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Wang A, Yin J, Liu Y, Zhu R, Zhao J, Zhou J, Liu H, Ding P, Zhang G. Identification of linear B-cell epitope on the structure protein p49 of African Swine Fever Virus (ASFV). Int J Biol Macromol 2024; 280:135983. [PMID: 39326597 DOI: 10.1016/j.ijbiomac.2024.135983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 09/02/2024] [Accepted: 09/22/2024] [Indexed: 09/28/2024]
Abstract
African swine fever (ASF), a viral disease affecting both domestic pigs and wild boars, is caused by the African swine fever virus (ASFV). Currently, an effective vaccine is lacking. The structural protein p49, encoded by the B438L gene, is vital for the virus's capsid structure and architecture. Research indicates its potential as a vaccine target. In this study, mAbs against ASFV p49 were generated using the hybridoma technique. The full-length B438L sequence was divided into 5 segments (B1 ∼ B5) via the overlapping polypeptide method, and an expression vector was constructed for expression and purification. Three hybridoma cell lines recognized epitope regions, with 3B12 and 6F1 recognizing the B4 (aa 234-362) fragment, and 3B12, 6F1, and 7C5 reacting with the B5 (aa 312-438) segment. The amino acid sequence (aa 333-438) was further divided into three segments (B6 ∼ B8) for verification. Results from Dot-ELISA and peptide ELISA confirmed that 333-YQTHYMENIVTLVPR-347 and 383-NNYIPKYTGGIGDSK-397 were the major B cell antigenic, highly conserved across ASFV strains. Interestingly, the motif 333-YQTHYMENIVTLVPR-347 was highly conserved, except for a single substitution (T → S) in three residues. This study identifies the B cell epitope of p49 protein, providing insights into ASFV p49 protein structure and function and supporting the development of ASFV-related vaccine products.
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Affiliation(s)
- Aiping Wang
- Longhu Laboratory, Zhengzhou 451100, China; School of Life Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Jiajia Yin
- School of Life Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Yankai Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Ruixin Zhu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Jianguo Zhao
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Jingming Zhou
- Longhu Laboratory, Zhengzhou 451100, China; School of Life Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Hongliang Liu
- Longhu Laboratory, Zhengzhou 451100, China; School of Life Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Peiyang Ding
- Longhu Laboratory, Zhengzhou 451100, China; School of Life Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Gaiping Zhang
- Longhu Laboratory, Zhengzhou 451100, China; School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China.
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2
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Talucci I, Maric HM. Epitope landscape in autoimmune neurological disease and beyond. Trends Pharmacol Sci 2024; 45:768-780. [PMID: 39181736 DOI: 10.1016/j.tips.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/08/2024] [Accepted: 07/19/2024] [Indexed: 08/27/2024]
Abstract
Autoantibody binding has a central role in autoimmune diseases and has also been linked to cancer, infections, and behavioral disorders. Autoimmune neurological diseases remain misclassified also due to an incomplete understanding of the underlying disease-specific epitopes. Such epitopes are crucial for both pathology and diagnosis, but have historically been overlooked. Recent technological advancements have enabled the exploration of these epitopes, potentially opening novel clinical avenues. The precise identification of novel B and T cell epitopes and their autoreactivity has led to the discovery of autoantigen-specific biomarkers for patients at high risk of autoimmune neurological diseases. In this review, we propose utilizing newly available synthetic and cellular-surface display technologies and guide epitope-focused studies to unlock the potential of disease-specific epitopes for improving diagnosis and treatments. Additionally, we offer recommendations to guide emerging epitope-focused studies to broaden the current landscape.
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Affiliation(s)
- Ivan Talucci
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Germany; Department of Neurology, University Hospital Würzburg, Germany
| | - Hans M Maric
- Rudolf Virchow Center for Integrative and Translational Bioimaging, University of Würzburg, Germany.
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3
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Zhang G, Kuang X, Zhang Y, Liu Y, Su Z, Zhang T, Wu Y. Machine-learning-based structural analysis of interactions between antibodies and antigens. Biosystems 2024; 243:105264. [PMID: 38964652 DOI: 10.1016/j.biosystems.2024.105264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 06/21/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Computational analysis of paratope-epitope interactions between antibodies and their corresponding antigens can facilitate our understanding of the molecular mechanism underlying humoral immunity and boost the design of new therapeutics for many diseases. The recent breakthrough in artificial intelligence has made it possible to predict protein-protein interactions and model their structures. Unfortunately, detecting antigen-binding sites associated with a specific antibody is still a challenging problem. To tackle this challenge, we implemented a deep learning model to characterize interaction patterns between antibodies and their corresponding antigens. With high accuracy, our model can distinguish between antibody-antigen complexes and other types of protein-protein complexes. More intriguingly, we can identify antigens from other common protein binding regions with an accuracy of higher than 70% even if we only have the epitope information. This indicates that antigens have distinct features on their surface that antibodies can recognize. Additionally, our model was unable to predict the partnerships between antibodies and their particular antigens. This result suggests that one antigen may be targeted by more than one antibody and that antibodies may bind to previously unidentified proteins. Taken together, our results support the precision of antibody-antigen interactions while also suggesting positive future progress in the prediction of specific pairing.
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Affiliation(s)
- Grace Zhang
- Staples High School, 70 North Avenue, Westport, CT, 06880, USA
| | - Xiaohan Kuang
- Data Science Institute, Vanderbilt University, 1001 19th Ave S, Nashville, TN, 37212, USA
| | - Yuhao Zhang
- Data Science Institute, Vanderbilt University, 1001 19th Ave S, Nashville, TN, 37212, USA
| | - Yunchao Liu
- Department of Computer Science, Vanderbilt University, 1400 18th Ave S, Nashville, TN, 37212, USA
| | - Zhaoqian Su
- Data Science Institute, Vanderbilt University, 1001 19th Ave S, Nashville, TN, 37212, USA
| | - Tom Zhang
- California Institute of Technology, 1200 East California Boulevard, Pasadena, CA, 91125, USA.
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY, 10461, USA.
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4
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Bisarad P, Kelbauskas L, Singh A, Taguchi AT, Trenchevska O, Woodbury NW. Predicting monoclonal antibody binding sequences from a sparse sampling of all possible sequences. Commun Biol 2024; 7:979. [PMID: 39134636 PMCID: PMC11319732 DOI: 10.1038/s42003-024-06650-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 07/29/2024] [Indexed: 08/15/2024] Open
Abstract
Previous work has shown that binding of target proteins to a sparse, unbiased sample of all possible peptide sequences is sufficient to train a machine learning model that can then predict, with statistically high accuracy, target binding to any possible peptide sequence of similar length. Here, highly sequence-specific molecular recognition is explored by measuring binding of 8 monoclonal antibodies (mAbs) with specific linear cognate epitopes to an array containing 121,715 near-random sequences about 10 residues in length. Network models trained on resulting sequence-binding values are used to predict the binding of each mAb to its cognate sequence and to an in silico generated one million random sequences. The model always ranks the binding of the cognate sequence in the top 100 sequences, and for 6 of the 8 mAbs, the cognate sequence ranks in the top ten. Practically, this approach has potential utility in selecting highly specific mAbs for therapeutics or diagnostics. More fundamentally, this demonstrates that very sparse random sampling of a large amino acid sequence spaces is sufficient to generate comprehensive models predictive of highly specific molecular recognition.
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Affiliation(s)
- Pritha Bisarad
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Pediatric Movement Disorders Program, Division of Pediatric Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, Phoenix, AZ, USA
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
| | - Laimonas Kelbauskas
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Biomorph Technologies, Chandler, AZ, USA
| | - Akanksha Singh
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, AZ, USA
- Prellis Biologics Inc., Berkeley, CA, USA
| | | | | | - Neal W Woodbury
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA.
- Center for Innovations in Medicine, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
- Center for Molecular Design and Biomimetics, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
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5
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Sonnentag SJ, Jenne F, Orian-Rousseau V, Nesterov-Mueller A. High-throughput screening for cell binding and repulsion peptides on multifunctionalized surfaces. Commun Biol 2024; 7:870. [PMID: 39020032 PMCID: PMC11255233 DOI: 10.1038/s42003-024-06541-7] [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: 10/11/2023] [Accepted: 07/03/2024] [Indexed: 07/19/2024] Open
Abstract
The adhesion of cells to the extracellular matrix engages cell surface receptors such as integrins, proteoglycans and other types of cell adhesion molecules such as CD44. To closely examine the determinants of cell adhesion, herein we describe the generation of high-density peptide arrays and test the growth of cells on these multifunctionalized surfaces. The peptide library used consists of over 11,000 different sequences, either random or derived from existing proteins. By applying this screen to SW620 mCherry colorectal cancer cells, we select for peptides with both maximum cell adhesion and maximum cell repulsion. All of these extreme properties are based on unique combinations of amino acids. Here, we identify peptides with maximum cell repulsion on secreted frizzled- and Dickkopf-related proteins. Peptides with strong cell repulsion are found at the poles of the TNF-alpha homotrimer. The formation of cellular patterns on alternating highly repulsive and adhesive peptides are examined. Our screen allows the identification of peptides suitable for biomedical and tissue engineering applications.
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Affiliation(s)
- Steffen J Sonnentag
- Institute of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131, Karlsruhe, Germany
| | - Felix Jenne
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131, Karlsruhe, Germany
| | - Véronique Orian-Rousseau
- Institute of Biological and Chemical Systems - Functional Molecular Systems, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131, Karlsruhe, Germany.
| | - Alexander Nesterov-Mueller
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131, Karlsruhe, Germany.
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6
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Thalén NB, Karlander M, Lundqvist M, Persson H, Hofström C, Turunen SP, Godzwon M, Volk AL, Malm M, Ohlin M, Rockberg J. Mammalian cell display with automated oligo design and library assembly allows for rapid residue level conformational epitope mapping. Commun Biol 2024; 7:805. [PMID: 38961245 PMCID: PMC11222437 DOI: 10.1038/s42003-024-06508-8] [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: 11/29/2023] [Accepted: 06/25/2024] [Indexed: 07/05/2024] Open
Abstract
Precise epitope determination of therapeutic antibodies is of great value as it allows for further comprehension of mechanism of action, therapeutic responsiveness prediction, avoidance of unwanted cross reactivity, and vaccine design. The golden standard for discontinuous epitope determination is the laborious X-ray crystallography method. Here, we present a combinatorial method for rapid mapping of discontinuous epitopes by mammalian antigen display, eliminating the need for protein expression and purification. The method is facilitated by automated workflows and tailored software for antigen analysis and oligonucleotide design. These oligos are used in automated mutagenesis to generate an antigen receptor library displayed on mammalian cells for direct binding analysis by flow cytometry. Through automated analysis of 33930 primers an optimized single condition cloning reaction was defined allowing for mutation of all surface-exposed residues of the receptor binding domain of SARS-CoV-2. All variants were functionally expressed, and two reference binders validated the method. Furthermore, epitopes of three novel therapeutic antibodies were successfully determined followed by evaluation of binding also towards SARS-CoV-2 Omicron BA.2. We find the method to be highly relevant for rapid construction of antigen libraries and determination of antibody epitopes, especially for the development of therapeutic interventions against novel pathogens.
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Affiliation(s)
- Niklas Berndt Thalén
- Department Protein science, KTH-Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Maximilian Karlander
- Department Protein science, KTH-Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Magnus Lundqvist
- Department Protein science, KTH-Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Helena Persson
- Science for Life Laboratory, Drug Discovery and Development Platform & School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Camilla Hofström
- Science for Life Laboratory, Drug Discovery and Development Platform & School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - S Pauliina Turunen
- Science for Life Laboratory, Drug Discovery and Development Platform & School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | | | - Anna-Luisa Volk
- Department Protein science, KTH-Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Magdalena Malm
- Department Protein science, KTH-Royal Institute of Technology, Stockholm, SE-106 91, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Johan Rockberg
- Department Protein science, KTH-Royal Institute of Technology, Stockholm, SE-106 91, Sweden.
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7
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Ray P, Ledgerwood-Lee M, Brickner H, Clark AE, Garretson A, Graham R, Van Zant W, Carlin AF, Aronoff-Spencer ES. Design and Development of an Antigen Test for SARS-CoV-2 Nucleocapsid Protein to Validate the Viral Quality Assurance Panels. Viruses 2024; 16:662. [PMID: 38793544 PMCID: PMC11125937 DOI: 10.3390/v16050662] [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: 03/30/2024] [Revised: 04/19/2024] [Accepted: 04/21/2024] [Indexed: 05/26/2024] Open
Abstract
The continuing mutability of the SARS-CoV-2 virus can result in failures of diagnostic assays. To address this, we describe a generalizable bioinformatics-to-biology pipeline developed for the calibration and quality assurance of inactivated SARS-CoV-2 variant panels provided to Radical Acceleration of Diagnostics programs (RADx)-radical program awardees. A heuristic genetic analysis based on variant-defining mutations demonstrated the lowest genetic variance in the Nucleocapsid protein (Np)-C-terminal domain (CTD) across all SARS-CoV-2 variants. We then employed the Shannon entropy method on (Np) sequences collected from the major variants, verifying the CTD with lower entropy (less prone to mutations) than other Np regions. Polyclonal and monoclonal antibodies were raised against this target CTD antigen and used to develop an Enzyme-linked immunoassay (ELISA) test for SARS-CoV-2. Blinded Viral Quality Assurance (VQA) panels comprised of UV-inactivated SARS-CoV-2 variants (XBB.1.5, BF.7, BA.1, B.1.617.2, and WA1) and distractor respiratory viruses (CoV 229E, CoV OC43, RSV A2, RSV B, IAV H1N1, and IBV) were assembled by the RADx-rad Diagnostics core and tested using the ELISA described here. The assay tested positive for all variants with high sensitivity (limit of detection: 1.72-8.78 ng/mL) and negative for the distractor virus panel. Epitope mapping for the monoclonal antibodies identified a 20 amino acid antigenic peptide on the Np-CTD that an in-silico program also predicted for the highest antigenicity. This work provides a template for a bioinformatics pipeline to select genetic regions with a low propensity for mutation (low Shannon entropy) to develop robust 'pan-variant' antigen-based assays for viruses prone to high mutational rates.
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Affiliation(s)
- Partha Ray
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Melissa Ledgerwood-Lee
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Howard Brickner
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Alex E. Clark
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Aaron Garretson
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Rishi Graham
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Westley Van Zant
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Aaron F. Carlin
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
- Department of Pathology, University of California, San Diego, CA 92093, USA
| | - Eliah S. Aronoff-Spencer
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
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8
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Timofeeva AM, Sedykh SE, Litvinova EA, Dolgushin SA, Matveev AL, Tikunova NV, Nevinsky GA. Binding of Natural Antibodies Generated after COVID-19 and Vaccination with Individual Peptides Corresponding to the SARS-CoV-2 S-Protein. Vaccines (Basel) 2024; 12:426. [PMID: 38675808 PMCID: PMC11053827 DOI: 10.3390/vaccines12040426] [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: 03/20/2024] [Revised: 04/14/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The rapid development of vaccines is a crucial objective in modern biotechnology and molecular pharmacology. In this context, conducting research to expedite the selection of a potent immunogen is imperative. The candidate vaccine should induce the production of antibodies that can recognize the immunogenic epitopes of the target protein, resembling the ones found in recovered patients. One major challenge in vaccine development is the absence of straightforward and reliable techniques to determine the extent to which the spectrum of antibodies produced after vaccination corresponds to antibodies found after recovery. This paper describes a newly developed method to detect antibodies specific to immunogenic epitopes of the target protein in blood plasma and to compare them with antibody spectra generated post vaccination. Comparing the antibody pool generated in the human body after recovering from an infectious disease with the pool formed through vaccination can become a universal method for screening candidate vaccines. This method will enable the identification of candidate vaccines that can induce the production of antibodies similar to those generated in response to a natural infection. Implementing this approach will facilitate the rapid development of new vaccines, even when faced with a pandemic.
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Affiliation(s)
- Anna M. Timofeeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (S.E.S.); (A.L.M.); (N.V.T.)
- Advanced Engineering School, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Sergey E. Sedykh
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (S.E.S.); (A.L.M.); (N.V.T.)
- Advanced Engineering School, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ekaterina A. Litvinova
- Physical Engineering Faculty, Novosibirsk State Technical University, Novosibirsk 630073, Russia
| | | | - Andrey L. Matveev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (S.E.S.); (A.L.M.); (N.V.T.)
| | - Nina V. Tikunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (S.E.S.); (A.L.M.); (N.V.T.)
- Advanced Engineering School, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Georgy A. Nevinsky
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (S.E.S.); (A.L.M.); (N.V.T.)
- Advanced Engineering School, Novosibirsk State University, Novosibirsk 630090, Russia
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9
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Garg P, Hsueh SCC, Plotkin SS. Testing the feasibility of targeting a conserved region on the S2 domain of the SARS-CoV-2 spike protein. Biophys J 2024; 123:992-1005. [PMID: 38491772 PMCID: PMC11052916 DOI: 10.1016/j.bpj.2024.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 10/02/2023] [Accepted: 03/11/2024] [Indexed: 03/18/2024] Open
Abstract
The efficacy of vaccines against the SARS-CoV-2 virus significantly declines with the emergence of mutant strains, prompting investigation into the feasibility of targeting highly conserved but often cryptic regions on the S2 domain of spike protein. Using tools from molecular dynamics, we find that exposure of a conserved S2 epitope located in the central helices below the receptor binding domains would require large-scale motion beyond receptor binding domain up-down motion, but, along the reaction coordinates we explored, it is unlikely to be exposed by such large-scale dynamic fluctuations of the S1 domain without any external facilitating factors, despite some previous computational evidence suggesting transient exposure of this region. Furthermore, glycans, particularly those on N165 and N234, hinder S2-exposing opening dynamics, and thus stabilize spike in addition to immunologically shielding the protein surface. Although the S2 epitope region examined here is central to large-scale conformational changes during viral entry, free energy landscape analysis obtained using the path coordinate formalism reveals no inherent "loaded spring" effect, suggesting that a vaccine immunogen would tend to present the epitope in a prefusion-like conformation and may be effective in neutralization. These findings contribute to a deeper understanding of the dynamic origins of the function of the spike protein, as well as further characterizing the feasibility of the S2 epitope as a therapeutic target.
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Affiliation(s)
- Pranav Garg
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada
| | - Shawn C C Hsueh
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, University of British Columbia, Vancouver, British Columbia, Canada; Genome Sciences and Technology Program, University of British Columbia, Vancouver, British Columbia, Canada.
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10
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Maguire C, Wang C, Ramasamy A, Fonken C, Morse B, Lopez N, Wylie D, Melamed E. Molecular Mimicry as a Mechanism of Viral Immune Evasion and Autoimmunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.583134. [PMID: 38496443 PMCID: PMC10942439 DOI: 10.1101/2024.03.08.583134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Mimicry of host protein structures ("molecular mimicry") is a common mechanism employed by viruses to evade the host's immune system. To date, studies have primarily evaluated molecular mimicry in the context of full protein structural mimics. However, recent work has demonstrated that short linear amino acid (AA) molecular mimics can elicit cross-reactive antibodies and T-cells from the host, which may contribute to development and progression of autoimmunity. Despite this, the prevalence of molecular mimics throughout the human virome has not been fully explored. In this study, we evaluate 134 human infecting viruses and find significant usage of linear mimicry across the virome, particularly those in the herpesviridae and poxviridae families. Furthermore, we identify that proteins involved in cellular replication and inflammation, those expressed from autosomes, the X chromosome, and in thymic cells are over-enriched in viral mimicry. Finally, we demonstrate that short linear mimicry from Epstein-Barr virus (EBV) is significantly higher in auto-antibodies found in multiple sclerosis patients to a greater degree than previously appreciated. Our results demonstrate that human-infecting viruses frequently leverage mimicry in the course of their infection, point to substantial evolutionary pressure for mimicry, and highlight mimicry's important role in human autoimmunity. Clinically, our findings could translate to development of novel therapeutic strategies that target viral infections linked to autoimmunity, with the goal of eliminating disease-associated latent viruses and preventing their reactivation.
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Affiliation(s)
- Cole Maguire
- The University of Texas at Austin, Department of Neurology
| | - Chumeng Wang
- The University of Texas at Austin, Department of Neurology
| | | | - Cara Fonken
- The University of Texas at Austin, Department of Neurology
| | - Brinkley Morse
- The University of Texas at Austin, Department of Neurology
| | - Nathan Lopez
- The University of Texas at Austin, Department of Neurology
| | - Dennis Wylie
- The University of Texas at Austin, Center for Biomedical Research Support
| | - Esther Melamed
- The University of Texas at Austin, Department of Neurology
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11
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Oliveira L, Neumann P, Mata-Sucre Y, Kuo YT, Marques A, Schubert V, Macas J. KNL1 and NDC80 represent new universal markers for the detection of functional centromeres in plants. Chromosome Res 2024; 32:3. [PMID: 38403686 DOI: 10.1007/s10577-024-09747-x] [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: 01/05/2024] [Revised: 01/25/2024] [Accepted: 02/08/2024] [Indexed: 02/27/2024]
Abstract
Centromere is the chromosomal site of kinetochore assembly and microtubule attachment for chromosome segregation. Given its importance, markers that allow specific labeling of centromeric chromatin throughout the cell cycle and across all chromosome types are sought for facilitating various centromere studies. Antibodies against the N-terminal region of CENH3 are commonly used for this purpose, since CENH3 is the near-universal marker of functional centromeres. However, because the N-terminal region of CENH3 is highly variable among plant species, antibodies directed against this region usually function only in a small group of closely related species. As a more versatile alternative, we present here antibodies targeted to the conserved domains of two outer kinetochore proteins, KNL1 and NDC80. Sequence comparison of these domains across more than 350 plant species revealed a high degree of conservation, particularly within a six amino acid motif, FFGPVS in KNL1, suggesting that both antibodies would function in a wide range of plant species. This assumption was confirmed by immunolabeling experiments in angiosperm (monocot and dicot) and gymnosperm species, including those with mono-, holo-, and meta-polycentric chromosomes. In addition to centromere labeling on condensed chromosomes during cell division, both antibodies detected the corresponding regions in the interphase nuclei of most species tested. These results demonstrated that KNL1 and NDC80 are better suited for immunolabeling centromeres than CENH3, because antibodies against these proteins offer incomparably greater versatility across different plant species which is particularly convenient for studying the organization and function of the centromere in non-model species.
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Affiliation(s)
- Ludmila Oliveira
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Pavel Neumann
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Yennifer Mata-Sucre
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Laboratório de Citogenética E Evolução Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Yi-Tzu Kuo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - André Marques
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Jiří Macas
- Biology Centre, Institute of Plant Molecular Biology, Czech Academy of Sciences, České Budějovice, Czech Republic.
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12
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Specht AG, Ginese M, Kurtz SL, Elkins KL, Specht H, Beamer G. Host Genetic Background Influences BCG-Induced Antibodies Cross-Reactive to SARS-CoV-2 Spike Protein. Vaccines (Basel) 2024; 12:242. [PMID: 38543876 PMCID: PMC10975245 DOI: 10.3390/vaccines12030242] [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: 01/23/2024] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 04/01/2024] Open
Abstract
Mycobacterium bovis Bacillus Calmette-Guérin (BCG) protects against childhood tuberculosis; and unlike most vaccines, BCG broadly impacts immunity to other pathogens and even some cancers. Early in the COVID-19 pandemic, epidemiological studies identified a protective association between BCG vaccination and outcomes of SARS-CoV-2, but the associations in later studies were inconsistent. We sought possible reasons and noticed the study populations often lived in the same country. Since individuals from the same regions can share common ancestors, we hypothesized that genetic background could influence associations between BCG and SARS-CoV-2. To explore this hypothesis in a controlled environment, we performed a pilot study using Diversity Outbred mice. First, we identified amino acid sequences shared by BCG and SARS-CoV-2 spike protein. Next, we tested for IgG reactive to spike protein from BCG-vaccinated mice. Sera from some, but not all, BCG-vaccinated Diversity Outbred mice contained higher levels of IgG cross-reactive to SARS-CoV-2 spike protein than sera from BCG-vaccinated C57BL/6J inbred mice and unvaccinated mice. Although larger experimental studies are needed to obtain mechanistic insight, these findings suggest that genetic background may be an important variable contributing to different associations observed in human randomized clinical trials evaluating BCG vaccination on SARS-CoV-2 and COVID-19.
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Affiliation(s)
- Aubrey G. Specht
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (A.G.S.); (M.G.)
| | - Melanie Ginese
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA 01536, USA; (A.G.S.); (M.G.)
| | - Sherry L. Kurtz
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA; (S.L.K.); (K.L.E.)
| | - Karen L. Elkins
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA; (S.L.K.); (K.L.E.)
| | - Harrison Specht
- Department of Bioengineering and Barnett Institute, Northeastern University, Boston, MA 02115, USA;
| | - Gillian Beamer
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
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13
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Wenson L, Leino M, Jarvius M, Heldin J, Koos B, Söderberg O. The method developer's guide to oligonucleotide design. Expert Rev Proteomics 2024; 21:65-80. [PMID: 38363709 DOI: 10.1080/14789450.2024.2318565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
INTRODUCTION Development of new methods is essential to make great leaps in science, opening up new avenues for research, but the process behind method development is seldom described. AREAS COVERED Over the last twenty years we have been developing several new methods, such as in situ PLA, proxHCR, and MolBoolean, using oligonucleotide-conjugated antibodies to visualize protein-protein interactions. Herein, we describe the rationale behind the oligonucleotide systems of these methods. The main objective of this paper is to provide researchers with a description on how we thought when we designed those methods. We also describe in detail how the methods work and how one should interpret results. EXPERT OPINION Understanding how the methods work is important in selecting an appropriate method for your experiments. We also hope that this paper may be an inspiration for young researchers to enter the field of method development. Seeing a problem is a motivation to develop a solution.
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Affiliation(s)
- Leonie Wenson
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical center, Uppsala, Sweden
| | - Mattias Leino
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical center, Uppsala, Sweden
| | - Malin Jarvius
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical center, Uppsala, Sweden
| | - Johan Heldin
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical center, Uppsala, Sweden
| | - Björn Koos
- Klinik für Anästhesiologie, Intensivmedizin und Schmerztherapie, Universitätsklinikum Knappschaftskrankenhaus Bochum-Langendreer, Ruhr-Universität Bochum, Bochum, Germany
| | - Ola Söderberg
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical center, Uppsala, Sweden
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14
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Sun R, Qian MG, Zhang X. T and B cell epitope analysis for the immunogenicity evaluation and mitigation of antibody-based therapeutics. MAbs 2024; 16:2324836. [PMID: 38512798 PMCID: PMC10962608 DOI: 10.1080/19420862.2024.2324836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/26/2024] [Indexed: 03/23/2024] Open
Abstract
The surge in the clinical use of therapeutic antibodies has reshaped the landscape of pharmaceutical therapy for many diseases, including rare and challenging conditions. However, the administration of exogenous biologics could potentially trigger unwanted immune responses such as generation of anti-drug antibodies (ADAs). Real-world experiences have illuminated the clear correlation between the ADA occurrence and unsatisfactory therapeutic outcomes as well as immune-related adverse events. By retrospectively examining research involving immunogenicity analysis, we noticed the growing emphasis on elucidating the immunogenic epitope profiles of antibody-based therapeutics aiming for mechanistic understanding the immunogenicity generation and, ideally, mitigating the risks. As such, we have comprehensively summarized here the progress in both experimental and computational methodologies for the characterization of T and B cell epitopes of therapeutics. Furthermore, the successful practice of epitope-driven deimmunization of biotherapeutics is exceptionally highlighted in this article.
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Affiliation(s)
- Ruoxuan Sun
- Global Drug Metabolism, Pharmacokinetics & Modeling, Preclinical & Translational Sciences, Takeda Development Center Americas, Inc. (TDCA), Cambridge, MA, USA
| | - Mark G. Qian
- Global Drug Metabolism, Pharmacokinetics & Modeling, Preclinical & Translational Sciences, Takeda Development Center Americas, Inc. (TDCA), Cambridge, MA, USA
| | - Xiaobin Zhang
- Global Drug Metabolism, Pharmacokinetics & Modeling, Preclinical & Translational Sciences, Takeda Development Center Americas, Inc. (TDCA), Cambridge, MA, USA
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15
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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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16
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Zhang G, Su Z, Zhang T, Wu Y. Machine-learning-based Structural Analysis of Interactions between Antibodies and Antigens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570397. [PMID: 38106177 PMCID: PMC10723427 DOI: 10.1101/2023.12.06.570397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Computational analysis of paratope-epitope interactions between antibodies and their corresponding antigens can facilitate our understanding of the molecular mechanism underlying humoral immunity and boost the design of new therapeutics for many diseases. The recent breakthrough in artificial intelligence has made it possible to predict protein-protein interactions and model their structures. Unfortunately, detecting antigen-binding sites associated with a specific antibody is still a challenging problem. To tackle this challenge, we implemented a deep learning model to characterize interaction patterns between antibodies and their corresponding antigens. With high accuracy, our model can distinguish between antibody-antigen complexes and other types of protein-protein complexes. More intriguingly, we can identify antigens from other common protein binding regions with an accuracy of higher than 70% even if we only have the epitope information. This indicates that antigens have distinct features on their surface that antibodies can recognize. Additionally, our model was unable to predict the partnerships between antibodies and their particular antigens. This result suggests that one antigen may be targeted by more than one antibody and that antibodies may bind to previously unidentified proteins. Taken together, our results support the precision of antibody-antigen interactions while also suggesting positive future progress in the prediction of specific pairing.
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Affiliation(s)
- Grace Zhang
- Staples High School, 70 North Avenue, Westport, CT 06880
| | - Zhaoqian Su
- Data Science Institute, Vanderbilt University, 1001 19th Ave S, Nashville, TN, 37212
| | - Tom Zhang
- California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461
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17
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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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18
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Bach E, Fitzgerald SF, Williams-MacDonald SE, Mitchell M, Golde WT, Longbottom D, Nisbet AJ, Dinkla A, Sullivan E, Pinapati RS, Tan JC, Joosten LAB, Roest HJ, Østerbye T, Koets AP, Buus S, McNeilly TN. Genome-wide epitope mapping across multiple host species reveals significant diversity in antibody responses to Coxiella burnetii vaccination and infection. Front Immunol 2023; 14:1257722. [PMID: 37954609 PMCID: PMC10637584 DOI: 10.3389/fimmu.2023.1257722] [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: 07/12/2023] [Accepted: 09/19/2023] [Indexed: 11/14/2023] Open
Abstract
Coxiella burnetii is an important zoonotic bacterial pathogen of global importance, causing the disease Q fever in a wide range of animal hosts. Ruminant livestock, in particular sheep and goats, are considered the main reservoir of human infection. Vaccination is a key control measure, and two commercial vaccines based on formalin-inactivated C. burnetii bacterins are currently available for use in livestock and humans. However, their deployment is limited due to significant reactogenicity in individuals previously sensitized to C. burnetii antigens. Furthermore, these vaccines interfere with available serodiagnostic tests which are also based on C. burnetii bacterin antigens. Defined subunit antigen vaccines offer significant advantages, as they can be engineered to reduce reactogenicity and co-designed with serodiagnostic tests to allow discrimination between vaccinated and infected individuals. This study aimed to investigate the diversity of antibody responses to C. burnetii vaccination and/or infection in cattle, goats, humans, and sheep through genome-wide linear epitope mapping to identify candidate vaccine and diagnostic antigens within the predicted bacterial proteome. Using high-density peptide microarrays, we analyzed the seroreactivity in 156 serum samples from vaccinated and infected individuals to peptides derived from 2,092 open-reading frames in the C. burnetii genome. We found significant diversity in the antibody responses within and between species and across different types of C. burnetii exposure. Through the implementation of three different vaccine candidate selection methods, we identified 493 candidate protein antigens for protein subunit vaccine design or serodiagnostic evaluation, of which 65 have been previously described. This is the first study to investigate multi-species seroreactivity against the entire C. burnetii proteome presented as overlapping linear peptides and provides the basis for the selection of antigen targets for next-generation Q fever vaccines and diagnostic tests.
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Affiliation(s)
- Emil Bach
- Department of Immunology & Microbiology, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | | | | | - Annemieke Dinkla
- Department of Bacteriology, Host-Pathogen Interaction and Diagnostic Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Eric Sullivan
- Nimble Therapeutics, Inc., Madison, WI, United States
| | | | - John C. Tan
- Nimble Therapeutics, Inc., Madison, WI, United States
| | - Leo A. B. Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | - Hendrik-Jan Roest
- Department of Bacteriology, Host-Pathogen Interaction and Diagnostic Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
- Ministry of Agriculture, Nature and Food Quality, Den Haag, Netherlands
- Department of Infection and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Thomas Østerbye
- Department of Immunology & Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Ad P. Koets
- Department of Bacteriology, Host-Pathogen Interaction and Diagnostic Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Søren Buus
- Department of Immunology & Microbiology, University of Copenhagen, Copenhagen, Denmark
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19
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Das A, Santhosh S, Giridhar M, Behr J, Michel T, Schaudy E, Ibáñez-Redín G, Lietard J, Somoza MM. Dipodal Silanes Greatly Stabilize Glass Surface Functionalization for DNA Microarray Synthesis and High-Throughput Biological Assays. Anal Chem 2023; 95:15384-15393. [PMID: 37801728 PMCID: PMC10586054 DOI: 10.1021/acs.analchem.3c03399] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/22/2023] [Indexed: 10/08/2023]
Abstract
Glass is by far the most common substrate for biomolecular arrays, including high-throughput sequencing flow cells and microarrays. The native glass hydroxyl surface is modified by using silane chemistry to provide appropriate functional groups and reactivities for either in situ synthesis or surface immobilization of biologically or chemically synthesized biomolecules. These arrays, typically of oligonucleotides or peptides, are then subjected to long incubation times in warm aqueous buffers prior to fluorescence readout. Under these conditions, the siloxy bonds to the glass are susceptible to hydrolysis, resulting in significant loss of biomolecules and concomitant loss of signal from the assay. Here, we demonstrate that functionalization of glass surfaces with dipodal silanes results in greatly improved stability compared to equivalent functionalization with standard monopodal silanes. Using photolithographic in situ synthesis of DNA, we show that dipodal silanes are compatible with phosphoramidite chemistry and that hybridization performed on the resulting arrays provides greatly improved signal and signal-to-noise ratios compared with surfaces functionalized with monopodal silanes.
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Affiliation(s)
- Arya Das
- Technical
University of Munich, Germany, TUM School
of Natural Sciences, Boltzmannstraße 10, 85748 Garching, Germany
- Leibniz-Institute
for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 30, 85354 Freising, Germany
| | - Santra Santhosh
- Technical
University of Munich, Germany, TUM School
of Natural Sciences, Boltzmannstraße 10, 85748 Garching, Germany
- Leibniz-Institute
for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 30, 85354 Freising, Germany
| | - Maya Giridhar
- Leibniz-Institute
for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 30, 85354 Freising, Germany
| | - Jürgen Behr
- Leibniz-Institute
for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 30, 85354 Freising, Germany
| | - Timm Michel
- Leibniz-Institute
for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 30, 85354 Freising, Germany
- Technical
University of Munich, Germany, TUM School
of Life Sciences, Alte
Akademie 8, 85354 Freising, Germany
| | - Erika Schaudy
- Institute
of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Gisela Ibáñez-Redín
- Institute
of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Jory Lietard
- Institute
of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Mark M. Somoza
- Leibniz-Institute
for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 30, 85354 Freising, Germany
- Institute
of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
- Chair
of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
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20
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Greisen PJ, Yi L, Zhou R, Zhou J, Johansson E, Dong T, Liu H, Johnsen LB, Lund S, Svensson LA, Zhu H, Thomas N, Yang Z, Østergaard H. Computational design of N-linked glycans for high throughput epitope profiling. Protein Sci 2023; 32:e4726. [PMID: 37421602 PMCID: PMC10521239 DOI: 10.1002/pro.4726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/12/2023] [Accepted: 07/06/2023] [Indexed: 07/10/2023]
Abstract
Efficient identification of epitopes is crucial for drug discovery and design as it enables the selection of optimal epitopes, expansion of lead antibody diversity, and verification of binding interface. Although high-resolution low throughput methods like x-ray crystallography can determine epitopes or protein-protein interactions accurately, they are time-consuming and can only be applied to a limited number of complexes. To overcome these limitations, we have developed a rapid computational method that incorporates N-linked glycans to mask epitopes or protein interaction surfaces, thereby providing a mapping of these regions. Using human coagulation factor IXa (fIXa) as a model system, we computationally screened 158 positions and expressed 98 variants to test experimentally for epitope mapping. We were able to delineate epitopes rapidly and reliably through the insertion of N-linked glycans that efficiently disrupted binding in a site-selective manner. To validate the efficacy of our method, we conducted ELISA experiments and high-throughput yeast surface display assays. Furthermore, x-ray crystallography was employed to verify the results, thereby recapitulating through the method of N-linked glycans a coarse-grained mapping of the epitope.
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Affiliation(s)
| | - Li Yi
- Global Research TechnologiesNovo Nordisk A/SMaaloevDenmark
| | - Rong Zhou
- Discovery Technology China, Novo Nordisk Research CentreNovo Nordisk A/SBeijingChina
| | - Jian Zhou
- Discovery Technology China, Novo Nordisk Research CentreNovo Nordisk A/SBeijingChina
| | - Eva Johansson
- Global Research TechnologiesNovo Nordisk A/SMaaloevDenmark
| | - Tiantang Dong
- Discovery Technology China, Novo Nordisk Research CentreNovo Nordisk A/SBeijingChina
| | - Haimo Liu
- Discovery Technology China, Novo Nordisk Research CentreNovo Nordisk A/SBeijingChina
| | | | - Søren Lund
- Global Research TechnologiesNovo Nordisk A/SMaaloevDenmark
| | | | - Haisun Zhu
- Discovery Technology China, Novo Nordisk Research CentreNovo Nordisk A/SBeijingChina
| | - Nidhin Thomas
- Digital Science and InnovationNovo Nordisk A/SSeattleUSA
| | - Zhiru Yang
- Discovery Technology China, Novo Nordisk Research CentreNovo Nordisk A/SBeijingChina
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21
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Angaitkar P, Janghel RR, Sahu TP. DL-TCNN: Deep Learning-based Temporal Convolutional Neural Network for prediction of conformational B-cell epitopes. 3 Biotech 2023; 13:297. [PMID: 37575599 PMCID: PMC10412510 DOI: 10.1007/s13205-023-03716-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 07/24/2023] [Indexed: 08/15/2023] Open
Abstract
Prediction of conformational B-cell epitopes (CBCE) is an essential phase for vaccine design, drug invention, and accurate disease diagnosis. Many laboratorial and computational approaches have been developed to predict CBCE. However, laboratorial experiments are costly and time consuming, leading to the popularity of Machine Learning (ML)-based computational methods. Although ML methods have succeeded in many domains, achieving higher accuracy in CBCE prediction remains a challenge. To overcome this drawback and consider the limitations of ML methods, this paper proposes a novel DL-based framework for CBCE prediction, leveraging the capabilities of deep learning in the medical domain. The proposed model is named Deep Learning-based Temporal Convolutional Neural Network (DL-TCNN), which hybridizes empirical hyper-tuned 1D-CNN and TCN. TCN is an architecture that employs causal convolutions and dilations, adapting well to sequential input with extensive receptive fields. To train the proposed model, physicochemical features are firstly extracted from antigen sequences. Next, the Synthetic Minority Oversampling Technique (SMOTE) is applied to address the class imbalance problem. Finally, the proposed DL-TCNN is employed for the prediction of CBCE. The model's performance is evaluated and validated on a benchmark antigen-antibody dataset. The DL-TCNN achieves 94.44% accuracy, and 0.989 AUC score for the training dataset, 78.53% accuracy, and 0.661 AUC score for the validation dataset; and 85.10% accuracy, 0.855 AUC score for the testing dataset. The proposed model outperforms all the existing CBCE methods.
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Affiliation(s)
- Pratik Angaitkar
- Department of Information Technology, National Institute of Technology, Raipur, G.E. Road, Raipur, C.G. 492010 India
| | - Rekh Ram Janghel
- Department of Information Technology, National Institute of Technology, Raipur, G.E. Road, Raipur, C.G. 492010 India
| | - Tirath Prasad Sahu
- Department of Information Technology, National Institute of Technology, Raipur, G.E. Road, Raipur, C.G. 492010 India
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22
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Buks R, Alnabulsi A, Zindrili R, Alnabulsi A, Wang A, Wang T, Martin SAM. Catch of the Day: New Serum Amyloid A (SAA) Antibody Is a Valuable Tool to Study Fish Health in Salmonids. Cells 2023; 12:2097. [PMID: 37626907 PMCID: PMC10453338 DOI: 10.3390/cells12162097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/08/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Serum amyloid A (SAA) proteins belong to a family of acute-phase reactants, playing an integral role in defending the organism from pathological damage. Despite a wealth of data on the regulation of SAA transcripts in teleosts, there is only limited information on these proteins' abundance in fish. The aim of this study is to characterise SAA protein levels in salmonids using a newly developed antibody specific to salmonid SAA. The salmonid SAA antibody detected SAA and accurately discriminated between stimulated and control specimens from rainbow trout macrophage cell line (RTS-11) in vitro, as well as rainbow trout challenged with Aeromonas salmonicida- or flagellin-stimulated Atlantic salmon in vivo. The presence of SAA protein was analysed in RTS-11 cell line supernatants, liver, and spleen samples using ELISA, immunoblotting, and immunohistochemistry. This study is the first to characterise SAA protein levels in salmonids in vivo and in vitro. The newly developed salmonid SAA antibody was able to discriminate between stimulated and unstimulated specimens, showing that it can be used to study the acute-phase response in salmonids with the potential to be further developed into assays to monitor and evaluate health in wild and farmed fish.
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Affiliation(s)
- Ralfs Buks
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK
- Vertebrate Antibodies Ltd., Aberdeen AB24 2TZ, UK
| | | | - Rodanthi Zindrili
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK
| | | | - Alex Wang
- Vertebrate Antibodies Ltd., Aberdeen AB24 2TZ, UK
| | - Tiehui Wang
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK
| | - Samuel A. M. Martin
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, UK
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23
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Mitchell MM, Leng Y, Boppana S, Britt WJ, Gutierrez Sanchez LH, Elledge SJ. Signatures of AAV-2 immunity are enriched in children with severe acute hepatitis of unknown etiology. Sci Transl Med 2023; 15:eadh9917. [PMID: 37494473 PMCID: PMC10501808 DOI: 10.1126/scitranslmed.adh9917] [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: 03/27/2023] [Accepted: 06/21/2023] [Indexed: 07/28/2023]
Abstract
Severe acute hepatitis of unknown etiology in children is under investigation in 35 countries. Although several potential etiologic agents have been investigated, a clear cause for the liver damage observed in these cases remains to be identified. Using VirScan, a high-throughput antibody profiling technology, we probed the antibody repertoires of nine cases of severe acute hepatitis of unknown etiology treated at Children's of Alabama and compared their antibody responses with 38 pediatric and 470 adult controls. We report increased adeno-associated dependoparvovirus A (AAV-A) breadth in cases relative to controls and adeno-associated virus 2 (AAV-2) peptide responses that were conserved in seven of nine cases but rarely observed in pediatric and adult controls. These findings suggest that AAV-2 is a likely etiologic agent of severe acute hepatitis of unknown etiology.
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Affiliation(s)
- Moriah M. Mitchell
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Program in Systems, Synthetic, and Quantitative Biology, Harvard University, Boston, MA 02115, USA
| | - Yumei Leng
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Suresh Boppana
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - William J. Britt
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Luz Helena Gutierrez Sanchez
- Division of Gastroenterology, Hepatitis, and Nutrition, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Stephen J. Elledge
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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24
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Su L, Huang W, Neill FH, Estes MK, Atmar RL, Palzkill T. Mapping human norovirus antigens during infection reveals the breadth of the humoral immune response. NPJ Vaccines 2023; 8:87. [PMID: 37280322 PMCID: PMC10242225 DOI: 10.1038/s41541-023-00683-1] [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: 10/12/2022] [Accepted: 05/25/2023] [Indexed: 06/08/2023] Open
Abstract
Human noroviruses (HuNoV) are the leading cause of acute gastroenteritis worldwide. The humoral immune response plays an important role in clearing HuNoV infections and elucidating the antigenic landscape of HuNoV during an infection can shed light on antibody targets to inform vaccine design. Here, we utilized Jun-Fos-assisted phage display of a HuNoV genogroup GI.1 genomic library and deep sequencing to simultaneously map the epitopes of serum antibodies of six individuals infected with GI.1 HuNoV. We found both unique and common epitopes that were widely distributed among both nonstructural proteins and the major capsid protein. Recurring epitope profiles suggest immunodominant antibody footprints among these individuals. Analysis of sera collected longitudinally from three individuals showed the presence of existing epitopes in the pre-infection sera, suggesting these individuals had prior HuNoV infections. Nevertheless, newly recognized epitopes surfaced seven days post-infection. These new epitope signals persisted by 180 days post-infection along with the pre-infection epitopes, suggesting a persistent production of antibodies recognizing epitopes from previous and new infections. Lastly, analysis of a GII.4 genotype genomic phage display library with sera of three persons infected with GII.4 virus revealed epitopes that overlapped with those identified in GI.1 affinity selections, suggesting the presence of GI.1/GII.4 cross-reactive antibodies. The results demonstrate that genomic phage display coupled with deep sequencing can characterize HuNoV antigenic landscapes from complex polyclonal human sera to reveal the timing and breadth of the human humoral immune response to infection.
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Affiliation(s)
- Lynn Su
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Wanzhi Huang
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Frederick H Neill
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Robert L Atmar
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
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25
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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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26
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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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27
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Ricci AD, Bracco L, Salas-Sarduy E, Ramsey JM, Nolan MS, Lynn MK, Altcheh J, Ballering GE, Torrico F, Kesper N, Villar JC, Marcipar IS, Marco JD, Agüero F. The Trypanosoma cruzi Antigen and Epitope Atlas: antibody specificities in Chagas disease patients across the Americas. Nat Commun 2023; 14:1850. [PMID: 37012236 PMCID: PMC10070320 DOI: 10.1038/s41467-023-37522-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
During an infection the immune system produces pathogen-specific antibodies. These antibody repertoires become specific to the history of infections and represent a rich source of diagnostic markers. However, the specificities of these antibodies are mostly unknown. Here, using high-density peptide arrays we examined the human antibody repertoires of Chagas disease patients. Chagas disease is a neglected disease caused by Trypanosoma cruzi, a protozoan parasite that evades immune mediated elimination and mounts long-lasting chronic infections. We describe a proteome-wide search for antigens, characterised their linear epitopes, and show their reactivity on 71 individuals from diverse human populations. Using single-residue mutagenesis we revealed the core functional residues for 232 of these epitopes. Finally, we show the diagnostic performance of identified antigens on challenging samples. These datasets enable the study of the Chagas antibody repertoire at an unprecedented depth and granularity, while also providing a rich source of serological biomarkers.
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Affiliation(s)
- Alejandro D Ricci
- Instituto de Investigaciones Biotecnológicas (IIB) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad de San Martín (UNSAM), San Martín, Buenos Aires, Argentina
| | - Leonel Bracco
- Instituto de Investigaciones Biotecnológicas (IIB) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad de San Martín (UNSAM), San Martín, Buenos Aires, Argentina
| | - Emir Salas-Sarduy
- Instituto de Investigaciones Biotecnológicas (IIB) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina
- Escuela de Bio y Nanotecnologías (EByN), Universidad de San Martín (UNSAM), San Martín, Buenos Aires, Argentina
| | - Janine M Ramsey
- Centro Regional de Investigación en Salud Pública, Instituto Nacional de Salud Pública, Tapachula, México
| | - Melissa S Nolan
- Laboratory of Vector-borne and Zoonotic Diseases, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - M Katie Lynn
- Laboratory of Vector-borne and Zoonotic Diseases, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Jaime Altcheh
- Hospital de Niños "Ricardo Gutierrez", Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
- Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas (IMIPP) - GCBA-CONICET, Buenos Aires, Argentina
| | - Griselda E Ballering
- Hospital de Niños "Ricardo Gutierrez", Ciudad Autónoma de Buenos Aires, Buenos Aires, Argentina
| | | | - Norival Kesper
- LIM-49, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brasil
| | - Juan C Villar
- Facultad de Ciencias de la Salud, Universidad Autónoma de Bucaramanga y Fundación Cardioinfantil - Instituto de Cardiología, Bogotá, Colombia
| | - Iván S Marcipar
- Facultad de Ciencias Médicas y Facultad de Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Jorge D Marco
- Instituto de Patología Experimental, Universidad Nacional de Salta - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Salta, Argentina
| | - Fernán Agüero
- Instituto de Investigaciones Biotecnológicas (IIB) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Martín, Buenos Aires, Argentina.
- Escuela de Bio y Nanotecnologías (EByN), Universidad de San Martín (UNSAM), San Martín, Buenos Aires, Argentina.
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28
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Hogan JM, Lee PS, Wong SC, West SM, Morishige WH, Bee C, Tapia GC, Rajpal A, Strop P, Dollinger G. Residue-Level Characterization of Antibody Binding Epitopes Using Carbene Chemical Footprinting. Anal Chem 2023; 95:3922-3931. [PMID: 36791402 DOI: 10.1021/acs.analchem.2c03091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Characterization of antibody binding epitopes is an important factor in therapeutic drug discovery, as the binding site determines and drives antibody pharmacology and pharmacokinetics. Here, we present a novel application of carbene chemical footprinting with mass spectrometry for identification of antibody binding epitopes at the single-residue level. Two different photoactivated diazirine reagents provide complementary labeling information allowing structural refinement of the antibody binding interface. We applied this technique to map the epitopes of multiple MICA and CTLA-4 antibodies and validated the findings with X-ray crystallography and yeast surface display epitope mapping. The characterized epitopes were used to understand biolayer interferometry-derived competitive binding results at the structural level. We show that carbene footprinting provides fast and high-resolution epitope information critical in the antibody selection process and enables mechanistic understanding of function to accelerate the drug discovery process.
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Affiliation(s)
- Jason M Hogan
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Peter S Lee
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Susan C Wong
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Sean M West
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Winse H Morishige
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Christine Bee
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Gamze Camdere Tapia
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Arvind Rajpal
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Pavel Strop
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
| | - Gavin Dollinger
- Discovery Biotherapeutics, Bristol Myers Squibb, 700 Bay Road, Redwood City, California 94063, United States
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29
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Raghavan M, Kalantar KL, Duarte E, Teyssier N, Takahashi S, Kung AF, Rajan JV, Rek J, Tetteh KKA, Drakeley C, Ssewanyana I, Rodriguez-Barraquer I, Greenhouse B, DeRisi JL. Antibodies to repeat-containing antigens in Plasmodium falciparum are exposure-dependent and short-lived in children in natural malaria infections. eLife 2023; 12:e81401. [PMID: 36790168 PMCID: PMC10005774 DOI: 10.7554/elife.81401] [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: 06/26/2022] [Accepted: 02/14/2023] [Indexed: 02/16/2023] Open
Abstract
Protection against Plasmodium falciparum, which is primarily antibody-mediated, requires recurrent exposure to develop. The study of both naturally acquired limited immunity and vaccine induced protection against malaria remains critical for ongoing eradication efforts. Towards this goal, we deployed a customized P. falciparum PhIP-seq T7 phage display library containing 238,068 tiled 62-amino acid peptides, covering all known coding regions, including antigenic variants, to systematically profile antibody targets in 198 Ugandan children and adults from high and moderate transmission settings. Repeat elements - short amino acid sequences repeated within a protein - were significantly enriched in antibody targets. While breadth of responses to repeat-containing peptides was twofold higher in children living in the high versus moderate exposure setting, no such differences were observed for peptides without repeats, suggesting that antibody responses to repeat-containing regions may be more exposure dependent and/or less durable in children than responses to regions without repeats. Additionally, short motifs associated with seroreactivity were extensively shared among hundreds of antigens, potentially representing cross-reactive epitopes. PfEMP1 shared motifs with the greatest number of other antigens, partly driven by the diversity of PfEMP1 sequences. These data suggest that the large number of repeat elements and potential cross-reactive epitopes found within antigenic regions of P. falciparum could contribute to the inefficient nature of malaria immunity.
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Affiliation(s)
- Madhura Raghavan
- University of California, San FranciscoSan FranciscoUnited States
| | | | - Elias Duarte
- University of California, BerkeleyBerkeleyUnited States
| | - Noam Teyssier
- University of California, San FranciscoSan FranciscoUnited States
| | - Saki Takahashi
- University of California, San FranciscoSan FranciscoUnited States
| | - Andrew F Kung
- University of California, San FranciscoSan FranciscoUnited States
| | - Jayant V Rajan
- University of California, San FranciscoSan FranciscoUnited States
| | - John Rek
- Infectious Diseases Research CollaborationKampalaUganda
| | - Kevin KA Tetteh
- London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Chris Drakeley
- London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Isaac Ssewanyana
- Infectious Diseases Research CollaborationKampalaUganda
- London School of Hygiene and Tropical MedicineLondonUnited Kingdom
| | - Isabel Rodriguez-Barraquer
- University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Bryan Greenhouse
- University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Joseph L DeRisi
- University of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
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Multiplexed Bead-Based Peptide Immunoassays for the Detection of Antibody Reactivities. Methods Mol Biol 2023; 2628:505-533. [PMID: 36781804 DOI: 10.1007/978-1-0716-2978-9_30] [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: 02/15/2023]
Abstract
Antigenic peptides are commonly used in serological test settings such as enzyme-linked immunosorbent assays (ELISA) to determine reactive antibodies (ABs) from serum or plasma samples. The use of synthetic peptides provides advantages like lower production effort and easier incorporation of specific chemical modifications compared to full-length antigenic proteins. Multiplexed antibody (AB) profiling methods such as microarray technologies enable the simultaneous identification of multiple novel biomarkers for the use in early disease diagnostics, vaccine development, or monitoring of immune responses. Despite various benefits they still show major limitations which can be overcome with bead-based assay technologies like the multi-analyte profiling (xMAP) technology developed by Luminex. In this chapter we introduce our established workflow for AB profiling with a multiplexed bead-based peptide immunoassay. The workflow is based on copper-catalyzed click chemistry to immobilize designed synthetic peptides onto uniquely color-coded paramagnetic beads in an orientation-specific manner. The individual peptide-coupled beads can be distinguished by their unique emission spectra during readout in the xMAP instrument and therefore allow testing of up to 500 different antigenic peptides in one multiplexed reaction. The multistep process described in this chapter is divided into separate sections for peptide design, coupling of functionalized peptides to MagPlex beads via click chemistry, confirmation of successful peptide immobilization, processing of serum or plasma samples, or preferably purified IgG thereof, with the multiplexed bead-based peptide immunoassay and subsequent data export and analysis.
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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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Designing multi-epitope mRNA construct as a universal influenza vaccine candidate for future epidemic/pandemic preparedness. Int J Biol Macromol 2023; 226:885-899. [PMID: 36521707 DOI: 10.1016/j.ijbiomac.2022.12.066] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/25/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
Despite the availability of prevention and treatment strategies and advancing immunization approaches, the influenza virus remains a global threat that continues to plague humanity with unpredictable pandemics. Due to the unusual genetic variability and segmented genome, the reassortment between different strains of influenza is facilitated and the viruses continuously evolve and adapt to the host cell's immunity. This underlies the seasonal vaccine mismatches that decrease the vaccine efficacy and increase the risk of outbreaks. Thus, the development of a universal vaccine covering all the influenza A and B strains would reduce the pervasiveness of the influenza virus. In the current study, a potentially universal influenza multi-epitope vaccine was designed based on the experimentally tested conserved T cell and B cell epitopes of hemagglutinin (HA), neuraminidase (NA), nucleoprotein (NP), and matrix-2 proton channel (M2) of the virus. The immune simulation and molecular docking of the vaccine construct with TLR2, TLR3, and TLR4 elicited the favorable immunogenicity of the vaccine and the formation of stable complexes, respectively. Ultimately, based on the immunoinformatics analysis, the universal mRNA multi-epitope vaccine designed in this study might have a protection potential against the various subtypes of influenza A and B.
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Systematic Evaluation of Antigenic Stimulation in Chronic Lymphocytic Leukemia: Humoral Immunity as Biomarkers for Disease Evolution. Cancers (Basel) 2023; 15:cancers15030891. [PMID: 36765855 PMCID: PMC9913429 DOI: 10.3390/cancers15030891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/12/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is the most common leukemia in the Western world. Studies of CLL antibody reactivity have shown differential targets to autoantigens and antimicrobial molecular motifs that support the current hypothesis of CLL pathogenesis. METHODS In this study, we conducted a quantitative serum analysis of 7 immunoglobulins in CLL and monoclonal B-cell lymphocytosis (MBL) patients (bead-suspension protein arrays) and a serological profile (IgG and IgM) study of autoantibodies and antimicrobial antigens (protein microarrays). RESULTS Significant differences in the IgA levels were observed according to disease progression and evolution as well as significant alterations in IgG1 according to IGHV mutational status. More representative IgG autoantibodies in the cohort were against nonmutagenic proteins and IgM autoantibodies were against vesicle proteins. Antimicrobial IgG and IgM were detected against microbes associated with respiratory tract infections. CONCLUSIONS Quantitative differences in immunoglobulin serum levels could be potential biomarkers for disease progression. In the top 5 tumoral antigens, we detected autoantibodies (IgM and IgG) against proteins related to cell homeostasis and metabolism in the studied cohort. The top 5 microbial antigens were associated with respiratory and gastrointestinal infections; moreover, the subsets with better prognostics were characterized by a reactivation of Cytomegalovirus. The viral humoral response could be a potential prognosis biomarker for disease progression.
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Garcia-Montojo M, Simula ER, Fathi S, McMahan C, Ghosal A, Berry JD, Cudkowicz M, Elkahloun A, Johnson K, Norato G, Jensen P, James T, Sechi LA, Nath A. Antibody Response to HML-2 May Be Protective in Amyotrophic Lateral Sclerosis. Ann Neurol 2022; 92:782-792. [PMID: 36053951 DOI: 10.1002/ana.26466] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 07/28/2022] [Accepted: 07/28/2022] [Indexed: 01/07/2023]
Abstract
OBJECTIVES Reactivation of HERV-K(HML-2) has been found in subsets of individuals with amyotrophic lateral sclerosis (ALS). This study examines the antibody response against HML-2 in ALS and analyzes its clinical relevance. METHODS Antibodies to HML-2 envelope (env) were analyzed using a peptide array for epitope mapping and by a peptide enzyme-linked immunosorbent assay (ELISA) in 242 healthy donors, and 243 ALS and 85 multiple sclerosis (MS) individuals. Extracellular levels of HML-2 were analyzed by digital polymerase chain reaction (PCR). RESULTS Antibodies in the sera of ALS individuals recognized more HML-2 env peptides compared to healthy controls (p < 0.0001). ALS individuals had higher levels of HML-2 than healthy donors (p = 0.02) and higher antibody levels against a select HML-2 env peptide compared to healthy donors or individuals with multiple sclerosis (p < 0.0001). 55.14% of ALS compared to 21.16% of healthy donors and 13.10% of MS individuals had antibodies against the HML-2 peptide (AUC = 0.769, p < 0.0001). Levels of extracellular HML-2 DNA in serum (p = 0.02) and the number of HML-2 env peptides recognized by ALS sera (p = 0.02) correlated with disease duration. Among ALS individuals, lower levels of HML-2 antibodies were associated with a definite diagnosis per EL Escorial criteria (p = 0.03), and with a lower predicted (p = 0.02) and observed survival (p = 0.03). INTERPRETATION There is a differential antibody response against specific epitopes of HML-2 env in ALS and controls, suggesting epitope spreading, likely due to persistent antigenic exposure following reactivation of the viral genes. Low levels of antibodies to HML-2 env in ALS are associated with poor prognosis and decreased survival probability. ANN NEUROL 2022;92:782-792.
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Affiliation(s)
- Marta Garcia-Montojo
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Elena Rita Simula
- Department of Biomedical Sciences, Division of Microbiology and Virology, University of Sassari, Sassari, Italy
| | - Saeed Fathi
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Cynthia McMahan
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Anubrata Ghosal
- Sean M. Healey & AMG Center for ALS and the Neurology Clinical Research Institute, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - James D Berry
- Sean M. Healey & AMG Center for ALS and the Neurology Clinical Research Institute, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Merit Cudkowicz
- Sean M. Healey & AMG Center for ALS and the Neurology Clinical Research Institute, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Abdel Elkahloun
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Kory Johnson
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Gina Norato
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Peter Jensen
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Tony James
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Leonardo A Sechi
- Department of Biomedical Sciences, Division of Microbiology and Virology, University of Sassari, Sassari, Italy.,Struttura Complessa Microbiologia e Virologia, Azienda Ospedaliera Universitaria Sassari, Sassari, Italy
| | - Avindra Nath
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
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Matalkah F, Rhodes S, Ramamurthy V, Stoilov P. The mAB 13A4 monoclonal antibody to the mouse PROM1 protein recognizes a structural epitope. PLoS One 2022; 17:e0274958. [PMID: 36215230 PMCID: PMC9550058 DOI: 10.1371/journal.pone.0274958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 09/08/2022] [Indexed: 11/18/2022] Open
Abstract
PROM1 (CD133, AC133) is a protein that is required for the maintenance of primary cilia. Mutation in the Prom1 gene in humans and animal models are associated with several forms of retinal degeneration. mAB 13A4 is the main reagent used to detect the mouse PROM1 protein. We endeavored to map the epitope of the rat monoclonal antibody mAB 13A4 to the mouse PROM1 protein. Deletion mutagenesis demonstrated that mAB 13A4 recognizes a structural epitope that is stabilized by two of the extracellular domains of PROM1. Furthermore, the affinity of mAB 13A4 to the major PROM1 isoform in photoreceptor cells is significantly reduced due to the inclusion of a photoreceptor-specific alternative exon in the third extracellular domain. Interestingly, a deletion in the photoreceptor specific isoform of six amino acids adjacent to the alternative exon restored the affinity of mAB 13A4 to PROM1. The results of the mutagenesis are consistent with the computationally predicted helical bundle structure of PROM1 and point to the utility of mAB 13A4 for evaluating the effect of mutations on the PROM1 structure. Our results show that the PROM1 isoform composition needs to be considered when interpreting tissue and developmental expression data produced by mAB 13A4.
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Affiliation(s)
- Fatimah Matalkah
- Department of Biochemistry and Molecular Medicine, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia, United States of America
| | - Scott Rhodes
- Department of Biochemistry and Molecular Medicine, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia, United States of America
| | - Visvanathan Ramamurthy
- Department of Biochemistry and Molecular Medicine, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia, United States of America
- Department of Ophthalmology and Visual Sciences, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia, United States of America
| | - Peter Stoilov
- Department of Biochemistry and Molecular Medicine, Robert C. Byrd Health Sciences Center, West Virginia University, Morgantown, West Virginia, United States of America
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Focused B cell response to recurring gluten motif with implications for epitope spreading in celiac disease. Cell Rep 2022; 41:111541. [DOI: 10.1016/j.celrep.2022.111541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/16/2022] [Accepted: 09/29/2022] [Indexed: 11/19/2022] Open
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Torres JM, Borja C, Gibert L, Ribot F, Olivares EG. Twentieth-Century Paleoproteomics: Lessons from Venta Micena Fossils. BIOLOGY 2022; 11:1184. [PMID: 36009810 PMCID: PMC9404968 DOI: 10.3390/biology11081184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/28/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022]
Abstract
Proteomics methods can identify amino acid sequences in fossil proteins, thus making it possible to determine the ascription or proximity of a fossil to other species. Before mass spectrometry was used to study fossil proteins, earlier studies used antibodies to recognize their sequences. Lowenstein and colleagues, at the University of San Francisco, pioneered the identification of fossil proteins with immunological methods. His group, together with Olivares's group at the University of Granada, studied the immunological reactions of proteins from the controversial Orce skull fragment (VM-0), a 1.3-million-year-old fossil found at the Venta Micena site in Orce (Granada province, southern Spain) and initially assigned to a hominin. However, discrepancies regarding the morphological features of the internal face of the fossil raised doubts about this ascription. In this article, we review the immunological analysis of the proteins extracted from VM-0 and other Venta Micena fossils assigned to hominins and to other mammals, and explain how these methods helped to determine the species specificity of these fossils and resolve paleontological controversies.
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Affiliation(s)
- Jesús M. Torres
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Universidad de Granada, 18016 Granada, Spain; (J.M.T.); (C.B.)
| | - Concepción Borja
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Universidad de Granada, 18016 Granada, Spain; (J.M.T.); (C.B.)
| | - Luis Gibert
- Departament de Geoquímica, Petrologia i Prospecció Geològica, Universitat de Barcelona, 08028 Barcelona, Spain;
| | - Francesc Ribot
- Museo de Prehistoria y Paleontología Josep Gibert, 18858 Orce, Spain;
| | - Enrique G. Olivares
- Departamento de Bioquímica y Biología Molecular III e Inmunología, Universidad de Granada, 18016 Granada, Spain; (J.M.T.); (C.B.)
- Instituto de Biopatología y Medicina Regenerativa, Centro de Investigación Biomédica, Universidad de Granada, 18100 Armilla, Spain
- Unidad de Gestión Clínica Laboratorios, Hospital Clínico Universitario San Cecilio, 18016 Granada, Spain
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Ghafouri F, Ahangari Cohan R, Samimi H, Hosseini Rad S M A, Naderi M, Noorbakhsh F, Haghpanah V. Development of a Multiepitope Vaccine Against SARS-CoV-2: Immunoinformatics Study. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2022; 3:e36100. [PMID: 35891920 PMCID: PMC9302570 DOI: 10.2196/36100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 05/16/2022] [Accepted: 07/04/2022] [Indexed: 11/21/2022]
Abstract
Background Since the first appearance of SARS-CoV-2 in China in December 2019, the world witnessed the emergence of the SARS-CoV-2 outbreak. Due to the high transmissibility rate of the virus, there is an urgent need to design and develop vaccines against SARS-CoV-2 to prevent more cases affected by the virus. Objective A computational approach is proposed for vaccine design against the SARS-CoV-2 spike (S) protein, as the key target for neutralizing antibodies, and envelope (E) protein, which contains a conserved sequence feature. Methods We used previously reported epitopes of S protein detected experimentally and further identified a collection of predicted B-cell and major histocompatibility (MHC) class II–restricted T-cell epitopes derived from E proteins with an identical match to SARS-CoV-2 E protein. Results The in silico design of our candidate vaccine against the S and E proteins of SARS-CoV-2 demonstrated a high affinity to MHC class II molecules and effective results in immune response simulations. Conclusions Based on the results of this study, the multiepitope vaccine designed against the S and E proteins of SARS-CoV-2 may be considered as a new, safe, and efficient approach to combatting the COVID-19 pandemic.
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Affiliation(s)
- Fatemeh Ghafouri
- Department of Biotechnology Faculty of Life Sciences and Biotechnology Shahid Beheshti University Tehran Iran
| | - Reza Ahangari Cohan
- Department of Nanobiotechnology New Technologies Research Group Pasteur Institute of Iran Tehran Iran
| | - Hilda Samimi
- Endocrinology and Metabolism Research Center Endocrinology and Metabolism Clinical Sciences Institute Tehran University of Medical Sciences Tehran Iran
| | | | - Mahmood Naderi
- Digestive Diseases Research Center Digestive Diseases Research Institute Tehran University of Medical Sciences Tehran Iran
| | - Farshid Noorbakhsh
- Department of Immunology School of Medicine Tehran University of Medical Sciences Tehran Iran
| | - Vahid Haghpanah
- Endocrinology and Metabolism Research Center Endocrinology and Metabolism Clinical Sciences Institute Tehran University of Medical Sciences Tehran Iran
- Personalized Medicine Research Center Endocrinology and Metabolism Clinical Sciences Institute Tehran University of Medical Sciences Tehran Iran
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Yang L, Liang T, Pierson LM, Wang H, Fletcher JK, Wang S, Bao D, Zhang L, Huang Z, Zheng W, Zhang X, Park H, Li Y, Robinson JE, Feehan AK, Lyon CJ, Cao J, Morici LA, Li C, Roy CJ, Yu X, Hu T. SARS-CoV-2 Epitopes following Infection and Vaccination Overlap Known Neutralizing Antibody Sites. RESEARCH (WASHINGTON, D.C.) 2022; 2022:9769803. [PMID: 35928300 PMCID: PMC9297724 DOI: 10.34133/2022/9769803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/27/2022] [Indexed: 11/06/2022]
Abstract
Identification of epitopes targeted following virus infection or vaccination can guide vaccine design and development of therapeutic interventions targeting functional sites, but can be laborious. Herein, we employed peptide microarrays to map linear peptide epitopes (LPEs) recognized following SARS-CoV-2 infection and vaccination. LPEs detected by nonhuman primate (NHP) and patient IgMs after SARS-CoV-2 infection extensively overlapped, localized to functionally important virus regions, and aligned with reported neutralizing antibody binding sites. Similar LPE overlap occurred after infection and vaccination, with LPE clusters specific to each stimulus, where strong and conserved LPEs mapping to sites known or likely to inhibit spike protein function. Vaccine-specific LPEs tended to map to sites known or likely to be affected by structural changes induced by the proline substitutions in the mRNA vaccine's S protein. Mapping LPEs to regions of known functional importance in this manner may accelerate vaccine evaluation and discovery of targets for site-specific therapeutic interventions.
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Affiliation(s)
- Li Yang
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Te Liang
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing 100083, China
| | - Lane M. Pierson
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Hongye Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jesse K. Fletcher
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Shu Wang
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Duran Bao
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Lili Zhang
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Zhen Huang
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Wenshu Zheng
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Xiaomei Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Heewon Park
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Yuwen Li
- Hayward Genetics Center, Department of Pediatrics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - James E. Robinson
- Department of Pediatrics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Amy K. Feehan
- Infectious Disease Department, Ochsner Clinic Foundation, New Orleans, LA 70121, USA
| | - Christopher J. Lyon
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Jing Cao
- University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Lisa A. Morici
- Department of Microbiology & Immunology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Chenzhong Li
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Chad J. Roy
- Department of Microbiology & Immunology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Division of Microbiology, Tulane National Primate Research Center, 18703 Three Rivers Road, Covington, LA 70433, USA
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Tony Hu
- Center for Cellular and Molecular Diagnostics, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
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Paris G, Heidepriem J, Tsouka A, Liu Y, Mattes DS, Pinzón Martín S, Dallabernardina P, Mende M, Lindner C, Wawrzinek R, Rademacher C, Seeberger PH, Breitling F, Bischoff FR, Wolf T, Loeffler FF. Automated Laser-Transfer Synthesis of High-Density Microarrays for Infectious Disease Screening. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2200359. [PMID: 35429012 DOI: 10.1002/adma.202200359] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Laser-induced forward transfer (LIFT) is a rapid laser-patterning technique for high-throughput combinatorial synthesis directly on glass slides. A lack of automation and precision limits LIFT applications to simple proof-of-concept syntheses of fewer than 100 compounds. Here, an automated synthesis instrument is reported that combines laser transfer and robotics for parallel synthesis in a microarray format with up to 10 000 individual reactions cm- 2 . An optimized pipeline for amide bond formation is the basis for preparing complex peptide microarrays with thousands of different sequences in high yield with high reproducibility. The resulting peptide arrays are of higher quality than commercial peptide arrays. More than 4800 15-residue peptides resembling the entire Ebola virus proteome on a microarray are synthesized to study the antibody response of an Ebola virus infection survivor. Known and unknown epitopes that serve now as a basis for Ebola diagnostic development are identified. The versatility and precision of the synthesizer is demonstrated by in situ synthesis of fluorescent molecules via Schiff base reaction and multi-step patterning of precisely definable amounts of fluorophores. This automated laser transfer synthesis approach opens new avenues for high-throughput chemical synthesis and biological screening.
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Affiliation(s)
- Grigori Paris
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
- Department of System Dynamics and Friction Physics, Institute of Mechanics, Technical University of Berlin, Str. des 17. Juni 135, 10623, Berlin, Germany
| | - Jasmin Heidepriem
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Alexandra Tsouka
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Yuxin Liu
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Daniela S Mattes
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafe, Germany
| | - Sandra Pinzón Martín
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Pietro Dallabernardina
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Marco Mende
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Celina Lindner
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Robert Wawrzinek
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
| | - Christoph Rademacher
- Department of Pharmaceutical Sciences, University of Vienna, Althanstr. 14, Vienna, 1090, Austria
- Department of Microbiology and Immunobiology, Max F. Perutz Laboratories GmbH, Dr.-Bohr-Gasse 9, Vienna, 1030, Austria
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Frank Breitling
- Institute of Microstructure Technology, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafe, Germany
| | - Frank Ralf Bischoff
- Department of Functional Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Timo Wolf
- Infectious Diseases Unit, Department of Medicine, Goethe University Hospital, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany
| | - Felix F Loeffler
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Muehlenberg 1, 14476, Potsdam, Germany
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Shome M, Chung Y, Chavan R, Park JG, Qiu J, LaBaer J. Serum autoantibodyome reveals that healthy individuals share common autoantibodies. Cell Rep 2022; 39:110873. [PMID: 35649350 PMCID: PMC9221390 DOI: 10.1016/j.celrep.2022.110873] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 03/02/2022] [Accepted: 05/04/2022] [Indexed: 12/02/2022] Open
Abstract
Autoantibodies are a hallmark of both autoimmune disease and cancer, but
they also occur in healthy individuals. Here, we perform a meta-analysis of nine
datasets and focus on the common autoantibodies shared by healthy individuals.
We report 77 common autoantibodies based on the protein microarray data obtained
from probing 182 healthy individual sera on 7,653 human proteins and an
additional 90 healthy individual sera on 1,666 human proteins. There is no
gender bias; however, the number of autoantibodies increase with age, plateauing
around adolescence. We use a bioinformatics pipeline to determine possible
molecular-mimicry peptides that can contribute to the elicitation of these
common autoantibodies. There is enrichment of intrinsic properties of proteins
like hydrophilicity, basicity, aromaticity, and flexibility for common
autoantigens. Subcellular localization and tissue-expression analysis reveal
that several common autoantigens are sequestered from the circulating
autoantibodies. Shome et al. performed a meta-analysis to discover the common
autoantibodies found in healthy individuals. These common autoantibodies appear
and increase during youth and plateau at adolescence. Bioinformatics techniques
demonstrate the potential role of molecular mimicry in their production as well
as several common intrinsic biochemical properties.
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Affiliation(s)
- Mahasish Shome
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Yunro Chung
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA; College of Health Solutions, Arizona State University, Phoenix, AZ, USA
| | - Ramani Chavan
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Jin G Park
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Ji Qiu
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Joshua LaBaer
- Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
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Mishra M, Zahra A, Chauhan LV, Thakkar R, Ng J, Joshi S, Spitzer ED, Marcos LA, Lipkin WI, Mishra N. A Short Series of Case Reports of COVID-19 in Immunocompromised Patients. Viruses 2022; 14:v14050934. [PMID: 35632677 PMCID: PMC9145915 DOI: 10.3390/v14050934] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/13/2022] [Accepted: 04/26/2022] [Indexed: 01/08/2023] Open
Abstract
Immunocompromised individuals are at risk of prolonged SARS-CoV-2 infection due to weaker immunity, co-morbidities, and lowered vaccine effectiveness, which may evolve highly mutated variants of SARS-CoV-2. Nonetheless, limited data are available on the immune responses elicited by SARS-CoV-2 infection, reinfections, and vaccinations with emerging variants in immunocompromised patients. We analyzed clinical samples that were opportunistically collected from eight immunocompromised individuals for mutations in SARS-CoV-2 genomes, neutralizing antibody (NAb) titers against different SARS-CoV-2 variants, and the identification of immunoreactive epitopes using a high-throughput coronavirus peptide array. The viral genome analysis revealed two SARS-CoV-2 variants (20A from a deceased patient and an Alpha variant from a recovered patient) with an eight amino-acid (aa) deletion within the N-terminal domain (NTD) of the surface glycoprotein. A higher NAb titer was present against the prototypic USA/WA1/2020 strain in vaccinated immunocompromised patients. NAb titer was absent against the Omicron variant and the cultured virus of the 20A variant with eight aa deletions in non-vaccinated patients. Our data suggest that fatal SARS-CoV-2 infections may occur in immunocompromised individuals even with high titers of NAb post-vaccination. Moreover, persistent SARS-CoV-2 infection may lead to the emergence of newer variants with additional mutations favoring the survival and fitness of the pathogen that include deletions in NAb binding sites in the SARS-CoV-2 surface glycoprotein.
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Affiliation(s)
- Mitali Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
| | - Aleena Zahra
- Division of Infectious Diseases, Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; (A.Z.); (E.D.S.); (L.A.M.)
| | - Lokendra V. Chauhan
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
| | - Riddhi Thakkar
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
| | - James Ng
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
| | - Shreyas Joshi
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
| | - Eric D. Spitzer
- Division of Infectious Diseases, Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; (A.Z.); (E.D.S.); (L.A.M.)
| | - Luis A. Marcos
- Division of Infectious Diseases, Department of Medicine, Stony Brook University, Stony Brook, NY 11794, USA; (A.Z.); (E.D.S.); (L.A.M.)
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
- Correspondence: (W.I.L.); (N.M.)
| | - Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA; (M.M.); (L.V.C.); (R.T.); (J.N.); (S.J.)
- Correspondence: (W.I.L.); (N.M.)
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43
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Koch BF. SARS-CoV-2 and human retroelements: a case for molecular mimicry? BMC Genom Data 2022; 23:27. [PMID: 35395708 PMCID: PMC8992427 DOI: 10.1186/s12863-022-01040-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/16/2022] [Indexed: 01/12/2023] Open
Abstract
Background The factors driving the late phase of COVID-19 are still poorly understood. However, autoimmunity is an evolving theme in COVID-19’s pathogenesis. Additionally, deregulation of human retroelements (RE) is found in many viral infections, and has also been reported in COVID-19. Results Unexpectedly, coronaviruses (CoV) – including SARS-CoV-2 – harbour many RE-identical sequences (up to 35 base pairs), and some of these sequences are part of SARS-CoV-2 epitopes associated to COVID-19 severity. Furthermore, RE are expressed in healthy controls and human cells and become deregulated after SARS-CoV-2 infection, showing mainly changes in long interspersed nuclear element (LINE1) expression, but also in endogenous retroviruses. Conclusion CoV and human RE share coding sequences, which are targeted by antibodies in COVID-19 and thus could induce an autoimmune loop by molecular mimicry. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01040-2.
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Affiliation(s)
- Benjamin Florian Koch
- Department of Internal Medicine, Nephrology, Goethe University Hospital, Johann Wolfgang Goethe University Frankfurt/Main, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.
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44
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Laurén I, Havervall S, Ng H, Lord M, Pettke A, Greilert‐Norin N, Gabrielsson L, Chourlia A, Amoêdo‐Leite C, Josyula VS, Eltahir M, Kerzeli I, Falk AJ, Hober J, Christ W, Wiberg A, Hedhammar M, Tegel H, Burman J, Xu F, Pin E, Månberg A, Klingström J, Christoffersson G, Hober S, Nilsson P, Philipson M, Dönnes P, Lindsay R, Thålin C, Mangsbo S. Long-term SARS-CoV-2-specific and cross-reactive cellular immune responses correlate with humoral responses, disease severity, and symptomatology. Immun Inflamm Dis 2022; 10:e595. [PMID: 35349756 PMCID: PMC8962644 DOI: 10.1002/iid3.595] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 01/28/2022] [Accepted: 02/01/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Cellular immune memory responses post coronavirus disease 2019 (COVID-19) have been difficult to assess due to the risks of contaminating the immune response readout with memory responses stemming from previous exposure to endemic coronaviruses. The work herein presents a large-scale long-term follow-up study investigating the correlation between symptomology and cellular immune responses four to five months post seroconversion based on a unique severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific peptide pool that contains no overlapping peptides with endemic human coronaviruses. METHODS Peptide stimulated memory T cell responses were assessed with dual interferon-gamma (IFNγ) and interleukin (IL)-2 Fluorospot. Serological analyses were performed using a multiplex antigen bead array. RESULTS Our work demonstrates that long-term SARS-CoV-2-specific memory T cell responses feature dual IFNγ and IL-2 responses, whereas cross-reactive memory T cell responses primarily generate IFNγ in response to SARS-CoV-2 peptide stimulation. T cell responses correlated to long-term humoral immune responses. Disease severity as well as specific COVID-19 symptoms correlated with the magnitude of the SARS-CoV-2-specific memory T cell response four to five months post seroconversion. CONCLUSION Using a large cohort and a SARS-CoV-2-specific peptide pool we were able to substantiate that initial disease severity and symptoms correlate with the magnitude of the SARS-CoV-2-specific memory T cell responses.
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Affiliation(s)
- Ida Laurén
- Department of Pharmacy, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Sebastian Havervall
- Department of Clinical SciencesKarolinska Institute, Danderyd HospitalStockholmSweden
| | - Henry Ng
- Department of Medical Cell Biology, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Martin Lord
- Department of Pharmacy, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | | | - Nina Greilert‐Norin
- Department of Clinical SciencesKarolinska Institute, Danderyd HospitalStockholmSweden
| | - Lena Gabrielsson
- Department of Clinical SciencesKarolinska Institute, Danderyd HospitalStockholmSweden
| | - Aikaterini Chourlia
- Department of Pharmacy, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Catarina Amoêdo‐Leite
- Department of Medical Cell Biology, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Vijay S. Josyula
- Department of Medical Cell Biology, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Mohamed Eltahir
- Department of Pharmacy, Science for Life LaboratoryUppsala UniversityUppsalaSweden
- Department of Immunology, Genetics, and PathologyUppsala UniversityUppsalaSweden
| | - Iliana Kerzeli
- Department of Pharmacy, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - August J. Falk
- Division of Affinity Proteomics, Department of Protein ScienceKTH Royal Institute of Technology, Science for Life LaboratoryStockholmSweden
| | - Jonathan Hober
- Department of Clinical SciencesKarolinska Institute, Danderyd HospitalStockholmSweden
| | - Wanda Christ
- Department of Medicine HuddingeKarolinska Institute, Centre for Infectious MedicineStockholmSweden
| | - Anna Wiberg
- Department of Immunology, Genetics, and PathologyUppsala UniversityUppsalaSweden
| | - My Hedhammar
- Division of Protein Technology, Department of Protein ScienceKTH Royal Institute of TechnologyStockholmSweden
| | - Hanna Tegel
- Division of Protein Technology, Department of Protein ScienceKTH Royal Institute of TechnologyStockholmSweden
| | - Joachim Burman
- Department of NeuroscienceUppsala UniversityUppsalaSweden
| | - Feifei Xu
- Department of Medical Cell Biology, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Elisa Pin
- Division of Affinity Proteomics, Department of Protein ScienceKTH Royal Institute of Technology, Science for Life LaboratoryStockholmSweden
| | - Anna Månberg
- Division of Affinity Proteomics, Department of Protein ScienceKTH Royal Institute of Technology, Science for Life LaboratoryStockholmSweden
| | - Jonas Klingström
- Department of Medicine HuddingeKarolinska Institute, Centre for Infectious MedicineStockholmSweden
| | - Gustaf Christoffersson
- Department of Medical Cell Biology, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Sophia Hober
- Division of Protein Technology, Department of Protein ScienceKTH Royal Institute of TechnologyStockholmSweden
| | - Peter Nilsson
- Division of Affinity Proteomics, Department of Protein ScienceKTH Royal Institute of Technology, Science for Life LaboratoryStockholmSweden
| | - Mia Philipson
- Department of Medical Cell Biology, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | | | - Robin Lindsay
- Department of Medical Cell Biology, Science for Life LaboratoryUppsala UniversityUppsalaSweden
| | - Charlotte Thålin
- Department of Clinical SciencesKarolinska Institute, Danderyd HospitalStockholmSweden
| | - Sara Mangsbo
- Department of Pharmacy, Science for Life LaboratoryUppsala UniversityUppsalaSweden
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Resemblance-Ranking Peptide Library to Screen for Binders to Antibodies on a Peptidomic Scale. Int J Mol Sci 2022; 23:ijms23073515. [PMID: 35408876 PMCID: PMC8999133 DOI: 10.3390/ijms23073515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 02/04/2023] Open
Abstract
A novel resemblance-ranking peptide library with 160,000 10-meric peptides was designed to search for selective binders to antibodies. The resemblance-ranking principle enabled the selection of sequences that are most similar to the human peptidome. The library was synthesized with ultra-high-density peptide arrays. As proof of principle, screens for selective binders were performed for the therapeutic anti-CD20 antibody rituximab. Several features in the amino acid composition of antibody-binding peptides were identified. The selective affinity of rituximab increased with an increase in the number of hydrophobic amino acids in a peptide, mainly tryptophan and phenylalanine, while a total charge of the peptide remained relatively small. Peptides with a higher affinity exhibited a lower sum helix propensity. For the 30 strongest peptide binders, a substitutional analysis was performed to determine dissociation constants and the invariant amino acids for binding to rituximab. The strongest selective peptides had a dissociation constant in the hundreds of the nano-molar range. The substitutional analysis revealed a specific hydrophobic epitope for rituximab. To show that conformational binders can, in principle, be detected in array format, cyclic peptide substitutions that are similar to the target of rituximab were investigated. Since the specific binders selected via the resemblance-ranking peptide library were based on the hydrophobic interactions that are widespread in the world of biomolecules, the library can be used to screen for potential linear epitopes that may provide information about the cross-reactivity of antibodies.
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Spencer Mangum D, Caywood E. A clinician’s guide to HLA matching in allogeneic hematopoietic stem cell transplant. Hum Immunol 2022; 83:687-694. [DOI: 10.1016/j.humimm.2022.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 02/14/2022] [Accepted: 03/02/2022] [Indexed: 12/26/2022]
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Suraritdechachai S, Lakkanasirorat B, Uttamapinant C. Molecular probes for cellular imaging of post-translational proteoforms. RSC Chem Biol 2022; 3:201-219. [PMID: 35360891 PMCID: PMC8826509 DOI: 10.1039/d1cb00190f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 01/04/2022] [Indexed: 12/29/2022] Open
Abstract
Specific post-translational modification (PTM) states of a protein affect its property and function; understanding their dynamics in cells would provide deep insight into diverse signaling pathways and biological processes. However, it is not trivial to visualize post-translational modifications in a protein- and site-specific manner, especially in a living-cell context. Herein, we review recent advances in the development of molecular imaging tools to detect diverse classes of post-translational proteoforms in individual cells, and their applications in studying precise roles of PTMs in regulating the function of cellular proteins.
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Affiliation(s)
- Surased Suraritdechachai
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| | - Benya Lakkanasirorat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
| | - Chayasith Uttamapinant
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC) Rayong Thailand
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48
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Anasir MI, Poh CL. Discovery of B-cell epitopes for development of dengue vaccines and antibody therapeutics. Med Microbiol Immunol 2022; 211:1-18. [PMID: 35059822 DOI: 10.1007/s00430-021-00726-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/04/2021] [Indexed: 10/19/2022]
Abstract
Dengue is one of the most frequently transmitted viral infections globally which creates a serious burden to the healthcare system in many countries in the tropical and subtropical regions. To date, no vaccine has demonstrated balanced protection against the four dengue serotypes. Dengvaxia as the only vaccine that has been licensed for use in endemic areas has shown an increased risk in dengue-naïve vaccines to develop severe dengue. A crucial element in protection from dengue infection is the neutralizing antibody responses. Therefore, the identification of protective linear B-cell epitopes can guide vaccine design and facilitate the development of monoclonal antibodies as dengue therapeutics. This review summarizes the identification of dengue B-cell epitopes within the envelope (E) protein of dengue that can be incorporated into peptide vaccine constructs. These epitopes have been identified through approaches such as bioinformatics, three-dimensional structure analysis of antibody-dengue complexes, mutagenesis/alanine scanning and escape mutant studies. Additionally, the therapeutic potential of monoclonal antibodies targeting the E protein of dengue is reviewed. This can provide a basis for the design of future dengue therapies.
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Affiliation(s)
- Mohd Ishtiaq Anasir
- Virology Unit, Infectious Disease Research Centre, Institute for Medical Research, National Institutes of Health, Setia Alam, Shah Alam, Selangor, Malaysia
- Centre for Virus and Vaccine Research, Sunway University, 5, Jalan Universiti, 47500, Bandar Sunway, Selangor, Malaysia
| | - Chit Laa Poh
- Centre for Virus and Vaccine Research, Sunway University, 5, Jalan Universiti, 47500, Bandar Sunway, Selangor, Malaysia.
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Polymorphisms in Cha o 1 and Cha o 2, major allergens of Japanese cypress (Chamaecyparis obtusa) pollen from a restricted region in Japan. PLoS One 2021; 16:e0261327. [PMID: 34962964 PMCID: PMC8714102 DOI: 10.1371/journal.pone.0261327] [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: 02/28/2021] [Accepted: 11/29/2021] [Indexed: 11/19/2022] Open
Abstract
Japanese cedar pollinosis is a major seasonal allergy in Japan, and Japanese cypress pollinosis is a growing concern because the cypress pollen season follows the cedar pollen season and cross-reactivity among allergens occurs between these closely related species. Allergens purified from pollen under unspecified collecting conditions can potentially heterogenous allergens profiles and batch to batch variability, and amino acid sequence variants in allergens possibly exist among trees. Polymorphisms have not been investigated for the cypress pollen major allergens, Cha o 1 and Cha o 2. Our aim was to examine the homogeneity of allergen amino acid sequences. DNA sequences of Cha o 1 and Cha o 2 from pollen collected from Chiba and Ibaraki prefectures and from needles of 47 plus trees located at seed orchards in Chiba Prefecture were examined by amplicon sequencing and amino acid substitutions were deduced. Sequence analysis of the pollen samples revealed that eight and seven residues of Cha o 2 were polymorphic, respectively. Thirteen residues in Cha o 2, including those residues identified in pollen, were deduced to be polymorphic for the plus trees. Cha o 2 expressed by the 47 plus trees included amino acid differences when compared with that of isoallergen Cha o 2.0101. No substitution was deduced in Cha o 1 for pollen taken from the two prefectures. One conservative amino acid substitution was deduced in Cha o 1 for the plus trees. Of the 47 plus trees examined, 38 were deduced to express only the isoallergen Cha o 1.0101 isoform, whereas eight trees were heterozygous and a single tree was homozygous for the non-synonymous mutation, which indicates relative uniformity of Cha o 1. Cha o 2 was found to be a heterogeneous allergen which suggests that studies using pollen from different trees may not give the same results.
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50
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Sheff JG, Kelly JF, Robotham A, Sulea T, Malenfant F, L'Abbé D, Duchesne M, Pelletier A, Lefebvre J, Acel A, Parat M, Gosselin M, Wu C, Fortin Y, Baardsnes J, Van Faassen H, Awrey S, Chafe SC, McDonald PC, Dedhar S, Lenferink AEG. Hydrogen-deuterium exchange mass spectrometry reveals three unique binding responses of mAbs directed to the catalytic domain of hCAIX. MAbs 2021; 13:1997072. [PMID: 34812124 PMCID: PMC8632303 DOI: 10.1080/19420862.2021.1997072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Human carbonic anhydrase (hCAIX), an extracellular enzyme that catalyzes the reversible hydration of CO2, is often overexpressed in solid tumors. This enzyme is instrumental in maintaining the survival of cancer cells in a hypoxic and acidic tumor microenvironment. Absent in most normal tissues, hCAIX is a promising therapeutic target for detection and treatment of solid tumors. Screening of a library of anti-hCAIX monoclonal antibodies (mAbs) previously identified three therapeutic candidates (mAb c2C7, m4A2 and m9B6) with distinct biophysical and functional characteristics. Selective binding to the catalytic domain was confirmed by yeast surface display and isothermal calorimetry, and deeper insight into the dynamic binding profiles of these mAbs upon binding were highlighted by bottom-up hydrogen-deuterium exchange mass spectrometry (HDX-MS). Here, a conformational and allosterically silent epitope was identified for the antibody-drug conjugate candidate c2C7. Unique binding profiles are described for both inhibitory antibodies, m4A2 and m9B6. M4A2 reduces the ability of the enzyme to hydrate CO2 by steric gating at the entrance of the catalytic cavity. Conversely, m9B6 disrupts the secondary structure that is necessary for substrate binding and hydration. The synergy of these two inhibitory mechanisms is demonstrated in in vitro activity assays and HDX-MS. Finally, the ability of m4A2 to modulate extracellular pH and intracellular metabolism is reported. By highlighting three unique modes by which hCAIX can be targeted, this study demonstrates both the utility of HDX-MS as an important tool in the characterization of anti-cancer biotherapeutics, and the underlying value of CAIX as a therapeutic target.
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Affiliation(s)
- Joey G Sheff
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - John F Kelly
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Anna Robotham
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Félix Malenfant
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Denis L'Abbé
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Mélanie Duchesne
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Alex Pelletier
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Jean Lefebvre
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Andrea Acel
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Marie Parat
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Mylene Gosselin
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Cunle Wu
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Yves Fortin
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Jason Baardsnes
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
| | - Henk Van Faassen
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, Ontario, Canada
| | - Shannon Awrey
- Department of Integrative Oncology, Bc Cancer Research Institute, Vancouver, BC, Canada
| | - Shawn C Chafe
- Department of Integrative Oncology, Bc Cancer Research Institute, Vancouver, BC, Canada
| | - Paul C McDonald
- Department of Integrative Oncology, Bc Cancer Research Institute, Vancouver, BC, Canada
| | - Shoukat Dedhar
- Department of Integrative Oncology, Bc Cancer Research Institute, Vancouver, BC, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada
| | - Anne E G Lenferink
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, Quebec, Canada
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