research field, holding tremendously vast possibilities for the development of reproductive medicine. This immunome-microbiome relationship influences the innate and adaptive immune responses, thereby affecting the onset and progression of reproductive disorders. However, the mechanisms governing these interactions remain elusive and require innovative approaches to gather more understanding. This comprehensive review examines the current knowledge on reproductive microbiomes across various parts of female reproductive tract, with special consideration of bidirectional interactions between microbiomes and the immune system. Additionally, it explores innate and adaptive immunity, focusing on immunoglobulin (Ig) A and IgM antibodies, their regulation, self-antigen tolerance mechanisms, and their roles in immune homeostasis. This review also highlights ongoing technological innovations in microbiota research, emphasizing the need for standardized detection and analysis methods. For instance, we evaluate the clinical utility of innovative technologies such as Phage ImmunoPrecipitation Sequencing (PhIP-Seq) and Microbial Flow Cytometry coupled to Next-Generation Sequencing (mFLOW-Seq). Despite ongoing advancements, we emphasize the need for further exploration in this field, as a deeper understanding of immunome-microbiome interactions holds promise for innovative diagnostic and therapeutic strategies for reproductive health, like infertility treatment and management of pregnancy.
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Affiliation(s)
| | - Vijayachitra Modhukur
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Reet Mändar
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
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21
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Carlton LH, McGregor R, Moreland NJ. Human antibody profiling technologies for autoimmune disease. Immunol Res 2023; 71:516-527. [PMID: 36690876 PMCID: PMC9870766 DOI: 10.1007/s12026-023-09362-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/12/2023] [Indexed: 01/25/2023]
Abstract
Autoimmune diseases are caused by the break-down in self-tolerance mechanisms and can result in the generation of autoantibodies specific to human antigens. Human autoantigen profiling technologies such as solid surface arrays and display technologies are powerful high-throughput technologies utilised to discover and map novel autoantigens associated with disease. This review compares human autoantigen profiling technologies including the application of these approaches in chronic and post-infectious autoimmune disease. Each technology has advantages and limitations that should be considered when designing new projects to profile autoantibodies. Recent studies that have utilised these technologies across a range of diseases have highlighted marked heterogeneity in autoantibody specificity between individuals as a frequent feature. This individual heterogeneity suggests that epitope spreading maybe an important mechanism in the pathogenesis of autoimmune disease in general and likely contributes to inflammatory tissue damage and symptoms. Studies focused on identifying autoantibody biomarkers for diagnosis should use targeted data analysis to identify the rarer public epitopes and antigens, common between individuals. Thus, utilisation of human autoantigen profiling technology, combined with different analysis approaches, can illuminate both pathogenesis and biomarker discovery.
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Affiliation(s)
- Lauren H Carlton
- School of Medical Sciences, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
| | - Reuben McGregor
- School of Medical Sciences, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Nicole J Moreland
- School of Medical Sciences, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
- Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
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22
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Rappazzo CG, Fernández-Quintero ML, Mayer A, Wu NC, Greiff V, Guthmiller JJ. Defining and Studying B Cell Receptor and TCR Interactions. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:311-322. [PMID: 37459189 PMCID: PMC10495106 DOI: 10.4049/jimmunol.2300136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/15/2023] [Indexed: 07/20/2023]
Abstract
BCRs (Abs) and TCRs (or adaptive immune receptors [AIRs]) are the means by which the adaptive immune system recognizes foreign and self-antigens, playing an integral part in host defense, as well as the emergence of autoimmunity. Importantly, the interaction between AIRs and their cognate Ags defies a simple key-in-lock paradigm and is instead a complex many-to-many mapping between an individual's massively diverse AIR repertoire, and a similarly diverse antigenic space. Understanding how adaptive immunity balances specificity with epitopic coverage is a key challenge for the field, and terms such as broad specificity, cross-reactivity, and polyreactivity remain ill-defined and are used inconsistently. In this Immunology Notes and Resources article, a group of experimental, structural, and computational immunologists define commonly used terms associated with AIR binding, describe methodologies to study these binding modes, as well as highlight the implications of these different binding modes for therapeutic design.
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Affiliation(s)
| | | | - Andreas Mayer
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Nicholas C. Wu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, 0372 Oslo, Norway
| | - Jenna J. Guthmiller
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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23
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Liebhoff AM, Venkataraman T, Morgenlander WR, Na M, Kula T, Waugh K, Morrison C, Rewers M, Longman R, Round J, Elledge S, Ruczinski I, Langmead B, Larman HB. Efficient encoding of large antigenic spaces by epitope prioritization with Dolphyn. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.30.551179. [PMID: 37577562 PMCID: PMC10418057 DOI: 10.1101/2023.07.30.551179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
We investigated a relatively underexplored component of the gut-immune axis by profiling the antibody response to gut phages using Phage Immunoprecipitation Sequencing (PhIP-Seq). To enhance this approach, we developed Dolphyn, a novel method that uses machine learning to select peptides from protein sets and compresses the proteome through epitope-stitching. Dolphyn improves the fraction of gut phage library peptides bound by antibodies from 10% to 31% in healthy individuals, while also reducing the number of synthesized peptides by 78%. In our study on gut phages, we discovered that the immune system develops antibodies to bacteria-infecting viruses in the human gut, particularly E.coli-infecting Myoviridae. Cost-effective PhIP-Seq libraries designed with Dolphyn enable the assessment of a wider range of proteins in a single experiment, thus facilitating the study of the gut-immune axis.
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Affiliation(s)
- Anna-Maria Liebhoff
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | | | - William R Morgenlander
- Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Miso Na
- Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Tomasz Kula
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA
| | - Kathleen Waugh
- Barbara Davis Center for Diabetes, University of Colorado Denver, Aurora, Colorado, USA
| | - Charles Morrison
- Behavioral, Clinical and Epidemiologic Sciences, FHI 360, Durham, NC, USA
| | - Marian Rewers
- Barbara Davis Center for Diabetes, University of Colorado Denver, Aurora, Colorado, USA
| | - Randy Longman
- Jill Roberts Institute for Research in IBD, Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - June Round
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Stephen Elledge
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins University, Baltimore, MD, USA
| | - Ben Langmead
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - H Benjamin Larman
- Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
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24
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Gordon-Lipkin EM, Banerjee P, Franco JLM, Tarasenko T, Kruk S, Thompson E, Gildea DE, Zhang S, Wolfsberg TG, Flegel WA, McGuire PJ. Primary oxidative phosphorylation defects lead to perturbations in the human B cell repertoire. Front Immunol 2023; 14:1142634. [PMID: 37483601 PMCID: PMC10361569 DOI: 10.3389/fimmu.2023.1142634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 06/09/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction The majority of studies on oxidative phosphorylation in immune cells have been performed in mouse models, necessitating human translation. To understand the impact of oxidative phosphorylation (OXPHOS) deficiency on human immunity, we studied children with primary mitochondrial disease (MtD). Methods scRNAseq analysis of peripheral blood mononuclear cells was performed on matched children with MtD (N = 4) and controls (N = 4). To define B cell function we performed phage display immunoprecipitation sequencing on a cohort of children with MtD (N = 19) and controls (N = 16). Results Via scRNAseq, we found marked reductions in select populations involved in the humoral immune response, especially antigen presenting cells, B cell and plasma populations, with sparing of T cell populations. MTRNR2L8, a marker of bioenergetic stress, was significantly elevated in populations that were most depleted. mir4485, a miRNA contained in the intron of MTRNR2L8, was co-expressed. Knockdown studies of mir4485 demonstrated its role in promoting survival by modulating apoptosis. To determine the functional consequences of our findings on humoral immunity, we studied the antiviral antibody repertoire in children with MtD and controls using phage display and immunoprecipitation sequencing. Despite similar viral exposomes, MtD displayed antiviral antibodies with less robust fold changes and limited polyclonality. Discussion Overall, we show that children with MtD display perturbations in the B cell repertoire which may impact humoral immunity and the ability to clear viral infections.
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Affiliation(s)
- Eliza M. Gordon-Lipkin
- Metabolism, Infection and Immunity Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Payal Banerjee
- Metabolism, Infection and Immunity Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Jose Luis Marin Franco
- Metabolism, Infection and Immunity Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Tatiana Tarasenko
- Metabolism, Infection and Immunity Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Shannon Kruk
- Metabolism, Infection and Immunity Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Elizabeth Thompson
- Metabolism, Infection and Immunity Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Derek E. Gildea
- Bioinformatics and Scientific Programming Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Suiyuan Zhang
- Bioinformatics and Scientific Programming Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Tyra G. Wolfsberg
- Bioinformatics and Scientific Programming Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | | | - Willy A. Flegel
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Peter J. McGuire
- Metabolism, Infection and Immunity Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
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25
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Diray-Arce J, Fourati S, Doni Jayavelu N, Patel R, Maguire C, Chang AC, Dandekar R, Qi J, Lee BH, van Zalm P, Schroeder A, Chen E, Konstorum A, Brito A, Gygi JP, Kho A, Chen J, Pawar S, Gonzalez-Reiche AS, Hoch A, Milliren CE, Overton JA, Westendorf K, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen L, Grubaugh ND, van Bakel H, Wilson M, Rajan J, Steen H, Eckalbar W, Cotsapas C, Langelier CR, Levy O, Altman MC, Maecker H, Montgomery RR, Haddad EK, Sekaly RP, Esserman D, Ozonoff A, Becker PM, Augustine AD, Guan L, Peters B, Kleinstein SH. Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients. Cell Rep Med 2023; 4:101079. [PMID: 37327781 PMCID: PMC10203880 DOI: 10.1016/j.xcrm.2023.101079] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 01/31/2023] [Accepted: 05/16/2023] [Indexed: 06/18/2023]
Abstract
The IMPACC cohort, composed of >1,000 hospitalized COVID-19 participants, contains five illness trajectory groups (TGs) during acute infection (first 28 days), ranging from milder (TG1-3) to more severe disease course (TG4) and death (TG5). Here, we report deep immunophenotyping, profiling of >15,000 longitudinal blood and nasal samples from 540 participants of the IMPACC cohort, using 14 distinct assays. These unbiased analyses identify cellular and molecular signatures present within 72 h of hospital admission that distinguish moderate from severe and fatal COVID-19 disease. Importantly, cellular and molecular states also distinguish participants with more severe disease that recover or stabilize within 28 days from those that progress to fatal outcomes (TG4 vs. TG5). Furthermore, our longitudinal design reveals that these biologic states display distinct temporal patterns associated with clinical outcomes. Characterizing host immune responses in relation to heterogeneity in disease course may inform clinical prognosis and opportunities for intervention.
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Affiliation(s)
- Joann Diray-Arce
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
| | - Slim Fourati
- Emory School of Medicine, Atlanta, GA 30322, USA
| | | | - Ravi Patel
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Cole Maguire
- The University of Texas at Austin, Austin, TX 78712, USA
| | - Ana C Chang
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Ravi Dandekar
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Jingjing Qi
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brian H Lee
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Patrick van Zalm
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew Schroeder
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Ernie Chen
- Yale School of Medicine, New Haven, CT 06510, USA
| | | | | | | | - Alvin Kho
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA
| | - Jing Chen
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - Annmarie Hoch
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Carly E Milliren
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA
| | | | | | - Charles B Cairns
- Drexel University, Tower Health Hospital, Philadelphia, PA 19104, USA
| | | | | | | | - Florian Krammer
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lindsey Rosen
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD 20814, USA
| | | | - Harm van Bakel
- Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael Wilson
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Jayant Rajan
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Hanno Steen
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Walter Eckalbar
- University of California San Francisco, San Francisco, CA 94115, USA
| | - Chris Cotsapas
- Yale School of Medicine, New Haven, CT 06510, USA; Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
| | | | - Ofer Levy
- Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
| | - Matthew C Altman
- Benaroya Research Institute, University of Washington, Seattle, WA 98101, USA
| | - Holden Maecker
- Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | | | - Elias K Haddad
- Drexel University, Tower Health Hospital, Philadelphia, PA 19104, USA
| | | | | | - Al Ozonoff
- Clinical and Data Coordinating Center, Boston Children's Hospital, Boston, MA 02115, USA; Precision Vaccines Program, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT & Harvard, Cambridge, MA 02142, USA
| | - Patrice M Becker
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD 20814, USA
| | - Alison D Augustine
- National Institute of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD 20814, USA
| | - Leying Guan
- Yale School of Public Health, New Haven, CT 06510, USA
| | - Bjoern Peters
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA
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26
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Andreu-Sánchez S, Bourgonje AR, Vogl T, Kurilshikov A, Leviatan S, Ruiz-Moreno AJ, Hu S, Sinha T, Vich Vila A, Klompus S, Kalka IN, de Leeuw K, Arends S, Jonkers I, Withoff S, Brouwer E, Weinberger A, Wijmenga C, Segal E, Weersma RK, Fu J, Zhernakova A. Phage display sequencing reveals that genetic, environmental, and intrinsic factors influence variation of human antibody epitope repertoire. Immunity 2023; 56:1376-1392.e8. [PMID: 37164013 DOI: 10.1016/j.immuni.2023.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/13/2022] [Accepted: 04/06/2023] [Indexed: 05/12/2023]
Abstract
Phage-displayed immunoprecipitation sequencing (PhIP-seq) has enabled high-throughput profiling of human antibody repertoires. However, a comprehensive overview of environmental and genetic determinants shaping human adaptive immunity is lacking. In this study, we investigated the effects of genetic, environmental, and intrinsic factors on the variation in human antibody repertoires. We characterized serological antibody repertoires against 344,000 peptides using PhIP-seq libraries from a wide range of microbial and environmental antigens in 1,443 participants from a population cohort. We detected individual-specificity, temporal consistency, and co-housing similarities in antibody repertoires. Genetic analyses showed the involvement of the HLA, IGHV, and FUT2 gene regions in antibody-bound peptide reactivity. Furthermore, we uncovered associations between phenotypic factors (including age, cell counts, sex, smoking behavior, and allergies, among others) and particular antibody-bound peptides. Our results indicate that human antibody epitope repertoires are shaped by both genetics and environmental exposures and highlight specific signatures of distinct phenotypes and genotypes.
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Affiliation(s)
- Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Thomas Vogl
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria; Center for Cancer Research, Medical University of Vienna, Wien, Austria.
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Angel J Ruiz-Moreno
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shixian Hu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shelley Klompus
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Iris N Kalka
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | - Karina de Leeuw
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Suzanne Arends
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Iris Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sebo Withoff
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Elisabeth Brouwer
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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27
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Bourgonje AR, Andreu-Sánchez S, Vogl T, Hu S, Vich Vila A, Gacesa R, Leviatan S, Kurilshikov A, Klompus S, Kalka IN, van Dullemen HM, Weinberger A, Visschedijk MC, Festen EAM, Faber KN, Wijmenga C, Dijkstra G, Segal E, Fu J, Zhernakova A, Weersma RK. Phage-display immunoprecipitation sequencing of the antibody epitope repertoire in inflammatory bowel disease reveals distinct antibody signatures. Immunity 2023; 56:1393-1409.e6. [PMID: 37164015 DOI: 10.1016/j.immuni.2023.04.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 12/13/2022] [Accepted: 04/14/2023] [Indexed: 05/12/2023]
Abstract
Inflammatory bowel diseases (IBDs), e.g., Crohn's disease (CD) and ulcerative colitis (UC), are chronic immune-mediated inflammatory diseases. A comprehensive overview of an IBD-specific antibody epitope repertoire is, however, lacking. Using high-throughput phage-display immunoprecipitation sequencing (PhIP-Seq), we identified antibodies against 344,000 antimicrobial, immune, and food antigens in 497 individuals with IBD compared with 1,326 controls. IBD was characterized by 373 differentially abundant antibody responses (202 overrepresented and 171 underrepresented), with 17% shared by both IBDs, 55% unique to CD, and 28% unique to UC. Antibody reactivities against bacterial flagellins dominated in CD and were associated with ileal involvement, fibrostenotic disease, and anti-Saccharomyces cerevisiae antibody positivity, but not with fecal microbiome composition. Antibody epitope repertoires accurately discriminated CD from controls (area under the curve [AUC] = 0.89), and similar discrimination was achieved when using only ten antibodies (AUC = 0.87). Individuals with IBD thus show a distinct antibody repertoire against selected peptides, allowing clinical stratification and discovery of immunological targets.
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Affiliation(s)
- Arno R Bourgonje
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sergio Andreu-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Thomas Vogl
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria; Center for Cancer Research, Medical University of Vienna, Wien, Austria
| | - Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Shelley Klompus
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Iris N Kalka
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hendrik M van Dullemen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Marijn C Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Klaas Nico Faber
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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28
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Yalcin D, Bennett SJ, Sheehan J, Trauth AJ, Tso FY, West JT, Hagensee ME, Ramsay AJ, Wood C. Longitudinal Variations in Antibody Responses against SARS-CoV-2 Spike Epitopes upon Serial Vaccinations. Int J Mol Sci 2023; 24:ijms24087292. [PMID: 37108460 PMCID: PMC10138620 DOI: 10.3390/ijms24087292] [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: 03/01/2023] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) impacted healthcare, the workforce, and worldwide socioeconomics. Multi-dose mono- or bivalent mRNA vaccine regimens have shown high efficacy in protection against SARS-CoV-2 and its emerging variants with varying degrees of efficacy. Amino acid changes, primarily in the receptor-binding domain (RBD), result in selection for viral infectivity, disease severity, and immune evasion. Therefore, many studies have centered around neutralizing antibodies that target the RBD and their generation achieved through infection or vaccination. Here, we conducted a unique longitudinal study, analyzing the effects of a three-dose mRNA vaccine regimen exclusively using the monovalent BNT162b2 (Pfizer/BioNTech) vaccine, systematically administered to nine previously uninfected (naïve) individuals. We compare changes in humoral antibody responses across the entire SARS-CoV-2 spike glycoprotein (S) using a high-throughput phage display technique (VirScan). Our data demonstrate that two doses of vaccination alone can achieve the broadest and highest magnitudes of anti-S response. Moreover, we present evidence of novel highly boosted non-RBD epitopes that strongly correlate with neutralization and recapitulate independent findings. These vaccine-boosted epitopes could facilitate multi-valent vaccine development and drug discovery.
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Affiliation(s)
- Dicle Yalcin
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Sydney J Bennett
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68516, USA
| | - Jared Sheehan
- Department of Microbiology, Immunology and Parasitology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Amber J Trauth
- Departments of Medicine, Section of Infectious Diseases, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - For Yue Tso
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - John T West
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Michael E Hagensee
- Departments of Medicine, Section of Infectious Diseases, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Alistair J Ramsay
- Department of Microbiology, Immunology and Parasitology, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
| | - Charles Wood
- Department of Interdisciplinary Oncology, Stanley S. Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68516, USA
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29
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Rackaityte E, Proekt I, Miller HS, Ramesh A, Brooks JF, Kung AF, Mandel-Brehm C, Yu D, Zamecnik C, Bair R, Vazquez SE, Sunshine S, Abram CL, Lowell CA, Rizzuto G, Wilson MR, Zikherman J, Anderson MS, DeRisi JL. Validation of a murine proteome-wide phage display library for the identification of autoantibody specificities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.07.535899. [PMID: 37066405 PMCID: PMC10104109 DOI: 10.1101/2023.04.07.535899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Autoimmunity is characterized by loss of tolerance to tissue-specific as well as systemic antigens, resulting in complex autoantibody landscapes. Here, we introduce and extensively validate the performance characteristics of a murine proteome-wide library for phage display immunoprecipitation and sequencing (PhIP-seq), to profile mouse autoantibodies. This system and library were validated using seven genetic mouse models across a spectrum of autoreactivity. Mice deficient in antibody production (Rag2-/- and μMT) were used to model non-specific peptide enrichments, while cross-reactivity was evaluated using anti-ovalbumin B cell receptor (BCR)-restricted OB1 mice as a proof of principle. The PhIP-seq approach was then utilized to interrogate three distinct autoimmune disease models. First, serum from Lyn-/- IgD+/- mice with lupus-like disease was used to identify nuclear and apoptotic bleb reactivities, lending support to the hypothesis that apoptosis is a shared origin of these antigens. Second, serum from non-obese diabetic (NOD) mice, a polygenic model of pancreas-specific autoimmunity, enriched peptides derived from both insulin and predicted pancreatic proteins. Lastly, Aire-/- mouse sera were used to identify numerous auto-antigens, many of which were also observed in previous studies of humans with autoimmune polyendocrinopathy syndrome type 1 (APS1) carrying recessive mutations in AIRE. Among these were peptides derived from Perilipin-1, a validated autoimmune biomarker of generalized acquired lipodystrophy in humans. Autoreactivity to Perilipin-1 correlated with lymphocyte infiltration in adipose tissue and underscores the approach in revealing previously unknown specificities. These experiments support the use of murine proteome-wide PhIP-seq for antigenic profiling and autoantibody discovery, which may be employed to study a range of immune perturbations in mouse models of autoimmunity.
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Affiliation(s)
- Elze Rackaityte
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
| | - Irina Proekt
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Haleigh S. Miller
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
- Biological and Medical Informatics Program, University of California San Francisco, San Francisco, CA USA
| | - Akshaya Ramesh
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Jeremy F. Brooks
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Andrew F. Kung
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
- Biological and Medical Informatics Program, University of California San Francisco, San Francisco, CA USA
| | - Caleigh Mandel-Brehm
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
| | - David Yu
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Colin Zamecnik
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Rebecca Bair
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Sara E. Vazquez
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Sara Sunshine
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
| | - Clare L. Abram
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Clifford A. Lowell
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Gabrielle Rizzuto
- Human Oncology & Pathogenesis Program and Department of Pathology & Laboratory Medicine, Memorial Sloan Kettering Cancer Center, NY, NY
| | - Michael R. Wilson
- Weill Institute for Neurosciences, Department of Neurology, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Julie Zikherman
- Division of Rheumatology, Rosalind Russell and Ephraim P. Engleman Rheumatology Research Center, Department of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Mark S. Anderson
- Diabetes Center, School of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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30
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Hosono Y, Sie B, Pinal-Fernandez I, Pak K, Mecoli CA, Casal-Dominguez M, Warner BM, Kaplan MJ, Albayda J, Danoff S, Lloyd TE, Paik JJ, Tiniakou E, Aggarwal R, Oddis CV, Moghadam-Kia S, Carmona-Rivera C, Milisenda JC, Grau-Junyent JM, Selva-O'Callaghan A, Christopher-Stine L, Larman HB, Mammen AL. Coexisting autoantibodies against transcription factor Sp4 are associated with decreased cancer risk in patients with dermatomyositis with anti-TIF1γ autoantibodies. Ann Rheum Dis 2023; 82:246-252. [PMID: 36008132 PMCID: PMC9870850 DOI: 10.1136/ard-2022-222441] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 08/11/2022] [Indexed: 01/27/2023]
Abstract
OBJECTIVES In dermatomyositis (DM), autoantibodies are associated with unique clinical phenotypes. For example, anti-TIF1γ autoantibodies are associated with an increased risk of cancer. The purpose of this study was to discover novel DM autoantibodies. METHODS Phage ImmunoPrecipitation Sequencing using sera from 43 patients with DM suggested that transcription factor Sp4 is a novel autoantigen; this was confirmed by showing that patient sera immunoprecipitated full-length Sp4 protein. Sera from 371 Johns Hopkins patients with myositis (255 with DM, 28 with antisynthetase syndrome, 40 with immune-mediated necrotising myopathy, 29 with inclusion body myositis and 19 with polymyositis), 80 rheumatological disease controls (25 with Sjogren's syndrome, 25 with systemic lupus erythematosus and 30 with rheumatoid arthritis (RA)) and 200 healthy comparators were screened for anti-SP4 autoantibodies by ELISA. A validation cohort of 46 anti-TIF1γ-positive patient sera from the University of Pittsburgh was also screened for anti-Sp4 autoantibodies. RESULTS Anti-Sp4 autoantibodies were present in 27 (10.5%) patients with DM and 1 (3.3%) patient with RA but not in other clinical groups. In patients with DM, 96.3% of anti-Sp4 autoantibodies were detected in those with anti-TIF1γ autoantibodies. Among 26 TIF1γ-positive patients with anti-Sp4 autoantibodies, none (0%) had cancer. In contrast, among 35 TIF1γ-positive patients without anti-Sp4 autoantibodies, 5 (14%, p=0.04) had cancer. In the validation cohort, among 15 TIF1γ-positive patients with anti-Sp4 autoantibodies, 2 (13.3%) had cancer. By comparison, among 31 TIF1γ-positive patients without anti-Sp4 autoantibodies, 21 (67.7%, p<0.001) had cancer. CONCLUSIONS Anti-Sp4 autoantibodies appear to identify a subgroup of anti-TIF1γ-positive DM patients with lower cancer risk.
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Affiliation(s)
- Yuji Hosono
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Brandon Sie
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Iago Pinal-Fernandez
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Neurology and Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Katherine Pak
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Christopher A Mecoli
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Maria Casal-Dominguez
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Neurology and Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Blake M Warner
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Mariana J Kaplan
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jemima Albayda
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sonye Danoff
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Thomas E Lloyd
- Department of Neurology and Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Julie J Paik
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Eleni Tiniakou
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Rohit Aggarwal
- Department of Medicine, Division of Rheumatology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Chester V Oddis
- Department of Medicine, Division of Rheumatology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Siamak Moghadam-Kia
- Department of Medicine, Division of Rheumatology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Carmelo Carmona-Rivera
- Systemic Autoimmunity Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | | | | | | | - Lisa Christopher-Stine
- Department of Neurology and Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - H Benjamin Larman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Andrew Lee Mammen
- Muscle Disease Unit, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Neurology and Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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31
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Henson SN, Elko EA, Swiderski PM, Liang Y, Engelbrektson AL, Piña A, Boyle AS, Fink Z, Facista SJ, Martinez V, Rahee F, Brown A, Kelley EJ, Nelson GA, Raspet I, Mead HL, Altin JA, Ladner JT. PepSeq: a fully in vitro platform for highly multiplexed serology using customizable DNA-barcoded peptide libraries. Nat Protoc 2023; 18:396-423. [PMID: 36385198 PMCID: PMC10339795 DOI: 10.1038/s41596-022-00766-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022]
Abstract
PepSeq is an in vitro platform for building and conducting highly multiplexed proteomic assays against customizable targets by using DNA-barcoded peptides. Starting with a pool of DNA oligonucleotides encoding peptides of interest, this protocol outlines a fully in vitro and massively parallel procedure for synthesizing the encoded peptides and covalently linking each to a corresponding cDNA tag. The resulting libraries of peptide/DNA conjugates can be used for highly multiplexed assays that leverage high-throughput sequencing to profile the binding or enzymatic specificities of proteins of interest. Here, we describe the implementation of PepSeq for fast and cost-effective epitope-level analysis of antibody reactivity across hundreds of thousands of peptides from <1 µl of serum or plasma input. This protocol includes the design of the DNA oligonucleotide library, synthesis of DNA-barcoded peptide constructs, binding of constructs to sample, preparation for sequencing and data analysis. Implemented in this way, PepSeq can be used for a number of applications, including fine-scale mapping of antibody epitopes and determining a subject's pathogen exposure history. The protocol is divided into two main sections: (i) design and synthesis of DNA-barcoded peptide libraries and (ii) use of libraries for highly multiplexed serology. Once oligonucleotide templates are in hand, library synthesis takes 1-2 weeks and can provide enough material for hundreds to thousands of assays. Serological assays can be conducted in 96-well plates and generate sequencing data within a further ~4 d. A suite of software tools, including the PepSIRF package, are made available to facilitate the design of PepSeq libraries and analysis of assay data.
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Affiliation(s)
- Sierra N Henson
- The Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Evan A Elko
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Piotr M Swiderski
- DNA/RNA Synthesis Laboratory, Department of Molecular Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Yong Liang
- DNA/RNA Synthesis Laboratory, Department of Molecular Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | | | - Alejandra Piña
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Annalee S Boyle
- The Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Zane Fink
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Vidal Martinez
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Fatima Rahee
- The Translational Genomics Research Institute (TGen), Phoenix, AZ, USA
| | - Annabelle Brown
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Erin J Kelley
- The Translational Genomics Research Institute (TGen), Flagstaff, AZ, USA
| | - Georgia A Nelson
- The Translational Genomics Research Institute (TGen), Flagstaff, AZ, USA
| | - Isaiah Raspet
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Heather L Mead
- The Translational Genomics Research Institute (TGen), Flagstaff, AZ, USA
| | - John A Altin
- The Translational Genomics Research Institute (TGen), Flagstaff, AZ, USA.
| | - Jason T Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA.
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Garand M, Huang SSY, Goessling LS, Wan F, Santillan DA, Santillan MK, Brar A, Wylie TN, Wylie KM, Eghtesady P. Virome Analysis and Association of Positive Coxsackievirus B Serology during Pregnancy with Congenital Heart Disease. Microorganisms 2023; 11:262. [PMID: 36838226 PMCID: PMC9963073 DOI: 10.3390/microorganisms11020262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/09/2023] [Accepted: 01/15/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND We have previously shown coxsackievirus B (CVB) to be a potent inducer of congenital heart disease (CHD) in mice. The clinical relevance of these findings in humans and the roles of other viruses in the pathogenesis of CHD remain unknown. METHODS We obtained plasma samples, collected at all trimesters, from 89 subjects (104 pregnancies), 73 healthy controls (88 pregnancies), and 16 with CHD-affected birth (16 pregnancies), from the Perinatal Family Tissue Bank (PFTB). We performed CVB IgG/IgM serological assays on plasma. We also used ViroCap sequencing and PCR to test for viral nucleic acid in plasma, circulating leukocytes from the buffy coat, and in the media of a co-culture system. RESULTS CVB IgG/IgM results indicated that prior exposure was 7.8 times more common in the CHD group (95% CI, 1.14-54.24, adj. p-value = 0.036). However, the CVB viral genome was not detected in plasma, buffy coat, or co-culture supernatant by molecular assays, although other viruses were detected. CONCLUSION Detection of viral nucleic acid in plasma was infrequent and specifically no CVB genome was detected. However, serology demonstrated that prior CVB exposure is higher in CHD-affected pregnancies. Further studies are warranted to understand the magnitude of the contribution of the maternal blood virome to the pathogenesis of CHD.
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Affiliation(s)
- Mathieu Garand
- Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susie S. Y. Huang
- Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lisa S. Goessling
- Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Fei Wan
- Department of Public Health Sciences and Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Donna A. Santillan
- Department of Obstetrics and Gynecology, University of Iowa, Iowa City, IA 52242, USA
| | - Mark K. Santillan
- Department of Obstetrics and Gynecology, University of Iowa, Iowa City, IA 52242, USA
| | - Anoop Brar
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Todd N. Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kristine M. Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Pirooz Eghtesady
- Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
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Nagy K, McBride R, Head SR, Ordoukhanian P, Law M. Low-Cost Peptide Microarrays for Mapping Continuous Antibody Epitopes. Methods Mol Biol 2023; 2578:63-81. [PMID: 36152281 DOI: 10.1007/978-1-0716-2732-7_6] [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: 06/16/2023]
Abstract
Understanding antibody specificity and defining response profiles to antigens continue to be essential to both vaccine research and therapeutic antibody development. Peptide scanning assays enable mapping of continuous epitopes in order to delineate antibody-antigen interactions beyond traditional immunoassay formats. We have developed a relatively low-cost method to generate peptide microarray slides for antibody binding studies that allow for interrogation of up to 1536 overlapping peptides derived from the target antigens on a single microslide. Using an IntavisAG MultiPep RS peptide synthesizer and a Digilab MicroGrid II 600 microarray printer robot, each peptide is tagged with a polyethylene glycol aminooxy terminus to improve peptide solubility, orientation, and conjugation efficiency to the slide surface. Interrogation of the surface can then be performed using polyclonal immune sera or monoclonal antibodies, and sensitive detection using an InnoScan 1100 AL scanner with fluorescent-conjugated secondary reagents maximizes conservation of reagents.
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Affiliation(s)
- Kenna Nagy
- Department of Immunology & Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ryan McBride
- Genomics Core, The Scripps Research Institute, La Jolla, CA, USA
| | - Steven R Head
- Genomics Core, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Mansun Law
- Department of Immunology & Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
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Comprehensive profiling of antibody responses to the human anellome using programmable phage display. Cell Rep 2022; 41:111754. [PMID: 36543141 DOI: 10.1016/j.celrep.2022.111754] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 09/23/2022] [Accepted: 11/09/2022] [Indexed: 12/24/2022] Open
Abstract
Anelloviruses represent a major constituent of the commensal human virome; however, little is known about their immunobiology. Here, we present "AnelloScan," a T7 phage library representing the open reading frame 1 (ORF1), ORF2, ORF3, and torque teno virus (TTV)-derived apoptosis-inducing protein (TAIP) sequences of more than 800 human anelloviruses and profile the antibody reactivities of serum samples from a cross-sectional cohort of 156 subjects by using phage-immunoprecipitation sequencing (PhIP-Seq). A majority of anellovirus peptides are not reactive in any of the subjects tested (n = ∼28,000; ∼85% of the library). Antibody-reactive peptides are largely restricted to the C-terminal region of the capsid protein ORF1. Moreover, using a longitudinal cohort of matched blood-transfusion donors and recipients, we find that most transmitted anelloviruses do not elicit a detectable antibody reactivity in the recipient and that the remainder elicit delayed responses appearing ∼100-150 days after transfusion.
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35
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Allergenic food protein consumption is associated with systemic IgG antibody responses in non-allergic individuals. Immunity 2022; 55:2454-2469.e6. [PMID: 36473469 DOI: 10.1016/j.immuni.2022.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 06/01/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022]
Abstract
Although food-directed immunoglobulin E (IgE) has been studied in the context of allergies, the prevalence and magnitude of IgG responses against dietary antigens are incompletely characterized in the general population. Here, we measured IgG binding against food and environmental antigens obtained from allergen databases and the immune epitope database (IEDB), represented in a phage displayed library of 58,233 peptides. By profiling blood samples of a large cohort representing the average adult Israeli population (n = 1,003), we showed that many food antigens elicited systemic IgG in up to 50% of individuals. Dietary intake of specific food protein correlated with antibody binding, suggesting that diet can shape the IgG epitope repertoire. Our work documents abundant systemic IgG responses against food antigens and provides a reference map of the exact immunogenic epitopes on a population scale, laying the foundation to unravel the role of food- and environmental antigen-directed antibody binding in disease contexts.
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36
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BIPS—A code base for designing and coding of a Phage ImmunoPrecipitation Oligo Library. PLoS Comput Biol 2022; 18:e1010663. [PMID: 36355866 PMCID: PMC9681064 DOI: 10.1371/journal.pcbi.1010663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 11/22/2022] [Accepted: 09/18/2022] [Indexed: 11/12/2022] Open
Abstract
BIPS (Build Phage ImmunoPrecipitation Sequencing library) is a software that converts a list of proteins into a custom DNA oligonucleotide library for the PhIP-Seq system. The tool creates constant-length oligonucleotides with internal barcodes, while maintaining the original length of the peptide. This allows using large libraries, of hundreds of thousands of oligonucleotides, while saving on the costs of sequencing and maintaining the accuracy of oligonucleotide reads identification. BIPS is available under GNU public license from: https://github.com/kalkairis/BuildPhIPSeqLibrary.
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37
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Schuettenberg A, Piña A, Metrailer M, Peláez-Sánchez RG, Agudelo-Flórez P, Lopez JÁ, Ryle L, Monroy FP, Altin JA, Ladner JT. Highly Multiplexed Serology for Nonhuman Mammals. Microbiol Spectr 2022; 10:e0287322. [PMID: 36125316 PMCID: PMC9602771 DOI: 10.1128/spectrum.02873-22] [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: 07/29/2022] [Accepted: 09/06/2022] [Indexed: 01/04/2023] Open
Abstract
Emerging infectious diseases represent a serious and ongoing threat to humans. Most emerging viruses are maintained in stable relationships with other species of animals, and their emergence within the human population results from cross-species transmission. Therefore, if we want to be prepared for the next emerging virus, we need to broadly characterize the diversity and ecology of viruses currently infecting other animals (i.e., the animal virosphere). High-throughput metagenomic sequencing has accelerated the pace of virus discovery. However, molecular assays can detect only active infections and only if virus is present within the sampled fluid or tissue at the time of collection. In contrast, serological assays measure long-lived antibody responses to infections, which can be detected within the blood, regardless of the infected tissues. Therefore, serological assays can provide a complementary approach for understanding the circulation of viruses, and while serological assays have historically been limited in scope, recent advancements allow thousands to hundreds of thousands of antigens to be assessed simultaneously using <1 μL of blood (i.e., highly multiplexed serology). The application of highly multiplexed serology for the characterization of the animal virosphere is dependent on the availability of reagents that can be used to capture or label antibodies of interest. Here, we evaluate the utility of commercial immunoglobulin-binding proteins (protein A and protein G) to enable highly multiplexed serology in 25 species of nonhuman mammals, and we describe a competitive fluorescence-linked immunosorbent assay (FLISA) that can be used as an initial screen for choosing the most appropriate capture protein for a given host species. IMPORTANCE Antibodies are generated in response to infections with viruses and other pathogens, and they help protect against future exposures. Mature antibodies are long lived, are highly specific, and can bind to their protein targets with high affinity. Thus, antibodies can also provide information about an individual's history of viral exposures, which has important applications for understanding the epidemiology and etiology of disease. In recent years, there have been large advances in the available methods for broadly characterizing antibody-binding profiles, but thus far, these have been utilized primarily with human samples only. Here, we demonstrate that commercial antibody-binding reagents can facilitate modern antibody assays for a wide variety of mammalian species, and we describe an inexpensive and fast approach for choosing the best reagent for each animal species. By studying antibody-binding profiles in captive and wild animals, we can better understand the distribution and prevalence of viruses that could spill over into humans.
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Affiliation(s)
- Alexa Schuettenberg
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Alejandra Piña
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Morgan Metrailer
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | | | | | - Juan Álvaro Lopez
- Microbiology School, Primary Immunodeficiencies Group, University of Antioquia, Medellín, Colombia
| | - Luke Ryle
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Fernando P. Monroy
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - John A. Altin
- The Translational Genomics Research Institute (TGen), Flagstaff, Arizona, USA
| | - Jason T. Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
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38
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Garand M, Huang SSY, Goessling LS, Santillan DA, Santillan MK, Brar A, Wylie TN, Wylie KM, Eghtesady P. A Case of Persistent Human Pegivirus Infection in Two Separate Pregnancies of a Woman. Microorganisms 2022; 10:1925. [PMID: 36296201 PMCID: PMC9610878 DOI: 10.3390/microorganisms10101925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 05/26/2024] Open
Abstract
Human pegivirus (HPgV) is best known for persistent, presumably non-pathogenic, infection and a propensity to co-infect with human immunodeficiency virus or hepatitis C virus. However, unique attributes, such as the increased risk of malignancy or immune modulation, have been recently recognized for HPgV. We have identified a unique case of a woman with high levels HPgV infection in two pregnancies, which occurred 4 years apart and without evidence of human immunodeficiency virus or hepatitis C virus infection. The second pregnancy was complicated by congenital heart disease. A high level of HPgV infection was detected in the maternal blood from different trimesters by RT-PCR and identified as HPgV type 1 genotype 2 in both pregnancies. In the second pregnancy, the decidua and intervillous tissue of the placenta were positive for HPgV by PCR but not the chorion or cord blood (from both pregnancies), suggesting no vertical transmission despite high levels of viremia. The HPgV genome sequence was remarkably conserved over the 4 years. Using VirScan, sera antibodies for HPgV were detected in the first trimester of both pregnancies. We observed the same anti-HPgV antibodies against the non-structural NS5 protein in both pregnancies, suggesting a similar non-E2 protein humoral immune response over time. To the best of our knowledge, this is the first report of persistent HPgV infection involving placental tissues with no clear indication of vertical transmission. Our results reveal a more elaborate viral-host interaction than previously reported, expand our knowledge about tropism, and opens avenues for exploring the replication sites of this virus.
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Affiliation(s)
- Mathieu Garand
- Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Susie S. Y. Huang
- Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lisa S. Goessling
- Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Donna A. Santillan
- Department of Obstetrics and Gynecology, University of Iowa, Iowa City, IA 52242, USA
| | - Mark K. Santillan
- Department of Obstetrics and Gynecology, University of Iowa, Iowa City, IA 52242, USA
| | - Anoop Brar
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Todd N. Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kristine M. Wylie
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Pirooz Eghtesady
- Division of Pediatric Cardiothoracic Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
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39
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Vogl T, Kalka IN, Klompus S, Leviatan S, Weinberger A, Segal E. Systemic antibody responses against human microbiota flagellins are overrepresented in chronic fatigue syndrome patients. SCIENCE ADVANCES 2022; 8:eabq2422. [PMID: 36149952 DOI: 10.1126/sciadv.abq2422] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating disease with an unclear etiology and pathogenesis. Both an involvement of the immune system and gut microbiota dysbiosis have been implicated in its pathophysiology. However, potential interactions between adaptive immune responses and the microbiota in ME/CFS have been incompletely characterized. Here, we profiled antibody responses of patients with severe ME/CFS and healthy controls against microbiota and viral antigens represented as a phage-displayed 244,000 variant library. Patients with severe ME/CFS exhibited distinct serum antibody epitope repertoires against flagellins of Lachnospiraceae bacteria. Training machine learning algorithms on this antibody-binding data demonstrated that immune responses against gut microbiota represent a unique layer of information beyond standard blood tests, providing improved molecular diagnostics for ME/CFS. Together, our results point toward an involvement of the microbiota-immune axis in ME/CFS and lay the foundation for comparative studies with inflammatory bowel diseases and illnesses characterized by long-term fatigue symptoms, including post-COVID-19 syndrome.
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Affiliation(s)
- Thomas Vogl
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Iris N Kalka
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shelley Klompus
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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40
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Chen A, Kammers K, Larman HB, Scharpf RB, Ruczinski I. Detecting antibody reactivities in Phage ImmunoPrecipitation Sequencing data. BMC Genomics 2022; 23:654. [PMID: 36109689 PMCID: PMC9476399 DOI: 10.1186/s12864-022-08869-y] [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: 02/02/2022] [Accepted: 08/31/2022] [Indexed: 11/10/2022] Open
Abstract
Phage ImmunoPrecipitation Sequencing (PhIP-Seq) is a recently developed technology to assess antibody reactivity, quantifying antibody binding towards hundreds of thousands of candidate epitopes. The output from PhIP-Seq experiments are read count matrices, similar to RNA-Seq data; however some important differences do exist. In this manuscript we investigated whether the publicly available method edgeR (Robinson et al., Bioinformatics 26(1):139-140, 2010) for normalization and analysis of RNA-Seq data is also suitable for PhIP-Seq data. We find that edgeR is remarkably effective, but improvements can be made and introduce a Bayesian framework specifically tailored for data from PhIP-Seq experiments (Bayesian Enrichment Estimation in R, BEER).
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Affiliation(s)
- Athena Chen
- grid.21107.350000 0001 2171 9311Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Kai Kammers
- grid.21107.350000 0001 2171 9311Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - H Benjamin Larman
- grid.21107.350000 0001 2171 9311Department of Pathology and the Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Robert B. Scharpf
- grid.21107.350000 0001 2171 9311Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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41
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Chen H, Li S, Wang J, He S, Wang D, Qian Z, Hu D, Qi F, Hu K, Luo C, Wang J. Simultaneous measurement of the antibody responses against SARS-CoV-2 and its multiple variants by a phage display mediated immuno-multiplex quantitative PCR-based assay. Front Microbiol 2022; 13:968036. [PMID: 36071962 PMCID: PMC9441900 DOI: 10.3389/fmicb.2022.968036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/18/2022] [Indexed: 11/14/2022] Open
Abstract
To combat the continued pandemic of COVID-19, multiplex serological assays have been developed to comprehensively monitor the humoral immune response and help to design new vaccination protocols to different SARS-CoV-2 variants. However, multiplex beads and stably transfected cell lines require stringent production and storage conditions, and assays based on flow cytometry is time-consuming and its application is therefore restricted. Here, we describe a phage display system to distinguish the differences of immune response to antigenic domains of multiple SARS-CoV-2 variants simultaneously. Compared with linear peptides, the recombinant antigens displayed on the phage surface have shown some function that requires the correct folding to form a stable structure, and the binding efficiency between the recombinant phage and existing antibodies is reduced by mutations on antigens known to be important for antigen–antibody interaction. By using Phage display mediated immuno-multiplex quantitative PCR (Pi-mqPCR), the binding efficiency between the antibody and antigens of different SARS-CoV-2 variants can be measured in one amplification reaction. Overall, these data show that this assay is a valuable tool to evaluate the humoral response to the same antigen of different SARS-CoV-2 variants or antigens of different pathogens. Combined with high-throughput DNA sequencing technology, this phage display system can be further applied in monitoring humoral immune response in a large population before and after vaccination.
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Affiliation(s)
- Hanyi Chen
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Shen Li
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Jiali Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Siqi He
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Dong Wang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Zhaohui Qian
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dandan Hu
- Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Fangfang Qi
- Department of Anatomy and Neurobiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Keping Hu
- The Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Andes Antibody Technology Hengshui LL Company, Hengshui City, China
| | - Chenyi Luo
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
- Shenzhen Research Institute, Beijing University of Chinese Medicine, Shenzhen, China
- *Correspondence: Chenyi Luo,
| | - Jianxun Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
- Shenzhen Research Institute, Beijing University of Chinese Medicine, Shenzhen, China
- Jianxun Wang,
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42
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Chen A, Kammers K, Larman HB, Scharpf RB, Ruczinski I. Detecting and quantifying antibody reactivity in PhIP-Seq data with BEER. Bioinformatics 2022; 38:4647-4649. [PMID: 35959988 PMCID: PMC9525010 DOI: 10.1093/bioinformatics/btac555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/05/2022] [Accepted: 08/09/2022] [Indexed: 12/24/2022] Open
Abstract
SUMMARY Because of their high abundance, easy accessibility in peripheral blood, and relative stability ex vivo, antibodies serve as excellent records of environmental exposures and immune responses. Phage Immuno-Precipitation Sequencing (PhIP-Seq) is the most efficient technique available for assessing antibody binding to hundreds of thousands of peptides at a cohort scale. PhIP-Seq is a high-throughput approach for assessing antibody reactivity to hundreds of thousands of candidate epitopes. Accurate detection of weakly reactive peptides is particularly important for characterizing the development and decline of antibody responses. Here, we present BEER (Bayesian Enrichment Estimation in R), a software package specifically developed for the quantification of peptide reactivity from PhIP-Seq experiments. BEER implements a hierarchical model and produces posterior probabilities for peptide reactivity and a fold change estimate to quantify the magnitude. BEER also offers functionality to infer peptide reactivity based on the edgeR package, though the improvement in speed is offset by slightly lower sensitivity compared to the Bayesian approach, specifically for weakly reactive peptides. AVAILABILITY AND IMPLEMENTATION BEER is implemented in R and freely available from the Bioconductor repository at https://bioconductor.org/packages/release/bioc/html/beer.html.
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Affiliation(s)
- Athena Chen
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Kai Kammers
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - H Benjamin Larman
- Department of Pathology and the Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Robert B Scharpf
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Rasquinha MT, Lasrado N, Petro-Turnquist E, Weaver E, Venkataraman T, Anderson D, Laserson U, Larman HB, Reddy J. PhIP-Seq Reveals Autoantibodies for Ubiquitously Expressed Antigens in Viral Myocarditis. BIOLOGY 2022; 11:biology11071055. [PMID: 36101433 PMCID: PMC9312229 DOI: 10.3390/biology11071055] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/09/2022] [Accepted: 07/11/2022] [Indexed: 12/01/2022]
Abstract
Simple Summary Myocarditis is the inflammation of the heart muscle, and viral infections are a common cause of this disease. Myocarditis in some patients can progress to dilated cardiomyopathy (DCM). The mouse model of coxsackievirus B3 (CVB3) is commonly used to understand this disease progression in DCM patients. In this paper, we have attempted to analyze antibodies for heart antigens that could be produced as a result of heart damage in animals infected with CVB3 using a technique called Phage ImmunoPrecipitation Sequencing (PhIP-Seq). The analyses led us to identify antibodies for several proteins that were not previously reported that may have relevance to human disease. Abstract Enteroviruses such as group B coxsackieviruses (CVB) are commonly suspected as causes of myocarditis that can lead to dilated cardiomyopathy (DCM), and the mouse model of CVB3 myocarditis is routinely used to understand DCM pathogenesis. Mechanistically, autoimmunity is suspected due to the presence of autoantibodies for select antigens. However, their role continues to be enigmatic, which also raises the question of whether the breadth of autoantibodies is sufficiently characterized. Here, we attempted to comprehensively analyze the autoantibody repertoire using Phage ImmunoPrecipitation Sequencing (PhIP-Seq), a versatile and high-throughput platform, in the mouse model of CVB3 myocarditis. First, PhIP-Seq analysis using the VirScan library revealed antibody reactivity only to CVB3 in the infected group but not in controls, thus validating the technique in this model. Second, using the mouse peptide library, we detected autoantibodies to 32 peptides from 25 proteins in infected animals that are ubiquitously expressed and have not been previously reported. Third, by using ELISA as a secondary assay, we confirmed antibody reactivity in sera from CVB3-infected animals to cytochrome c oxidase assembly factor 4 homolog (COA4) and phosphoinositide-3-kinase adaptor protein 1 (PIK3AP1), indicating the specificity of antibody detection by PhIP-Seq technology. Fourth, we noted similar antibody reactivity patterns in CVB3 and CVB4 infections, suggesting that the COA4- and PIK3AP1-reactive antibodies could be common to multiple CVB infections. The specificity of the autoantibodies was affirmed with influenza-infected animals that showed no reactivity to any of the antigens tested. Taken together, our data suggest that the autoantibodies identified by PhIP-Seq may have relevance to CVB pathogenesis, with a possibility that similar reactivity could be expected in human DCM patients.
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Affiliation(s)
- Mahima T. Rasquinha
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (M.T.R.); (N.L.)
| | - Ninaad Lasrado
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (M.T.R.); (N.L.)
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Erika Petro-Turnquist
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (E.P.-T.); (E.W.)
| | - Eric Weaver
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (E.P.-T.); (E.W.)
| | - Thiagarajan Venkataraman
- Division of Immunology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA;
| | - Daniel Anderson
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Uri Laserson
- Department of Genetics and Genomic Sciences and Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - H. Benjamin Larman
- Division of Immunology, Department of Pathology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA;
- Correspondence: (H.B.L.); (J.R.); Tel.: +1-(410)-614-6525 (H.B.L); +1-(402)-472-8541 (J.R.)
| | - Jay Reddy
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; (M.T.R.); (N.L.)
- Correspondence: (H.B.L.); (J.R.); Tel.: +1-(410)-614-6525 (H.B.L); +1-(402)-472-8541 (J.R.)
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Shrock EL, Shrock CL, Elledge SJ. VirScan: High-throughput Profiling of Antiviral Antibody Epitopes. Bio Protoc 2022; 12:e4464. [PMID: 35937932 PMCID: PMC9303818 DOI: 10.21769/bioprotoc.4464] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 06/03/2020] [Accepted: 06/08/2022] [Indexed: 12/29/2022] Open
Abstract
Profiling the specificities of antibodies can reveal a wealth of information about humoral immune responses and the antigens they target. Here, we present a protocol for VirScan, an application of the phage immunoprecipitation sequencing (PhIP-Seq) method for profiling the specificities of human antiviral antibodies. Accompanying this protocol is a video of the experimental procedure. VirScan and, more generally, PhIP-Seq are techniques that enable high-throughput antibody profiling by combining high-throughput DNA oligo synthesis and bacteriophage display with next-generation sequencing. In the VirScan method, human sera samples are screened against a library of peptides spanning the entire human viral proteome. Bound phage are immunoprecipitated and sequenced, identifying the viral peptides recognized by the antibodies. VirScan Is a powerful tool for uncovering individual viral exposure histories, mapping the epitope landscape of viruses of interest, and studying fundamental mechanisms of viral immunity. Graphical abstract.
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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, Brigham and Women’s Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA
| | | | - Stephen J. Elledge
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
,
Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA
,
*For correspondence:
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45
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Angkeow JW, Monaco DR, Chen A, Venkataraman T, Jayaraman S, Valencia C, Sie BM, Liechti T, Farhadi PN, Funez-dePagnier G, Sherman-Baust CA, Wong MQ, Ruczinski I, Caturegli P, Sears CL, Simner PJ, Round JL, Duggal P, Laserson U, Steiner TS, Sen R, Lloyd TE, Roederer M, Mammen AL, Longman RS, Rider LG, Larman HB. Phage display of environmental protein toxins and virulence factors reveals the prevalence, persistence, and genetics of antibody responses. Immunity 2022; 55:1051-1066.e4. [PMID: 35649416 PMCID: PMC9203978 DOI: 10.1016/j.immuni.2022.05.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 02/17/2022] [Accepted: 05/03/2022] [Indexed: 11/19/2022]
Abstract
Microbial exposures are crucial environmental factors that impact healthspan by sculpting the immune system and microbiota. Antibody profiling via Phage ImmunoPrecipitation Sequencing (PhIP-Seq) provides a high-throughput, cost-effective approach for detecting exposure and response to microbial protein products. We designed and constructed a library of 95,601 56-amino acid peptide tiles spanning 14,430 proteins with "toxin" or "virulence factor" keyword annotations. We used PhIP-Seq to profile the antibodies of ∼1,000 individuals against this "ToxScan" library. In addition to enumerating immunodominant antibody epitopes, we studied the age-dependent stability of the ToxScan profile and used a genome-wide association study to find that the MHC-II locus modulates bacterial epitope selection. We detected previously described anti-flagellin antibody responses in a Crohn's disease cohort and identified an association between anti-flagellin antibodies and juvenile dermatomyositis. PhIP-Seq with the ToxScan library is thus an effective tool for studying the environmental determinants of health and disease at cohort scale.
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Affiliation(s)
- Julia W Angkeow
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel R Monaco
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Athena Chen
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Thiagarajan Venkataraman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sahana Jayaraman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cristian Valencia
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Brandon M Sie
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thomas Liechti
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Payam N Farhadi
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, NIH, Bethesda, MD, USA
| | - Gabriela Funez-dePagnier
- Jill Roberts Institute for Research in IBD, Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Cheryl A Sherman-Baust
- Laboratory of Molecular Biology and Immunology, NIH/National Institute on Aging, Baltimore, MD, USA
| | - May Q Wong
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Patrizio Caturegli
- Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cynthia L Sears
- Departments of Medicine and Oncology, Johns Hopkins University School of Medicine, and Department of Molecular Microbiology & Immunology, Bloomberg School of Public Health, Baltimore, MD, USA
| | - Patricia J Simner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - June L Round
- Department of Pathology, Division of Microbiology and Immunology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Uri Laserson
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, NIH/National Institute on Aging, Baltimore, MD, USA
| | - Thomas E Lloyd
- Department of Neurology, Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Mario Roederer
- ImmunoTechnology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA
| | - Andrew L Mammen
- Muscle Disease Unit, Laboratory of Muscle Stem Cells and Gene Regulations, National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
| | - Randy S Longman
- Jill Roberts Institute for Research in IBD, Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lisa G Rider
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, NIH, Bethesda, MD, USA
| | - H Benjamin Larman
- Institute for Cell Engineering, Division of Immunology, Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Ma L, Ouyang H, Su A, Zhang Y, Pang D, Zhang T, Sun R, Wang W, Xie Z, Lv D. AbSE Workflow: Rapid Identification of the Coding Sequence and Linear Epitope of the Monoclonal Antibody at the Single-cell Level. ACS Synth Biol 2022; 11:1856-1864. [PMID: 35503752 DOI: 10.1021/acssynbio.2c00018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Monoclonal antibody (mAb) has been widely used in immunity research and disease diagnosis and therapy. Antibody sequence and epitope are the prerequisites and basis of mAb applications, which determine the properties of antibodies and make the preparation of antibody-based molecules controllable and reliable. Here, we present the antibody sequence and epitope identification (AbSE) workflow, a time-saving and cost-effective route for rapid determination of antibody sequence and linear epitope of mAb even at the single-cell level. The feasibility and accuracy of the AbSE workflow were demonstrated through the identification and validation of the coding sequence and epitope of antihuman serum albumin (antiHSA) mAb. It can be inferred that the AbSE workflow is a powerful and universal approach for paired antibody-epitope sequence identification. It may characterize antibodies not only on a single hybridoma cell but also on any other antibody-secreting cells.
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Affiliation(s)
- Lerong Ma
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - HongSheng Ouyang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
- Chongqing Research Institute, Jilin University, Chongqing 401123, China
- Chongqing Jitang Biotechnology Research Institute Co., Ltd., Chongqing 401123, China
- Shenzhen Kingsino Technology Co., Ltd., Shenzhen 518100, China
| | - Ang Su
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Yuanzhu Zhang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Daxin Pang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
- Chongqing Research Institute, Jilin University, Chongqing 401123, China
- Chongqing Jitang Biotechnology Research Institute Co., Ltd., Chongqing 401123, China
| | - Tao Zhang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Ruize Sun
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Wentao Wang
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Zicong Xie
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Dongmei Lv
- Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China
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Tiu CK, Zhu F, Wang LF, de Alwis R. Phage ImmunoPrecipitation Sequencing (PhIP-Seq): The Promise of High Throughput Serology. Pathogens 2022; 11:pathogens11050568. [PMID: 35631089 PMCID: PMC9143919 DOI: 10.3390/pathogens11050568] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary Determining the exposure or infection history of a person to a multitude of viruses is not an easy task. Typically, antibody tests detect antibodies against proteins (antigens) to only one or a few viruses. Here, we review an emerging technology called Phage ImmunoPrecipitation Sequencing (PhIP-Seq), that allows us to study the infection history of individuals to large numbers of viruses simultaneously. This technology uses bacteriophages to express and display viral antigens of choice, which are then bound by antigen-specific antibodies in patient samples. Antibody-bound bacteriophages are pulled down and identified through molecular techniques. This technology has been used in various infectious disease scenarios, including assessing exposure to different viruses, studying vaccine responses, and identifying viral cause of diseases. Despite inherent limitations in presenting only peptides, this technology holds great promise for future application in identifying novel pathogens, one health and pandemic preparedness. Abstract Phage ImmunoPrecipitation Sequencing (PhIP-Seq) is a high throughput serological technology that is revolutionizing the manner in which we track antibody profiles. In this review, we mainly focus on its application to viral infectious diseases. Through the pull-down of patient antibodies using peptide-tile-expressing T7 bacteriophages and detection using next-generation sequencing (NGS), PhIP-Seq allows the determination of antibody repertoires against peptide targets from hundreds of proteins and pathogens. It differs from conventional serological techniques in that PhIP-Seq does not require protein expression and purification. It also allows for the testing of many samples against the whole virome. PhIP-Seq has been successfully applied in many infectious disease investigations concerning seroprevalence, risk factors, time trends, etiology of disease, vaccinology, and emerging pathogens. Despite the inherent limitations of this technology, we foresee the future expansion of PhIP-Seq in both investigative studies and tracking of current, emerging, and novel viruses. Following the review of PhIP-Seq technology, its limitations, and applications, we recommend that PhIP-Seq be integrated into national surveillance programs and be used in conjunction with molecular techniques to support both One Health and pandemic preparedness efforts.
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Affiliation(s)
- Charles Kevin Tiu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (C.K.T.); (F.Z.); (L.-F.W.)
- SingHealth Duke-NUS Global Health Institute, Singapore 169857, Singapore
| | - Feng Zhu
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (C.K.T.); (F.Z.); (L.-F.W.)
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (C.K.T.); (F.Z.); (L.-F.W.)
- SingHealth Duke-NUS Global Health Institute, Singapore 169857, Singapore
| | - Ruklanthi de Alwis
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore 169857, Singapore; (C.K.T.); (F.Z.); (L.-F.W.)
- Viral Research and Experimental Medicine Centre (ViREMiCS), SingHealth Duke-NUS Academic Medical Centre, Singapore 169856, Singapore
- Correspondence:
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48
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Bourgonje AR, Vogl T, Segal E, Weersma RK. Antibody signatures in inflammatory bowel disease: current developments and future applications. Trends Mol Med 2022; 28:693-705. [DOI: 10.1016/j.molmed.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/01/2022] [Accepted: 05/03/2022] [Indexed: 11/25/2022]
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Valencia-Sanchez C, Knight AM, Hammami MB, Guo Y, Mills JR, Kryzer TJ, Piquet AL, Amin A, Heinzelmann M, Lucchinetti CF, Lennon VA, McKeon A, Pittock SJ, Dubey D. Characterisation of TRIM46 autoantibody-associated paraneoplastic neurological syndrome. J Neurol Neurosurg Psychiatry 2022; 93:196-200. [PMID: 34921120 PMCID: PMC9597704 DOI: 10.1136/jnnp-2021-326656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 11/22/2021] [Indexed: 02/03/2023]
Abstract
OBJECTIVES To report the expanded neurological presentations and oncological associations of tripartite motif-containing protein 46 (TRIM46)-IgG seropositive patients. METHODS Archived sera/cerebrospinal fluid (CSF) were evaluated by tissue-based immunofluorescence assay to identify patients with identical axon initial segment (AIS)-specific staining pattern. Phage immunoprecipitation sequencing (PhIP-Seq) was used to identify the putative autoantigen. RESULTS IgG in serum (17) and/or CSF (16) from 25 patients yielded unique AIS-specific staining on murine central nervous system (CNS) tissue. An autoantibody specific for TRIM46 was identified by PhIP-Seq, and autoantigen specificity was confirmed by transfected COS7 cell-based assay. Clinical information was available for 22 TRIM46-IgG seropositive patients. Fifteen were female (68%). Median age was 67 years (range 25-87). Fifteen (68%) patients presented with subacute cerebellar syndrome (six isolated; nine with CNS accompaniments: encephalopathy (three), brainstem signs (two), myelopathy (two), parkinsonism (one)). Other phenotypes included limbic encephalitis (three), encephalopathy with/without seizures (two), myelopathy (two). Eighteen (82%) had cancer: neuroendocrine carcinomas (9; pancreatic (3), small-cell lung (4), oesophagus (1), endometrium (1)), adenocarcinomas (6; lung (2), ovarian (2), endometrial (1), breast (1)), sarcoma (2) and gastrointestinal tumour (1). Neurological symptoms in three followed immune checkpoint inhibitor (ICI) administration. CONCLUSIONS This study supports TRIM46-IgG being a biomarker of paraneoplastic CNS disorders and expands the neurological phenotypes, oncological and ICI-related adverse event associations.
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Affiliation(s)
| | - Andrew M Knight
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - M Bakri Hammami
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Yong Guo
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | - John R Mills
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Thomas J Kryzer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Amanda L Piquet
- Department of Neurology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Anik Amin
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Morgan Heinzelmann
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - Vanda A Lennon
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA.,Department of Immunology, Mayo Clinic, Rochester, Minnesota, USA
| | - Andrew McKeon
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Sean J Pittock
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Divyanshu Dubey
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA .,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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Garrett ME, Galloway JG, Wolf C, Logue JK, Franko N, Chu HY, Matsen FA, Overbaugh JM. Comprehensive characterization of the antibody responses to SARS-CoV-2 Spike protein finds additional vaccine-induced epitopes beyond those for mild infection. eLife 2022; 11:73490. [PMID: 35072628 PMCID: PMC8887901 DOI: 10.7554/elife.73490] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Control of the COVID-19 pandemic will rely on SARS-CoV-2 vaccine-elicited antibodies to protect against emerging and future variants; an understanding of the unique features of the humoral responses to infection and vaccination, including different vaccine platforms, is needed to achieve this goal. Methods: The epitopes and pathways of escape for Spike-specific antibodies in individuals with diverse infection and vaccination history were profiled using Phage-DMS. Principal component analysis was performed to identify regions of antibody binding along the Spike protein that differentiate the samples from one another. Within these epitope regions, we determined potential sites of escape by comparing antibody binding of peptides containing wild-type residues versus peptides containing a mutant residue. Results: Individuals with mild infection had antibodies that bound to epitopes in the S2 subunit within the fusion peptide and heptad-repeat regions, whereas vaccinated individuals had antibodies that additionally bound to epitopes in the N- and C-terminal domains of the S1 subunit, a pattern that was also observed in individuals with severe disease due to infection. Epitope binding appeared to change over time after vaccination, but other covariates such as mRNA vaccine dose, mRNA vaccine type, and age did not affect antibody binding to these epitopes. Vaccination induced a relatively uniform escape profile across individuals for some epitopes, whereas there was much more variation in escape pathways in mildly infected individuals. In the case of antibodies targeting the fusion peptide region, which was a common response to both infection and vaccination, the escape profile after infection was not altered by subsequent vaccination. Conclusions: The finding that SARS-CoV-2 mRNA vaccination resulted in binding to additional epitopes beyond what was seen after infection suggests that protection could vary depending on the route of exposure to Spike antigen. The relatively conserved escape pathways to vaccine-induced antibodies relative to infection-induced antibodies suggests that if escape variants emerge they may be readily selected for across vaccinated individuals. Given that the majority of people will be first exposed to Spike via vaccination and not infection, this work has implications for predicting the selection of immune escape variants at a population level. Funding: This work was supported by NIH grants AI138709 (PI JMO) and AI146028 (PI FAM). JMO received support as the Endowed Chair for Graduate Education (FHCRC). The research of FAM was supported in part by a Faculty Scholar grant from the Howard Hughes Medical Institute and the Simons Foundation. Scientific Computing Infrastructure at Fred Hutch was funded by ORIP grant S10OD028685. When SARS-CoV-2 – the virus that causes COVID-19 – infects our bodies, our immune system reacts by producing small molecules called antibodies that stick to a part of the virus called the spike protein. Vaccines are thought to work by triggering the production of similar antibodies without causing disease. Some of the most effective antibodies against SARS-CoV-2 bind a specific area of the spike protein called the ‘receptor binding domain’ or RBD. When SARS-CoV-2 evolves it creates a challenge for our immune system: mutations, which are changes in the virus’s genetic code, can alter the shape of its spike protein, meaning that existing antibodies may no longer bind to it as effectively. This lowers the protection offered by past infection or vaccination, which makes it harder to tackle the pandemic. As it stands, it is not clear which mutations to the virus’s genetic code can affect antibody binding, especially to portions outside the RBD. To complicate things further, the antibodies people produce in response to mild infection, severe infection, and vaccination, while somewhat overlapping, exhibit some differences. Studying these differences could help minimize emergence of mutations that allow the virus to ‘escape’ the antibody response. A phage display library is a laboratory technique in which phages (viruses that infect bacteria) are used as a ‘repository’ for DNA fragments that code for a specific protein. The phages can then produce the protein (or fragments of it), and if the protein fragments bind to a target, it can be easily detected. Garrett, Galloway et al. exploited this technique to study how different portions of the SARS-CoV-2 spike protein were bound by antibodies. They made a phage library in which each phage encoded a portion of the spike protein with different mutations, and then exposed the different versions of the protein to antibodies from people who had experienced prior infection, vaccination, or both. The experiment showed that antibodies produced during severe infection or after vaccination bound to similar parts of the spike protein, while antibodies from people who had experienced mild infection targeted fewer areas. Garrett, Galloway et al. also found that mutations that affected the binding of antibodies produced after vaccination were more consistent than mutations that interfered with antibodies produced during infection. While these results show which mutations are most likely to help the virus escape existing antibodies, this does not mean that the virus will necessarily evolve in that direction. Indeed, some of the mutations may be impossible for the virus to acquire because they interfere with the virus’s ability to spread. Further studies could focus on revealing which of the mutations detected by Garrett, Galloway et al. are most likely to occur, to guide vaccine development in that direction. To help with this, Garrett, Galloway et al. have made the data accessible to other scientists and the public using a web tool.
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Affiliation(s)
- Meghan E Garrett
- Division of Human Biology, Fred Hutchinson Cancer Research Center
| | - Jared G Galloway
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center
| | - Caitlin Wolf
- Department of Medicine, University of Washington
| | | | | | - Helen Y Chu
- Department of Medicine, University of Washington
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