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Amjadi MF, Parker MH, Adyniec RR, Zheng Z, Robbins AM, Bashar SJ, Denny MF, McCoy SS, Ong IM, Shelef MA. Novel and unique rheumatoid factors cross-react with viral epitopes in COVID-19. J Autoimmun 2024; 142:103132. [PMID: 37956528 PMCID: PMC10957334 DOI: 10.1016/j.jaut.2023.103132] [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: 08/08/2023] [Revised: 10/05/2023] [Accepted: 10/12/2023] [Indexed: 11/15/2023]
Abstract
Rheumatoid factors (RFs), polyreactive antibodies canonically known to bind two conformational epitopes of IgG Fc, are a hallmark of rheumatoid arthritis but also can arise in other inflammatory conditions and infections. Also, infections may contribute to the development of rheumatoid arthritis and other autoimmune diseases. Recently, RFs only in rheumatoid arthritis were found to bind novel linear IgG epitopes as well as thousands of other rheumatoid arthritis autoantigens. Specific epitopes recognized by infection-induced polyreactive RFs remain undefined but could provide insights into loss of immune tolerance. Here, we identified novel linear IgG epitopes bound by RFs in COVID-19 but not rheumatoid arthritis or other conditions. The main COVID-19 RF was polyreactive, binding two IgG and multiple viral peptides with a tripeptide motif, as well as IgG Fc and SARS-CoV-2 spike proteins. In contrast, a rheumatoid arthritis-specific RF recognized IgG Fc, but not tripeptide motif-containing peptides or spike. Thus, RFs have disease-specific IgG reactivity and distinct polyreactivities that reflect the broader immune response. Moreover, the polyreactivity of a virus-induced RF appears to be attributable to a very short peptide motif. These findings refine our understanding of RFs and provide new insights into how viral infections may contribute to autoimmunity.
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Affiliation(s)
- Maya F Amjadi
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Maxwell H Parker
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Ryan R Adyniec
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Zihao Zheng
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA; Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
| | - Alex M Robbins
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - S Janna Bashar
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael F Denny
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Sara S McCoy
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Irene M Ong
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA; Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Miriam A Shelef
- Department of Medicine, University of Wisconsin-Madison, Madison, WI, USA; William S. Middleton Memorial Veterans Hospital, Madison, WI, USA.
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Hoefges A, McIlwain SJ, Erbe AK, Mathers N, Xu A, Melby D, Tetreault K, Le T, Kim K, Pinapati RS, Garcia BH, Patel J, Heck M, Feils AS, Tsarovsky N, Hank JA, Morris ZS, Ong IM, Sondel PM. Antibody landscape of C57BL/6 mice cured of B78 melanoma via a combined radiation and immunocytokine immunotherapy regimen. Front Immunol 2023; 14:1221155. [PMID: 38077403 PMCID: PMC10701281 DOI: 10.3389/fimmu.2023.1221155] [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: 05/11/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Sera of immune mice that were previously cured of their melanoma through a combined radiation and immunocytokine immunotherapy regimen consisting of 12 Gy of external beam radiation and the intratumoral administration of an immunocytokine (anti-GD2 mAb coupled to IL-2) with long-term immunological memory showed strong antibody-binding against melanoma tumor cell lines via flow cytometric analysis. Using a high-density whole-proteome peptide array (of 6.090.593 unique peptides), we assessed potential protein-targets for antibodies found in immune sera. Sera from 6 of these cured mice were analyzed with this high-density, whole-proteome peptide array to determine specific antibody-binding sites and their linear peptide sequence. We identified thousands of peptides that were targeted by these 6 mice and exhibited strong antibody binding only by immune (after successful cure and rechallenge), not naïve (before tumor implantation) sera and developed a robust method to detect these differentially targeted peptides. Confirmatory studies were done to validate these results using 2 separate systems, a peptide ELISA and a smaller scale peptide array utilizing a slightly different technology. To the best of our knowledge, this is the first study of the full set of germline encoded linear peptide-based proteome epitopes that are recognized by immune sera from mice cured of cancer via radio-immunotherapy. We furthermore found that although the generation of B-cell repertoire in immune development is vastly variable, and numerous epitopes are identified uniquely by immune serum from each of these 6 immune mice evaluated, there are still several epitopes and proteins that are commonly recognized by at least half of the mice studied. This suggests that every mouse has a unique set of antibodies produced in response to the curative therapy, creating an individual "fingerprint." Additionally, certain epitopes and proteins stand out as more immunogenic, as they are recognized by multiple mice in the immune group.
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Affiliation(s)
- Anna Hoefges
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
| | - Sean J. McIlwain
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, United States
| | - Amy K. Erbe
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
| | - Nicholas Mathers
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
| | - Angie Xu
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
| | - Drew Melby
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
| | - Kaitlin Tetreault
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, United States
| | - Trang Le
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, United States
| | - Kyungmann Kim
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, United States
| | | | | | - Jigar Patel
- Nimble Therapeutics, Inc., Madison, WI, United States
| | - Mackenzie Heck
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
| | - Arika S. Feils
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
| | - Noah Tsarovsky
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
| | - Jacquelyn Ann Hank
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
| | - Zachary Scott Morris
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
| | - Irene M. Ong
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, United States
- Department of Obstetrics and Gynecology, University of Wisconsin, Madison, WI, United States
| | - Paul Mark Sondel
- Department of Human Oncology, University of Wisconsin, Madison, WI, United States
- Department of Pediatrics, University of Wisconsin, Madison, WI, United States
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3
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Parker M, Zheng Z, Lasarev M, Alexandridis RA, Newton MA, Shelef MA, McCoy SS. Novel autoantibodies help diagnose anti-SSA antibody negative Sjögren's disease and predict abnormal labial salivary gland pathology. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.08.29.23294775. [PMID: 37693588 PMCID: PMC10491389 DOI: 10.1101/2023.08.29.23294775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Objectives Sj□gren's disease (SjD) diagnosis requires either positive anti-SSA antibodies or a labial salivary gland biopsy with a positive focus score (FS). One-third of SjD patients lack anti-SSA antibodies (SSA-), requiring a positive FS for diagnosis. Our objective was to identify novel autoantibodies to diagnose 'seronegative' SjD. Methods IgG binding to a high density whole human peptidome array was quantified using sera from SSA- SjD cases and matched non-autoimmune controls. We identified the highest bound peptides using empirical Bayesian statistical filters, which we confirmed in an independent cohort comprising SSA- SjD (n=76), sicca controls without autoimmunity (n=75), and autoimmune controls (SjD features but not meeting SjD criteria; n=41). In this external validation, we used non-parametric methods for peptide abundance and controlled false discovery rate in group comparisons. For predictive modeling, we used logistic regression, model selection methods, and cross-validation to identify clinical and peptide variables that predict SSA- SjD and FS positivity. Results IgG against a peptide from D-aminoacyl-tRNA deacylase (DTD2) was bound more in SSA- SjD than sicca controls (p=.004) and more than combined controls (sicca and autoimmune controls combined; p=0.003). IgG against peptides from retroelement silencing factor-1 (RESF1) and DTD2, were bound more in FS-positive than FS-negative participants (p=.010; p=0.012). A predictive model incorporating clinical variables showed good discrimination between SjD versus control (AUC 74%) and between FS-positive versus FS-negative (AUC 72%). Conclusion We present novel autoantibodies in SSA- SjD that have good predictive value for SSA- SjD and FS-positivity. KEY MESSAGES What is already known on this topic - Seronegative (anti-SSA antibody negative [SSA-]) Sjögren's disease (SjD) requires a labial salivary gland biopsy for diagnosis, which is challenging to obtain and interpret. What this study adds - We identified novel autoantibodies in SSA- SjD that, when combined with readily available clinical variables, provide good predictive ability to discriminate 1) SSA- SjD from control participants and 2) abnormal salivary gland biopsies from normal salivary gland biopsies. How this study might affect research, practice or policy - This study provides novel diagnostic antibodies addressing the critical need for improvement of SSA- SjD diagnostic tools.
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Hoefges A, McIlwain SJ, Erbe AK, Mathers N, Xu A, Melby D, Tetreault K, Le T, Kim K, Pinapati RS, Garcia B, Patel J, Heck M, Feils AS, Tsarovsky N, Hank JA, Morris ZS, Ong IM, Sondel PM. Antibody landscape of C57BL/6 mice cured of B78 melanoma via immunotherapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529012. [PMID: 36896021 PMCID: PMC9996675 DOI: 10.1101/2023.02.24.529012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Hoefges et al. utilized a whole-proteome peptide array approach to show that C57BL/6 mice develop a large repertoire of antibodies against linear peptide sequences of their melanoma after receiving a curative immunotherapy regimen consisting of radiation and an immunocytokine. Antibodies can play an important role in innate and adaptive immune responses against cancer, and in preventing infectious disease. Flow cytometry analysis of sera of immune mice that were previously cured of their melanoma through a combined immunotherapy regimen with long-term memory showed strong antibody-binding against melanoma tumor cell lines. Using a high-density whole-proteome peptide array, we assessed potential protein-targets for antibodies found in immune sera. Sera from 6 of these cured mice were analyzed with this high-density, whole-proteome peptide array to determine specific antibody-binding sites and their linear peptide sequence. We identified thousands of peptides that were targeted by 2 or more of these 6 mice and exhibited strong antibody binding only by immune, not naive sera. Confirmatory studies were done to validate these results using 2 separate ELISA-based systems. To the best of our knowledge, this is the first study of the "immunome" of protein-based epitopes that are recognized by immune sera from mice cured of cancer via immunotherapy.
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Affiliation(s)
- A Hoefges
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - S J McIlwain
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - A K Erbe
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - N Mathers
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - A Xu
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - D Melby
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - K Tetreault
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - T Le
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - K Kim
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | | | - B Garcia
- Nimble Therapeutics, Inc., Madison, WI, USA
| | - J Patel
- Nimble Therapeutics, Inc., Madison, WI, USA
| | - M Heck
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - A S Feils
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - N Tsarovsky
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - J A Hank
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - Z S Morris
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - I M Ong
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
- Department of Obstetrics and Gynecology, University of Wisconsin, Madison, WI, USA
| | - P M Sondel
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
- Department of Pediatrics, University of Wisconsin, Madison, WI, USA
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5
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McIlwain SJ, Hoefges A, Erbe AK, Sondel PM, Ong IM. Ranking Antibody Binding Epitopes and Proteins Across Samples from Whole Proteome Tiled Linear Peptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.23.536620. [PMID: 37162956 PMCID: PMC10168206 DOI: 10.1101/2023.04.23.536620] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Ultradense peptide binding arrays that can probe millions of linear peptides comprising the entire proteomes or immunomes of human or mouse, or numerous microbes, are powerful tools for studying the abundance of different antibody repertoire in serum samples to understand adaptive immune responses. There are few statistical analysis tools for exploring high-dimensional, significant and reproducible antibody targets for ultradense peptide binding arrays at the linear peptide, epitope (grouping of adjacent peptides), and protein level across multiple samples/subjects (I.e. epitope spread or immunogenic regions within each protein) for understanding the heterogeneity of immune responses. We developed HERON (Hierarchical antibody binding Epitopes and pROteins from liNear peptides), an R package, which allows users to identify immunogenic epitopes using meta-analyses and spatial clustering techniques to explore antibody targets at various resolution and confidence levels, that can be found consistently across a specified number of samples through the entire proteome to study antibody responses for diagnostics or treatment. Our approach estimates significance values at the linear peptide (probe), epitope, and protein level to identify top candidates for validation. We test the performance of predictions on all three levels using correlation between technical replicates and comparison of epitope calls on 2 datasets, which shows HERON's competitiveness in estimating false discovery rates and finding general and sample-level regions of interest for antibody binding. The code is available as an R package downloadable from http://github.com/Ong-Research/HERON.
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Affiliation(s)
- Sean J. McIlwain
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, WI
- University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, WI
| | - Anna Hoefges
- Department of Human Oncology, University of Wisconsin-Madison, WI
| | - Amy K. Erbe
- Department of Human Oncology, University of Wisconsin-Madison, WI
| | - Paul M. Sondel
- University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, WI
- Department of Human Oncology, University of Wisconsin-Madison, WI
- Department of Pediatrics, University of Wisconsin-Madison, WI
| | - Irene M. Ong
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, WI
- University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison, WI
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, WI
- Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison, WI
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6
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Mergaert AM, Zheng Z, Denny MF, Amjadi MF, Bashar SJ, Newton MA, Malmström V, Grönwall C, McCoy SS, Shelef MA. Rheumatoid factor and anti-modified protein antibody reactivities converge on IgG epitopes. Arthritis Rheumatol 2022; 74:984-991. [PMID: 35001558 DOI: 10.1002/art.42064] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/19/2021] [Accepted: 01/04/2022] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Rheumatoid arthritis (RA) patients often develop rheumatoid factors (RFs), antibodies that bind IgG Fc, and anti-modified protein antibodies (AMPAs), multi-reactive autoantibodies that commonly bind citrullinated, homocitrullinated, and acetylated antigens. Recently, antibodies that bind citrulline-containing IgG epitopes were discovered in RA, suggesting that additional undiscovered IgG epitopes could exist and that IgG could be a shared antigen for RFs and AMPAs. The objective of this study was to reveal new IgG epitopes in rheumatic disease and to determine if multi-reactive AMPAs bind IgG. METHODS Using RA, systemic lupus erythematosus, Sjögren's disease, and spondyloarthropathy sera, IgG binding to native, citrulline-containing, and homocitrulline-containing linear epitopes of the IgG constant region were evaluated by peptide array with highly bound epitopes further evaluated by ELISA. Monoclonal AMPA binding to IgG-derived peptides and IgG Fc was evaluated by ELISA. RESULTS Seropositive RA sera had high IgG binding to multiple citrulline- and homocitrulline-containing IgG-derived peptides, whereas anti-SSA+ Sjögren's disease sera had consistent binding to a single linear native epitope of IgG in the hinge region. Monoclonal AMPAs bound citrulline- and homocitrulline-containing IgG peptides and modified IgG Fc. CONCLUSION The repertoire of epitopes bound by AMPAs includes modified IgG epitopes, positioning IgG as a common antigen that connects the otherwise divergent reactivities of RFs and AMPAs.
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Affiliation(s)
- Aisha M Mergaert
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, USA.,Department of Medicine, University of Wisconsin-Madison, Madison, USA
| | - Zihao Zheng
- Department of Statistics, University of Wisconsin-Madison, Madison, USA.,Department of Medicine, University of Wisconsin-Madison, Madison, USA
| | - Michael F Denny
- Department of Medicine, University of Wisconsin-Madison, Madison, USA
| | - Maya F Amjadi
- Department of Medicine, University of Wisconsin-Madison, Madison, USA
| | - S Janna Bashar
- Department of Medicine, University of Wisconsin-Madison, Madison, USA
| | - Michael A Newton
- Department of Statistics, University of Wisconsin-Madison, Madison, USA
| | - Vivianne Malmström
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Caroline Grönwall
- Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sara S McCoy
- Department of Medicine, University of Wisconsin-Madison, Madison, USA
| | - Miriam A Shelef
- Department of Medicine, University of Wisconsin-Madison, Madison, USA.,William S. Middleton Memorial Veterans Hospital, Madison, USA
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