1
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Iaculli D, Ballet S. Discovery of Bioactive Peptides Through Peptide Scanning. J Pept Sci 2025; 31:e70029. [PMID: 40347116 DOI: 10.1002/psc.70029] [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: 02/27/2025] [Revised: 04/25/2025] [Accepted: 04/30/2025] [Indexed: 05/12/2025]
Abstract
Therapeutic peptides targeted at various diseases are becoming increasingly relevant for the pharmaceutical industry. Several of these drugs were originally designed by mimicking a segment of a protein of interest. As such, protein mimicry represents a promising strategy both in immunology, for the identification of B- and T-cell epitopes, as well as for the modulation of protein activity, including the disruption of protein-protein interactions (PPIs) and the interference with biological or pathological cellular functions. Several methods have been developed to pinpoint the (binding) epitopes of a protein or the regions responsible for biological activity. One of such strategies is the scanning of the protein or selected domains with synthetic overlapping peptides. As the mechanism of action of a mimetic peptide can be similar to that of the whole protein, this method offers a powerful tool for the investigation of protein function, along with providing a solid basis for the development of therapeutic candidates. This review gives a general overview of different applications of the peptide scanning methodology, describing a comparison of the preparation and use of solid-phase libraries (peptide arrays) with isolated peptide libraries and highlighting their strengths and most common applications.
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Affiliation(s)
- Debora Iaculli
- Research Group of Organic Chemistry, Departments of Chemistry and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Departments of Chemistry and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
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2
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Fernández de Santaella J, Koch NG, Widmer L, Nash MA. Amber Codon Mutational Scanning and Bioorthogonal PEGylation for Epitope Mapping of Antibody Binding Sites on Human Arginase-1. ACS Chem Biol 2025; 20:791-801. [PMID: 40168364 DOI: 10.1021/acschembio.4c00692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2025]
Abstract
Epitope mapping is crucial for understanding immunological responses to protein therapeutics. Here, we combined genetic code expansion and bacterial surface display to incorporate S-allylcysteine (SAC) into human arginase-1 (hArg1) via Methanococcoides burtonii pyrrolysyl-tRNA synthetase. Using an amber codon deep mutational scanning and sequencing workflow, we mapped SAC incorporation efficiency across the hArg1 sequence, providing insights into structural and sequence dependencies of noncanonical amino acid incorporation. We used mutually bioorthogonal allyl/tetrazine and azide/DBCO chemistries to achieve site-specific PEGylation and fluorescent labeling of hArg1, revealing insights into SAC side chain reactivity and solvent accessibility of residues in hArg1. This system was further applied to determine the binding epitope of a monoclonal antibody on the surface of hArg1, providing high-resolution data on the impact of PEGylation residue position on antibody binding. Our method produces high dimensional data of noncanonical amino acid incorporation efficiency, site-specific functionalization enabled by mutually bioorthogonal chemistries, and epitope mapping of therapeutic proteins.
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Affiliation(s)
- Jaime Fernández de Santaella
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4056 Basel, Switzerland
- National Center for Competence in Research (NCCR), Molecular Systems Engineering, 4058 Basel, Switzerland
| | - Nikolaj G Koch
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4056 Basel, Switzerland
| | - Lorenz Widmer
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4056 Basel, Switzerland
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4056 Basel, Switzerland
- National Center for Competence in Research (NCCR), Molecular Systems Engineering, 4058 Basel, Switzerland
- Swiss Nanoscience Institute, 4056 Basel, Switzerland
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3
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Wang Y, Gulati N, Regeenes R, Migliorini A, Oakie A, Nostro MC, Rocheleau JV. Modulating the Kinetics of a Fluorescence Anisotropy Immunoassay Using Tracer Point Mutations to Measure Human C-Peptide Secretion On-Chip. ACS OMEGA 2025; 10:11595-11606. [PMID: 40160725 PMCID: PMC11947798 DOI: 10.1021/acsomega.5c00761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2025] [Revised: 02/24/2025] [Accepted: 02/28/2025] [Indexed: 04/02/2025]
Abstract
Fluorescence anisotropy immunoassays (FAIAs) are widely used to quantify the concentration of target proteins based on competitive binding to a monoclonal antibody with a tracer. We recently designed an FAIA to measure mouse C-peptide secretion from living islets in a continuous-flow microfluidic device (InsC-chip). To develop a similar assay for human C-peptide, we selected two monoclonal antibodies (Ab1 and Ab2) that initially showed a low dynamic range and slow kinetics. One option to measure this assay on-chip was to extend the length of the mixing channels. However, this strategy would increase dispersion and ultimately lower the temporal resolution of secreted C-peptide. To shorten the time-to-reach equilibrium for Ab1, we reengineered the tracer based on a comparison between the human and mouse C-peptide sequences, resulting in >30-fold shorter time-to-reach equilibrium. To increase the relatively small dynamic range for Ab2, we used partial epitope mapping and targeted point mutations to increase the dynamic range by 45%. Finally, we validated both FAIAs by measuring depolarization-induced secretion from individual human stem cell-derived islets in our InsC-chip. These data demonstrate a strategy to optimize FAIA kinetics to be measured in continuous-flow microfluidic devices.
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Affiliation(s)
- Yufeng Wang
- Advanced
Diagnostics, Toronto General Hospital Research
Institute, Toronto M5G 1L7, Canada
- Institute
of Biomedical Engineering, University of
Toronto, Toronto M5S 3G9, Canada
| | - Nitya Gulati
- Advanced
Diagnostics, Toronto General Hospital Research
Institute, Toronto M5G 1L7, Canada
- Institute
of Biomedical Engineering, University of
Toronto, Toronto M5S 3G9, Canada
| | - Romario Regeenes
- Advanced
Diagnostics, Toronto General Hospital Research
Institute, Toronto M5G 1L7, Canada
- Institute
of Biomedical Engineering, University of
Toronto, Toronto M5S 3G9, Canada
| | - Adriana Migliorini
- McEwen
Stem Cell Institute, University Health Network, Toronto M5G 1L7, Canada
| | - Amanda Oakie
- McEwen
Stem Cell Institute, University Health Network, Toronto M5G 1L7, Canada
| | - Maria Cristina Nostro
- McEwen
Stem Cell Institute, University Health Network, Toronto M5G 1L7, Canada
- Departments
of Medicine and Physiology, University of
Toronto, Toronto M5S 1A8, Canada
| | - Jonathan V. Rocheleau
- Advanced
Diagnostics, Toronto General Hospital Research
Institute, Toronto M5G 1L7, Canada
- Institute
of Biomedical Engineering, University of
Toronto, Toronto M5S 3G9, Canada
- Departments
of Medicine and Physiology, University of
Toronto, Toronto M5S 1A8, Canada
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4
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Scalsky R, Dwivedi A, Stabler TC, Mbambo G, Ouattara A, Lyke KE, Takala-Harrison S, Silva JC. Whole-genome sieve analysis: Identification of protective malaria antigens by leveraging allele-specific vaccine efficacy. Vaccine 2025; 50:126783. [PMID: 39923546 DOI: 10.1016/j.vaccine.2025.126783] [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: 05/06/2024] [Revised: 01/18/2025] [Accepted: 01/21/2025] [Indexed: 02/11/2025]
Abstract
Discovery of new protective malaria antigens will enable the development of novel vaccine formulations with potentially higher efficacy. While several high-throughput experimental approaches enable the identification of novel immunogens, none so far has been designed to selectively identify protective antigens. Here, we propose that sieve analysis conducted on the whole genome (SAWG) can be used specifically for this purpose. We review available medium- to high-throughput methods for antigen identification and contextualize the need for the identification of protective antigens. We then provide the rationale for why SAWG is ideally suited for the identification of protective antigens in recombining pathogens with large genome size, describe conditions for optimal use, and discuss potential pitfalls. Most importantly, this approach can be applied to the discovery of new protective targets in any recombining organism for which there is a whole organism-based vaccine that can be safely deployed in a disease-endemic region.
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Affiliation(s)
- Ryan Scalsky
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
| | - Ankit Dwivedi
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Thomas C Stabler
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Gillian Mbambo
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA
| | - Amed Ouattara
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, USA
| | - Kirsten E Lyke
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, USA
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, USA
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, USA; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA; Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (NOVA), Lisbon, Portugal.
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5
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Kotliar IB, Bendes A, Dahl L, Chen Y, Saarinen M, Ceraudo E, Dodig-Crnković T, Uhlén M, Svenningsson P, Schwenk JM, Sakmar TP. Multiplexed mapping of the interactome of GPCRs with receptor activity-modifying proteins. SCIENCE ADVANCES 2024; 10:eado9959. [PMID: 39083597 PMCID: PMC11290489 DOI: 10.1126/sciadv.ado9959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/25/2024] [Indexed: 08/02/2024]
Abstract
Receptor activity-modifying proteins (RAMPs) form complexes with G protein-coupled receptors (GPCRs) and may regulate their cellular trafficking and pharmacology. RAMP interactions have been identified for about 50 GPCRs, but only a few GPCR-RAMP complexes have been studied in detail. To elucidate a comprehensive GPCR-RAMP interactome, we created a library of 215 dual epitope-tagged (DuET) GPCRs representing all GPCR subfamilies and coexpressed each GPCR with each of the three RAMPs. Screening the GPCR-RAMP pairs with customized multiplexed suspension bead array (SBA) immunoassays, we identified 122 GPCRs that showed strong evidence for interaction with at least one RAMP. We screened for interactions in three cell lines and found 23 endogenously expressed GPCRs that formed complexes with RAMPs. Mapping the GPCR-RAMP interactome expands the current system-wide functional characterization of RAMP-interacting GPCRs to inform the design of selective therapeutics targeting GPCR-RAMP complexes.
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Affiliation(s)
- Ilana B. Kotliar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Annika Bendes
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Leo Dahl
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Yuanhuang Chen
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Marcus Saarinen
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Emilie Ceraudo
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY, USA
| | - Tea Dodig-Crnković
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Per Svenningsson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Basal and Clinical Neuroscience, King’s College London, London, UK
| | - Jochen M. Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Solna, Sweden
| | - Thomas P. Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, NY, USA
- Department of Neurobiology, Care Sciences and Society, Section for Neurogeriatrics, Karolinska Institutet, Solna, Sweden
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6
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Grauslund LR, Ständer S, Veggi D, Andreano E, Rand KD, Norais N. Epitope Mapping of Human Polyclonal Antibodies to the fHbp Antigen of a Neisseria Meningitidis Vaccine by Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS). Mol Cell Proteomics 2024; 23:100734. [PMID: 38342408 PMCID: PMC10959699 DOI: 10.1016/j.mcpro.2024.100734] [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: 11/02/2022] [Revised: 12/22/2023] [Accepted: 02/08/2024] [Indexed: 02/13/2024] Open
Abstract
Antigen-antibody interactions play a key role in the immune response post vaccination and the mechanism of action of antibody-based biopharmaceuticals. 4CMenB is a multicomponent vaccine against Neisseria meningitidis serogroup B in which factor H binding protein (fHbp) is one of the key antigens. In this study, we use hydrogen/deuterium exchange mass spectrometry (HDX-MS) to identify epitopes in fHbp recognized by polyclonal antibodies (pAb) from two human donors (HDs) vaccinated with 4CMenB. Our HDX-MS data reveal several epitopes recognized by the complex mixture of human pAb. Furthermore, we show that the pAb from the two HDs recognize the same epitope regions. Epitope mapping of total pAb and purified fHbp-specific pAb from the same HD reveals that the two antibody samples recognize the same main epitopes, showing that HDX-MS based epitope mapping can, in this case at least, be performed directly using total IgG pAb samples that have not undergone Ab-selective purification. Two monoclonal antibodies (mAb) were previously produced from B-cell repertoire sequences from one of the HDs and used for epitope mapping of fHbp with HDX-MS. The epitopes identified for the pAb from the same HD in this study, overlap with the epitopes recognized by the two individual mAbs. Overall, HDX-MS epitope mapping appears highly suitable for simultaneous identification of epitopes recognized by pAb from human donors and to thus both guide vaccine development and study basic human immunity to pathogens, including viruses.
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Affiliation(s)
- Laura R Grauslund
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark; GSK Vaccines, GSK, Siena, Italy
| | - Susanne Ständer
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark; GSK Vaccines, GSK, Siena, Italy
| | | | - Emanuele Andreano
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark.
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7
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Murtas C, Bruschi M, Spinelli S, Kajana X, Verrina EE, Angeletti A, Caridi G, Candiano G, Feriozzi S, Prunotto M, Ghiggeri GM. Novel biomarkers and pathophysiology of membranous nephropathy: PLA2R and beyond. Clin Kidney J 2024; 17:sfad228. [PMID: 38213493 PMCID: PMC10783244 DOI: 10.1093/ckj/sfad228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Indexed: 01/13/2024] Open
Abstract
Research on membranous nephropathy truly exploded in the last 15 years. This happened because of the application of new techniques (laser capture microdissection, mass spectrometry, protein G immunoprecipitation, arrays) to the study of its pathogenesis. After the discovery of PLA2R as the major target antigen, many other antigens were identified and others are probably ongoing. Clinical and pathophysiology rebounds of new discoveries are relevant in terms of diagnosis and prognosis and it is time to make a first assessment of the innovative issues. In terms of classification, target antigens can be divided into: 'membrane antigens' and 'second wave' antigens. The first group consists of antigens constitutionally expressed on the podocyte membrane (as PLA2R) that may become a target of an autoimmune process because of perturbation of immune-tolerance. 'Second wave' antigens are antigens neo-expressed by the podocyte or by infiltrating cells after a stressing event: this allows the immune system to produce antibodies against them that intensify and maintain glomerular damage. With this abundance of target antigens it is not possible, at the moment, to test all antibodies at the bedside. In the absence of this possibility, the role of histological evaluation is still irreplaceable.
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Affiliation(s)
- Corrado Murtas
- Nephrology and Dialysis Unit, Ospedale Belcolle, ASL Viterbo, Viterbo, Italy
| | - Maurizio Bruschi
- Department of Experimental Medicine (DIMES) University of Genoa, Italy
- Nephrology, Dialysis and Transplantation Unit, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Sonia Spinelli
- Nephrology, Dialysis and Transplantation Unit, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Xhuliana Kajana
- Nephrology, Dialysis and Transplantation Unit, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Enrico E Verrina
- Nephrology, Dialysis and Transplantation Unit, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Andrea Angeletti
- Nephrology, Dialysis and Transplantation Unit, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Gianluca Caridi
- Nephrology, Dialysis and Transplantation Unit, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Giovanni Candiano
- Nephrology, Dialysis and Transplantation Unit, IRCCS Istituto Giannina Gaslini, Genova, Italy
| | - Sandro Feriozzi
- Nephrology and Dialysis Unit, Ospedale Belcolle, ASL Viterbo, Viterbo, Italy
| | - Marco Prunotto
- Institute of Pharmaceutical Sciences of Western Switzerland, School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Gian Marco Ghiggeri
- Nephrology, Dialysis and Transplantation Unit, IRCCS Istituto Giannina Gaslini, Genova, Italy
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8
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Röwer C, Olaleye OO, Bischoff R, Glocker MO. Mass Spectrometric ITEM-ONE and ITEM-TWO Analyses Confirm and Refine an Assembled Epitope of an Anti-Pertuzumab Affimer. Biomolecules 2023; 14:24. [PMID: 38254624 PMCID: PMC10813730 DOI: 10.3390/biom14010024] [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: 10/18/2023] [Revised: 12/13/2023] [Accepted: 12/21/2023] [Indexed: 01/24/2024] Open
Abstract
Intact Transition Epitope Mapping-One-step Non-covalent force Exploitation (ITEM-ONE) analysis reveals an assembled epitope on the surface of Pertuzumab, which is recognized by the anti-Pertuzumab affimer 00557_709097. It encompasses amino acid residues NSGGSIYNQRFKGR, which are part of CDR2, as well as residues FTLSVDR, which are located on the variable region of Pertuzumab's heavy chain and together form a surface area of 1381.46 Å2. Despite not being part of Pertuzumab's CDR2, the partial sequence FTLSVDR marks a unique proteotypic Pertuzumab peptide. Binding between intact Pertuzumab and the anti-Pertuzumab affimer was further investigated using the Intact Transition Epitope Mapping-Thermodynamic Weak-force Order (ITEM-TWO) approach. Quantitative analysis of the complex dissociation reaction in the gas phase afforded a quasi-equilibrium constant (KD m0g#) of 3.07 × 10-12. The experimentally determined apparent enthalpy (ΔHm0g#) and apparent free energy (ΔGm0g#) of the complex dissociation reaction indicate that the opposite reaction-complex formation-is spontaneous at room temperature. Due to strong binding to Pertuzumab and because of recognizing Pertuzumab's unique partial amino acid sequences, the anti-Pertuzumab affimer 00557_709097 is considered excellently suitable for implementation in Pertuzumab quantitation assays as well as for the accurate therapeutic drug monitoring of Pertuzumab in biological fluids.
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Affiliation(s)
- Claudia Röwer
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, 18057 Rostock, Germany
| | - Oladapo O. Olaleye
- Department of Analytical Biochemistry, Faculty of Science & Engineering, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, Faculty of Science & Engineering, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Michael O. Glocker
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, 18057 Rostock, Germany
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9
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Kotliar IB, Bendes A, Dahl L, Chen Y, Saarinen M, Ceraudo E, Dodig-Crnković T, Uhle’n M, Svenningsson P, Schwenk JM, Sakmar TP. Expanding the GPCR-RAMP interactome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568247. [PMID: 38045268 PMCID: PMC10690247 DOI: 10.1101/2023.11.22.568247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Receptor activity-modifying proteins (RAMPs) can form complexes with G protein-coupled receptors (GPCRs) and regulate their cellular trafficking and pharmacology. RAMP interactions have been identified for about 50 GPCRs, but only a few GPCR-RAMP complexes have been studied in detail. To elucidate a complete interactome between GPCRs and the three RAMPs, we developed a customized library of 215 Dual Epitope-Tagged (DuET) GPCRs representing all GPCR subfamilies. Using a multiplexed suspension bead array (SBA) assay, we identified 122 GPCRs that showed strong evidence for interaction with at least one RAMP. We screened for native interactions in three cell lines and found 23 GPCRs that formed complexes with RAMPs. Mapping the GPCR-RAMP interactome expands the current system-wide functional characterization of RAMP-interacting GPCRs to inform the design of selective GPCR-targeted therapeutics.
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Affiliation(s)
- Ilana B. Kotliar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University; 1230 York Ave., New York, 10065, USA
| | - Annika Bendes
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology; Solna, 171 65, Sweden
| | - Leo Dahl
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology; Solna, 171 65, Sweden
| | - Yuanhuang Chen
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University; 1230 York Ave., New York, 10065, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY 10065, USA
| | - Marcus Saarinen
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Emilie Ceraudo
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University; 1230 York Ave., New York, 10065, USA
| | - Tea Dodig-Crnković
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology; Solna, 171 65, Sweden
| | - Mathias Uhle’n
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology; Solna, 171 65, Sweden
| | - Per Svenningsson
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Basal and Clinical Neuroscience, King’s College London, London, UK
| | - Jochen M. Schwenk
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology; Solna, 171 65, Sweden
| | - Thomas P. Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University; 1230 York Ave., New York, 10065, USA
- Department of Neurobiology, Care Sciences and Society, Section for Neurogeriatrics, Karolinska Institutet; Solna, 171 64, Sweden
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10
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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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11
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Tewey MA, Coulibaly D, Lawton JG, Stucke EM, Zhou AE, Berry AA, Bailey JA, Pike A, Dara A, Ouattara A, Lyke KE, Ifeonu O, Laurens MB, Adams M, Takala-Harrison S, Niangaly A, Kouriba B, Koné AK, Rowe JA, Doumbo OK, Patel JJ, Tan JC, Felgner PL, Plowe CV, Thera MA, Travassos MA. Natural immunity to malaria preferentially targets the endothelial protein C receptor-binding regions of PfEMP1s. mSphere 2023; 8:e0045123. [PMID: 37791774 PMCID: PMC10597466 DOI: 10.1128/msphere.00451-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 10/05/2023] Open
Abstract
Antibody responses to variant surface antigens (VSAs) produced by the malaria parasite Plasmodium falciparum may contribute to age-related natural immunity to severe malaria. One VSA family, P. falciparum erythrocyte membrane protein-1 (PfEMP1), includes a subset of proteins that binds endothelial protein C receptor (EPCR) in human hosts and potentially disrupts the regulation of inflammatory responses, which may lead to the development of severe malaria. We probed peptide microarrays containing segments spanning five PfEMP1 EPCR-binding domain variants with sera from 10 Malian adults and 10 children to determine the differences between adult and pediatric immune responses. We defined serorecognized peptides and amino acid residues as those that elicited a significantly higher antibody response than malaria-naïve controls. We aimed to identify regions consistently serorecognized among adults but not among children across PfEMP1 variants, potentially indicating regions that drive the development of immunity to severe malaria. Adult sera consistently demonstrated broader and more intense serologic responses to constitutive PfEMP1 peptides than pediatric sera, including peptides in EPCR-binding domains. Both adults and children serorecognized a significantly higher proportion of EPCR-binding peptides than peptides that do not directly participate in receptor binding, indicating a preferential development of serologic responses at functional residues. Over the course of a single malaria transmission season, pediatric serological responses increased between the start and the peak of the season, but waned as the transmission season ended. IMPORTANCE Severe malaria and death related to malaria disproportionately affect sub-Saharan children under 5 years of age, commonly manifesting as cerebral malaria and/or severe malarial anemia. In contrast, adults in malaria-endemic regions tend to experience asymptomatic or mild disease. Our findings indicate that natural immunity to malaria targets specific regions within the EPCR-binding domain, particularly peptides containing EPCR-binding residues. Epitopes containing these residues may be promising targets for vaccines or therapeutics directed against severe malaria. Our approach provides insight into the development of natural immunity to a binding target linked to severe malaria by characterizing an "adult-like" response as recognizing a proportion of epitopes within the PfEMP1 protein, particularly regions that mediate EPCR binding. This "adult-like" response likely requires multiple years of malaria exposure, as increases in pediatric serologic response over a single malaria transmission season do not appear significant.
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Affiliation(s)
- Madison A. Tewey
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Drissa Coulibaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Jonathan G. Lawton
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Emily M. Stucke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Albert E. Zhou
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Andrea A. Berry
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jason A. Bailey
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Andrew Pike
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Antoine Dara
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Amed Ouattara
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kirsten E. Lyke
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Olukemi Ifeonu
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Matthew B. Laurens
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Matthew Adams
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Shannon Takala-Harrison
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Amadou Niangaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Bourema Kouriba
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Abdoulaye K. Koné
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - J. Alexandra Rowe
- Centre for Immunity, Infection and Evolution, Institute of Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Ogobara K. Doumbo
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | | | - John C. Tan
- Roche NimbleGen, Inc., Madison, Wisconsin, USA
| | - Philip L. Felgner
- Division of Infectious Diseases, Department of Medicine, University of California, Irvine, California, USA
| | - Christopher V. Plowe
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Mahamadou A. Thera
- Malaria Research and Training Center, University of Sciences, Techniques and Technologies, Bamako, Mali
| | - Mark A. Travassos
- Malaria Research Program, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
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12
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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: 9] [Impact Index Per Article: 4.5] [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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13
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Azulay A, Cohen-Lavi L, Friedman LM, McGargill MA, Hertz T. Mapping antibody footprints using binding profiles. CELL REPORTS METHODS 2023; 3:100566. [PMID: 37671022 PMCID: PMC10475849 DOI: 10.1016/j.crmeth.2023.100566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023]
Abstract
The increasing use of monoclonal antibodies (mAbs) in biology and medicine necessitates efficient methods for characterizing their binding epitopes. Here, we developed a high-throughput antibody footprinting method based on binding profiles. We used an antigen microarray to profile 23 human anti-influenza hemagglutinin (HA) mAbs using HA proteins of 43 human influenza strains isolated between 1918 and 2018. We showed that the mAb's binding profile can be used to characterize its influenza subtype specificity, binding region, and binding site. We present mAb-Patch-an epitope prediction method that is based on a mAb's binding profile and the 3D structure of its antigen. mAb-Patch was evaluated using four mAbs with known solved mAb-HA structures. mAb-Patch identifies over 67% of the true epitope when considering only 50-60 positions along the antigen. Our work provides proof of concept for utilizing antibody binding profiles to screen large panels of mAbs and to down-select antibodies for further functional studies.
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Affiliation(s)
- Asaf Azulay
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute of Biotechnology in the Negev, Beer-Sheva, Israel
| | - Liel Cohen-Lavi
- National Institute of Biotechnology in the Negev, Beer-Sheva, Israel
- Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Lilach M. Friedman
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute of Biotechnology in the Negev, Beer-Sheva, Israel
| | - Maureen A. McGargill
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Tomer Hertz
- The Shraga Segal Department of Microbiology, Immunology and Genetics, Ben-Gurion University of the Negev, Beer-Sheva, Israel
- National Institute of Biotechnology in the Negev, Beer-Sheva, Israel
- Vaccine and Infectious Disease Division, Fred Hutch Cancer Research Center, Seattle, WA, USA
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14
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Rowley AH, Arrollo D, Shulman ST, Torres A, O’Brien A, Wylie K, Kim KYA, Baker SC. Analysis of Plasmablasts From Children With Kawasaki Disease Reveals Evidence of a Convergent Antibody Response to a Specific Protein Epitope. J Infect Dis 2023; 228:412-421. [PMID: 36808252 PMCID: PMC10428203 DOI: 10.1093/infdis/jiad048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 02/20/2023] Open
Abstract
BACKGROUND Kawasaki disease (KD) is a febrile illness of young childhood that can result in coronary artery aneurysms and death. Coronavirus disease 2019 (COVID-19) mitigation strategies resulted in a marked decrease in KD cases worldwide, supporting a transmissible respiratory agent as the cause. We previously reported a peptide epitope recognized by monoclonal antibodies (MAbs) derived from clonally expanded peripheral blood plasmablasts from 3 of 11 KD children, suggesting a common disease trigger in a subset of patients with KD. METHODS We performed amino acid substitution scans to develop modified peptides with improved recognition by KD MAbs. We prepared additional MAbs from KD peripheral blood plasmablasts and assessed MAb characteristics that were associated with binding to the modified peptides. RESULTS We report a modified peptide epitope that is recognized by 20 MAbs from 11 of 12 KD patients. These MAbs predominantly use heavy chain VH3-74; two-thirds of VH3-74 plasmablasts from these patients recognize the epitope. The MAbs were nonidentical between patients but share a common complementarity-determining region 3 (CDR3) motif. CONCLUSIONS These results demonstrate a convergent VH3-74 plasmablast response to a specific protein antigen in children with KD, supporting one predominant causative agent in the etiopathogenesis of the illness.
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Affiliation(s)
- Anne H Rowley
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Microbiology/Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - David Arrollo
- Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Stanford T Shulman
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Abigail Torres
- Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Amornrat O’Brien
- Department of Microbiology and Immunology, Loyola University Stritch School of Medicine, Maywood, Illinois, USA
| | - Kristine Wylie
- Department of Pediatrics, Washington University in St Louis, St Louis, Missouri, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, Missouri, USA
| | - Kwang-Youn A Kim
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Susan C Baker
- Department of Microbiology and Immunology, Loyola University Stritch School of Medicine, Maywood, Illinois, USA
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15
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Davey NE, Simonetti L, Ivarsson Y. The next wave of interactomics: Mapping the SLiM-based interactions of the intrinsically disordered proteome. Curr Opin Struct Biol 2023; 80:102593. [PMID: 37099901 DOI: 10.1016/j.sbi.2023.102593] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/09/2023] [Accepted: 03/17/2023] [Indexed: 04/28/2023]
Abstract
Short linear motifs (SLiMs) are a unique and ubiquitous class of protein interaction modules that perform key regulatory functions and drive dynamic complex formation. For decades, interactions mediated by SLiMs have accumulated through detailed low-throughput experiments. Recent methodological advances have opened this previously underexplored area of the human interactome to high-throughput protein-protein interaction discovery. In this article, we discuss that SLiM-based interactions represent a significant blind spot in the current interactomics data, introduce the key methods that are illuminating the elusive SLiM-mediated interactome of the human cell on a large scale, and discuss the implications for the field.
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Affiliation(s)
- Norman E Davey
- Division of Cancer Biology, The Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK.
| | - Leandro Simonetti
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, Box 576, Husargatan 3, 751 23, Uppsala, Sweden.
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16
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Jethva PN, Gross ML. Hydrogen Deuterium Exchange and other Mass Spectrometry-based Approaches for Epitope Mapping. FRONTIERS IN ANALYTICAL SCIENCE 2023; 3:1118749. [PMID: 37746528 PMCID: PMC10512744 DOI: 10.3389/frans.2023.1118749] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Antigen-antibody interactions are a fundamental subset of protein-protein interactions responsible for the "survival of the fittest". Determining the interacting interface of the antigen, called an epitope, and that on the antibody, called a paratope, is crucial to antibody development. Because each antigen presents multiple epitopes (unique footprints), sophisticated approaches are required to determine the target region for a given antibody. Although X-ray crystallography, Cryo-EM, and nuclear magnetic resonance can provide atomic details of an epitope, they are often laborious, poor in throughput, and insensitive. Mass spectrometry-based approaches offer rapid turnaround, intermediate structural resolution, and virtually no size limit for the antigen, making them a vital approach for epitope mapping. In this review, we describe in detail the principles of hydrogen deuterium exchange mass spectrometry in application to epitope mapping. We also show that a combination of MS-based approaches can assist or complement epitope mapping and push the limit of structural resolution to the residue level. We describe in detail the MS methods used in epitope mapping, provide our perspective about the approaches, and focus on elucidating the role that HDX-MS is playing now and in the future by organizing a discussion centered around several improvements in prototype instrument/applications used for epitope mapping. At the end, we provide a tabular summary of the current literature on HDX-MS-based epitope mapping.
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Affiliation(s)
- Prashant N. Jethva
- Department of Chemistry, Washington University in St. Louis, St Louis, MO 63130, USA
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St Louis, MO 63130, USA
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17
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Olaleye O, Graf C, Spanov B, Govorukhina N, Groves MR, van de Merbel NC, Bischoff R. Determination of Binding Sites on Trastuzumab and Pertuzumab to Selective Affimers Using Hydrogen-Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:775-783. [PMID: 36960982 PMCID: PMC10080681 DOI: 10.1021/jasms.3c00069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 06/18/2023]
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a method to probe the solvent accessibility and conformational dynamics of a protein or a protein-ligand complex with respect to exchangeable amide hydrogens. Here, we present the application of HDX-MS to determine the binding sites of Affimer reagents to the monoclonal antibodies trastuzumab and pertuzumab, respectively. Intact and subunit level HDX-MS analysis of antibody-affimer complexes showed significant protection from HDX in the antibody Fab region upon affimer binding. Bottom-up HDX-MS experiments including online pepsin digestion revealed that the binding sites of the affimer reagents were mainly located in the complementarity-determining region (CDR) 2 of the heavy chain of the respective antibodies. Three-dimensional models of the binding interaction between the affimer reagents and the antibodies were built by homology modeling and molecular docking based on the HDX data.
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Affiliation(s)
- Oladapo Olaleye
- Analytical
Biochemistry, Department of Pharmacy, University
of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Christian Graf
- Novartis
Technical Research & Development Biologics, Hexal AG, Keltenring
1 + 3, 82041 Oberhaching, Germany
| | - Baubek Spanov
- Analytical
Biochemistry, Department of Pharmacy, University
of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Natalia Govorukhina
- Analytical
Biochemistry, Department of Pharmacy, University
of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Matthew R. Groves
- Drug
Design, Department of Pharmacy, University
of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Nico C. van de Merbel
- Analytical
Biochemistry, Department of Pharmacy, University
of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
- ICON
Bioanalytical Laboratories, Amerikaweg 18, 9407 TK Assen, The Netherlands
| | - Rainer Bischoff
- Analytical
Biochemistry, Department of Pharmacy, University
of Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
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18
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Leviatan S, Vogl T, Klompus S, Kalka IN, Weinberger A, Segal E. Allergenic food protein consumption is associated with systemic IgG antibody responses in non-allergic individuals. Immunity 2022; 55:2454-2469.e6. [PMID: 36473469 PMCID: PMC12103637 DOI: 10.1016/j.immuni.2022.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 06/01/2022] [Accepted: 11/09/2022] [Indexed: 12/12/2022]
Abstract
Although food-directed immunoglobulin E (IgE) has been studied in the context of allergies, the prevalence and magnitude of IgG responses against dietary antigens are incompletely characterized in the general population. Here, we measured IgG binding against food and environmental antigens obtained from allergen databases and the immune epitope database (IEDB), represented in a phage displayed library of 58,233 peptides. By profiling blood samples of a large cohort representing the average adult Israeli population (n = 1,003), we showed that many food antigens elicited systemic IgG in up to 50% of individuals. Dietary intake of specific food protein correlated with antibody binding, suggesting that diet can shape the IgG epitope repertoire. Our work documents abundant systemic IgG responses against food antigens and provides a reference map of the exact immunogenic epitopes on a population scale, laying the foundation to unravel the role of food- and environmental antigen-directed antibody binding in disease contexts.
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Affiliation(s)
- Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Thomas Vogl
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel; Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria; Center for Cancer Research, Medical University of Vienna, Wien, Austria.
| | - Shelley Klompus
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Iris N Kalka
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel; Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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19
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Faber E, Tshilwane SI, Van Kleef M, Pretorius A. The impact of Escherichia coli contamination products present in recombinant African horse sickness virus serotype 4 proteins on the innate and humoral immune responses. Mol Immunol 2022; 152:1-13. [DOI: 10.1016/j.molimm.2022.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/22/2022] [Accepted: 09/29/2022] [Indexed: 11/17/2022]
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20
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Bruschi M, Angeletti A, Kajana X, Moroni G, Sinico RA, Fredi M, Vaglio A, Cavagna L, Pratesi F, Migliorini P, Locatelli F, Pazzola G, Pesce G, Bagnasco M, Manfredi A, Ramirez GA, Esposito P, Negrini S, Bui F, Trezzi B, Emmi G, Cavazzana I, Binda V, Fenaroli P, Pisani I, Montecucco C, Santoro D, Scolari F, Volpi S, Mosca M, Tincani A, Candiano G, Verrina E, Franceschini F, Ravelli A, Prunotto M, Meroni PL, Ghiggeri GM. Evidence for charge-based mimicry in anti dsDNA antibody generation. J Autoimmun 2022; 132:102900. [PMID: 36087539 DOI: 10.1016/j.jaut.2022.102900] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/29/2022]
Abstract
Mechanisms for the generation of anti-dsDNA autoantibodies are still not completely elucidated. One theory states that dsDNA interacts for mimicry with antibodies raised versus other antigens but molecular features for mimicry are unknown. Here we show that, at physiological acid-base balance, anti-Annexin A1 binds IgG2 dsDNA in a competitive and dose-dependent way with Annexin A1 and that the competition between the two molecules is null at pH 9. On the other hand, these findings also show that dsDNA and Annexin A1 interact with their respective antibodies on a strictly pH-dependent basis: in both cases, the binding was minimal at pH 4 and maximal at pH9-10. The anionic charge of dsDNA is mainly conferred by the numerous phosphatidic residues. The epitope binding site of Annexin A1 for anti-Annexin A1 IgG2 was here characterized as a string of 34 amino acids at the NH2 terminus, 10 of which are anionic. Circulating levels of anti-dsDNA and anti-Annexin A1 IgG2 antibodies were strongly correlated in patients with systemic lupus erythematosus (n 496) and lupus nephritis (n 425) stratified for age, sex, etc. These results show that dsDNA competes with Annexin A1 for the binding with anti-Annexin A1 IgG2 on a dose and charged mediated base, being able to display an inhibition up to 75%. This study provides the first demonstration that dsDNA may interact with antibodies raised versus other anionic molecules (anti-Annexin A1 IgG2) because of charge mimicry and this interaction may contribute to anti-dsDNA antibodies generation.
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Affiliation(s)
- Maurizio Bruschi
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Andrea Angeletti
- Division of Nephrology, Dialysis and Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Xhuliana Kajana
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Gabriella Moroni
- Department of Biomedical Sciences, Humanitas University and IRCCS Humanitas Research Hospital, Milan, Italy
| | | | - Micaela Fredi
- Rheumatology and Clinical Immunology, ASST Spedali Civili and University of Brescia, Italy
| | - Augusto Vaglio
- Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", University of Florence, And Nephrology and Dialysis Unit, Meyer Children's Hospital, Florence, Italy
| | - Lorenzo Cavagna
- Division of Rheumatology, University and IRCCS Policlinico S. Matteo, Pavia, Italy
| | - Federico Pratesi
- Clinical Immunology Unit, Department of Internal Medicine, University of Pisa, Italy
| | - Paola Migliorini
- Clinical Immunology Unit, Department of Internal Medicine, University of Pisa, Italy
| | - Francesco Locatelli
- Division of Rheumatology, University and IRCCS Policlinico S. Matteo, Pavia, Italy
| | - Giulia Pazzola
- Nephrology and Dialysis, Arciospedale Santa Maria Nuova, Reggio Emilia, Italy
| | - Giampaola Pesce
- Medical and Radiometabolic Therapy Unit, Department of Internal Medicine, University of Genoa, Italy
| | - Marcello Bagnasco
- Medical and Radiometabolic Therapy Unit, Department of Internal Medicine, University of Genoa, Italy
| | - Angelo Manfredi
- Unit of Internal Medicine and Immunology, IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Pasquale Esposito
- Unit of Nephrology, Dialysis and Transplantation, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Simone Negrini
- Department of Internal Medicine, University of Genoa, Italy
| | - Federica Bui
- Division of Nephrology, University of Genoa and Policlinico San Martino, Genoa, Italy
| | - Barbara Trezzi
- Department of Medicine and Surgery, University of Milan, Bicocca, Italy
| | - Giacomo Emmi
- Lupus Clinic Department of Biomedicine, University of Florence, University Hospital Careggi, Florence, Italy
| | - Ilaria Cavazzana
- Rheumatology and Clinical Immunology, ASST Spedali Civili and University of Brescia, Italy
| | - Valentina Binda
- Department of Biomedical Sciences, Humanitas University and IRCCS Humanitas Research Hospital, Milan, Italy
| | - Paride Fenaroli
- Nephrology Unit, University Hospital, University of Parma, Parma, Italy
| | - Isabella Pisani
- Nephrology Unit, University Hospital, University of Parma, Parma, Italy
| | | | - Domenico Santoro
- Nephrology and Dialysis Unit, University of Messina and G Martino Hospital, Messina, Italy
| | - Francesco Scolari
- Division of Nephrology and Dialysis, University of Brescia and Ospedale di Montichiari, Brescia, Italy
| | - Stefano Volpi
- Division of Pediatric Rheumatology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Marta Mosca
- Rheumatologu Unit, Department of Clinical and Experimental Medicine, University of Pisa, Italy
| | - Angela Tincani
- Rheumatology and Clinical Immunology, ASST Spedali Civili and University of Brescia, Italy
| | - Giovanni Candiano
- Laboratory of Molecular Nephrology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Enrico Verrina
- Division of Nephrology, Dialysis and Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Franco Franceschini
- Rheumatology and Clinical Immunology, ASST Spedali Civili and University of Brescia, Italy
| | - Angelo Ravelli
- Division of Pediatric Rheumatology, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Marco Prunotto
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Pier Luigi Meroni
- Experimental Laboratory of Immunological and Rheumatologic Researches, IRCCS Istituto Auxologico Italiano, Milan, Italy.
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis and Transplantation, IRCCS Istituto Giannina Gaslini, Genoa, Italy.
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21
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Discovery of anti-Formin-like 1 protein (FMNL1) antibodies in membranous nephropathy and other glomerular diseases. Sci Rep 2022; 12:13659. [PMID: 35953506 PMCID: PMC9372176 DOI: 10.1038/s41598-022-17696-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/29/2022] [Indexed: 12/28/2022] Open
Abstract
Evidence has shown that podocyte-directed autoantibodies can cause membranous nephropathy (MN). In the present work we investigated sera of MN patients using a high-density peptide array covering the whole coding sequences of the human genome encompassing 7,499,126 tiled peptides. A panel of 21 proteins reactive to MN sera were identified. We focused our attention on Formin-like 1 (FMNL1), a protein expressed by macrophages in MN patients tissues. High levels of anti-FMNL1 IgG4 were demonstrated in sera of MN patients with an orthogonal methodology (ELISA) contemporary demonstrating FMNL1 positive cells in kidney co-staining with CD68 in glomeruli. High levels of circulating anti-FMNL1 IgG4 were associated with lack of remission of proteinuria, potentially indicating that autoantibodies directed against cells other than podocytes, involved in tissue repair, might play a role in MN disease progression. High serum levels of anti-FMNL1 IgGs were also observed in other non-autoimmune glomerolonephrites, i.e. idiopathic and genetic FSGS, IgAGN. These findings are suggestive of a broader role of those autoantibodies in other glomerular disease conditions.
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22
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Prifti DK, Lauzier A, Elowe S. A commercial ARHGEF17/TEM4 antibody cross-reacts with Nuclear Mitotic Apparatus protein 1 (NuMA). PLoS One 2022; 17:e0268848. [PMID: 35776709 PMCID: PMC9249204 DOI: 10.1371/journal.pone.0268848] [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: 05/06/2022] [Accepted: 05/20/2022] [Indexed: 11/18/2022] Open
Abstract
The Rho family Guanine nucleotide exchange factor (GEF) ARHGEF17 (also known as TEM4) is a large protein with only 3 annotated regions: an N-terminal actin-binding domain, a Rho-specific dbl homology (DH)- pleckstrin homology (PH) type GEF domain and a seven bladed β propeller fold at the C-terminus with unknown function. TEM4 has been implicated in numerous activities that rely on regulation of the cytoskeleton including cell migration, cell-cell junction formation and the spindle assembly checkpoint during mitosis. Here we have assessed the specificity of a TEM4 polyclonal antibody that has been commonly used as a Western blotting and immunocytochemistry probe for TEM4 in mammalian cells. We find that this antibody, in addition to its intended target, cross-reacts with the Nuclear Mitotic Apparatus Protein 1 (NuMA) in Western blotting and immunoprecipitation, and detects NuMA preferentially in immunocytochemistry. This cross-reactivity, with an abundant chromatin- and mitotic spindle-associated factor, is likely to affect the interpretation of experiments that make use of this antibody probe, in particular by immunocytochemistry and immunoprecipitation.
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Affiliation(s)
- Diogjena Katerina Prifti
- Programme en Biologie Cellulaire et Moléculaire, Faculté de Médicine Université Laval, Québec, Québec, Canada
- Centre de Recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe de Réproduction, Santé de la Mère et de l’enfant, Québec, Québec, Canada
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, l’ingénierie et les Applications des Protéines, Québec, Québec, Canada
| | - Annie Lauzier
- Centre de Recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe de Réproduction, Santé de la Mère et de l’enfant, Québec, Québec, Canada
| | - Sabine Elowe
- Centre de Recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe de Réproduction, Santé de la Mère et de l’enfant, Québec, Québec, Canada
- PROTEO-Regroupement Québécois de Recherche sur la Fonction, l’ingénierie et les Applications des Protéines, Québec, Québec, Canada
- Département de Pédiatrie, Faculté de Médicine, Université Laval et le Centre de Recherche sur le Cancer de l’Université Laval, Québec, Québec, Canada
- * E-mail:
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23
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Trejo-Zambrano MI, Gómez-Bañuelos E, Andrade F. Redox-Mediated Carbamylation As a Hapten Model Applied to the Origin of Antibodies to Modified Proteins in Rheumatoid Arthritis. Antioxid Redox Signal 2022; 36:389-409. [PMID: 33906423 PMCID: PMC8982126 DOI: 10.1089/ars.2021.0064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 04/16/2021] [Indexed: 12/23/2022]
Abstract
Significance: The production of antibodies to posttranslationally modified antigens is a hallmark in rheumatoid arthritis (RA). In particular, the presence of citrullination-associated antibodies, targeting both citrullinating enzymes (the peptidylarginine deiminases [PADs]) and citrullinated antigens (anticitrullinated protein antibodies [ACPAs]), has suggested that dysregulated citrullination is relevant for disease pathogenesis. Antibodies to other protein modifications with physicochemical similarities to citrulline, such as carbamylated-lysine and acetylated-lysine, have also gained interest in RA, but their mechanistic relation to ACPAs remains unclear. Recent Advances: Recent studies using RA-derived monoclonal antibodies have found that ACPAs are cross-reactive to carbamylated and acetylated peptides, challenging our understanding of the implications of such cross-reactivity. Critical Issues: Analogous to the classic antibody response to chemically modified proteins, we examine the possibility that antibodies to modified proteins in RA are more likely to resemble antihapten antibodies rather than autoantibodies. This potential shift in the autoantibody paradigm in RA offers the opportunity to explore new mechanisms involved in the origin and cross-reactivity of pathogenic antibodies in RA. In contrast to citrullination, carbamylation is a chemical modification associated with oxidative stress, it is highly immunogenic, and is considered in the group of posttranslational modification-derived products. We discuss the possibility that carbamylated proteins are antigenic drivers of cross-reacting antihapten antibodies that further create the ACPA response, and that ACPAs may direct the production of antibodies to PAD enzymes. Future Directions: Understanding the complexity of autoantibodies in RA is critical to develop tools to clearly define their origin, identify drivers of disease propagation, and develop novel therapeutics. Antioxid. Redox Signal. 36, 389-409.
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Affiliation(s)
| | - Eduardo Gómez-Bañuelos
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Felipe Andrade
- Division of Rheumatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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24
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Hanning KR, Minot M, Warrender AK, Kelton W, Reddy ST. Deep mutational scanning for therapeutic antibody engineering. Trends Pharmacol Sci 2021; 43:123-135. [PMID: 34895944 DOI: 10.1016/j.tips.2021.11.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/02/2021] [Accepted: 11/10/2021] [Indexed: 12/24/2022]
Abstract
The biophysical and functional properties of monoclonal antibody (mAb) drug candidates are often improved by protein engineering methods to increase the probability of clinical efficacy. One emerging method is deep mutational scanning (DMS) which combines the power of exhaustive protein mutagenesis and functional screening with deep sequencing and bioinformatics. The application of DMS has yielded significant improvements to the affinity, specificity, and stability of several preclinical antibodies alongside novel applications such as introducing multi-specific binding properties. DMS has also been applied directly on target antigens to precisely map antibody-binding epitopes and notably to profile the mutational escape potential of viral targets (e.g., SARS-CoV-2 variants). Finally, DMS combined with machine learning is enabling advances in the computational screening and engineering of therapeutic antibodies.
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Affiliation(s)
- Kyrin R Hanning
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand
| | - Mason Minot
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel 4058, Switzerland
| | - Annmaree K Warrender
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand
| | - William Kelton
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand.
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, Basel 4058, Switzerland.
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25
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Paull ML, Bozekowski JD, Daugherty PS. Mapping antibody binding using multiplexed epitope substitution analysis. J Immunol Methods 2021; 499:113178. [PMID: 34757083 DOI: 10.1016/j.jim.2021.113178] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 01/24/2023]
Abstract
A more complete understanding of antibody epitopes would aid the development of diagnostics, therapeutic antibodies, and vaccines. However, current methods for mapping antibody binding to epitopes require a targeted experimental approach, which limits throughput. To address these limitations, we developed Multiplexed Epitope Substitution Analysis (MESA) which can rapidly characterize various distinct epitopes using millions of antibody-binding peptides. We screened peptides from a random 12-mer library that bound to human serum antibody repertoires and determined their sequences using next-generation sequencing (NGS). Computationally, we divided target epitope sequences into overlapping k-mer subsequences and substituted the positions in each k-mer with all 20 amino acids, mimicking a saturation mutagenesis. We then determined enrichments of the substituted k-mers in the screened peptide dataset and used these enrichments to identify substitutions favored for binding at each position in the target epitope, ultimately revealing the precise binding motif. To validate MESA, we determined binding motifs for monoclonal antibodies spiked into serum, recovering the expected binding positions and amino acid preferences. To characterize epitopes bound by a population, we analyzed 50 serum specimens to determine the binding motifs within various target epitopes from common pathogens. Additionally, by analyzing various HSV-1 glycoprotein epitopes, MESA revealed unique binding signatures for HSV-1 seropositive specimens and demonstrated the variability of binding signatures within a population. These results demonstrate that MESA can rapidly identify and characterize binding motifs for an unlimited number of epitopes from a single experiment, accelerating discoveries and enhancing our understanding of antibody-epitope interactions.
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Affiliation(s)
- Michael L Paull
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Joel D Bozekowski
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA.
| | - Patrick S Daugherty
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106, USA
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26
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Identification of a specific surface epitope of OmpC for Escherichia coli O157:H7 with protein topology facilitated affinity mass spectrometry. Appl Microbiol Biotechnol 2021; 105:6819-6833. [PMID: 34432131 PMCID: PMC8426304 DOI: 10.1007/s00253-021-11511-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/04/2021] [Accepted: 08/07/2021] [Indexed: 11/03/2022]
Abstract
Abstract
The goal of this work was to identify the target protein and epitope of a previously reported Escherichia coli O157:H7 (ECO157)–specific monoclonal antibody (mAb) 2G12. mAb 2G12 has shown high specificity for the recovery and detection of ECO157. To achieve this goal, the target protein was first separated by two-dimensional gel electrophoresis (2-DE) and located by Western blot (WB). The protein spots were identified to be the outer membrane protein (Omp) C by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF–MS). After that, the target protein was purified by immunoaffinity chromatography (IAC) and subjected to in situ enzymatic cleavage of the vulnerable peptides. Eight eluted peptides of OmpC identified by liquid chromatography–tandem mass spectrometry (LC–MS/MS) were further mapped onto the homologous protein structure of E. coli OmpC (2IXX). The topology of OmpC showed that three peptides had extracellular loops. Epitope mapping with overlapping peptide library and sequence homology analysis revealed that the epitope consisted of a specific peptide, “LGVING,” and an adjacent conservative peptide, “TQTYNATRVGSLG.” Both peptides loop around the overall structure of the epitope. To test the availability of the epitope when ECO157 was grown under different osmolarity, pH, and nutrition levels, the binding efficacy of mAb 2G12 with ECO157 grown in these conditions was evaluated. Results further demonstrated the good stability of this epitope under potential stressful environmental conditions. In summary, this study revealed that mAb 2G12 targeted one specific and one conservative extracellular loop (peptide) of the OmpC present on ECO157, and the epitope was stable and accessible on ECO157 cells grown in different environment. Key points • OmpC is the target of a recently identified ECO157-specific mAb 2G12. • Eight peptides were identified from the OmpC by using LC–MS/MS. • The specificity of mAb 2G12 is mainly determined by the “LGVING” peptide. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-021-11511-8.
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27
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Yang J, Qi L, Chiang HC, Yuan B, Li R, Hu Y. BRCA1 Antibodies Matter. Int J Biol Sci 2021; 17:3239-3254. [PMID: 34421362 PMCID: PMC8375228 DOI: 10.7150/ijbs.63115] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/11/2021] [Indexed: 12/11/2022] Open
Abstract
Breast cancer susceptibility gene 1 (BRCA1) encodes a tumor suppressor that is frequently mutated in familial breast and ovarian cancer patients. BRCA1 functions in multiple important cellular processes including DNA damage repair, cell cycle checkpoint activation, protein ubiquitination, chromatin remodeling, transcriptional regulation, as well as R-loop formation and apoptosis. A large number of BRCA1 antibodies have been generated and become commercially available over the past three decades, however, many commercial antibodies are poorly characterized and, when widely used, led to unreliable data. In search of reliable and specific BRCA1 antibodies (Abs), particularly antibodies recognizing mouse BRCA1, we performed a rigorous validation of a number of commercially available anti-BRCA1 antibodies, using proper controls in a panel of validation applications, including Western blot (WB), immunoprecipitation (IP), immunoprecipitation-mass spectrometry (IP-MS), chromatin immunoprecipitation (ChIP) and immunofluorescence (IF). Furthermore, we assessed the specificity of these antibodies to detect mouse BRCA1 protein through the use of testis tissue and mouse embryonic fibroblasts (MEFs) from Brca1+/+ and Brca1Δ11/Δ11 mice. We find that Ab1, D-9, 07-434 (for recognizing human BRCA1) and 287.17, 440621, BR-64 (for recognizing mouse BRCA1) are specific with high quality performance in the indicated assays. We share these results here with the goal of helping the community combat the common challenges associated with anti-BRCA1 antibody specificity and reproducibility and, hopefully, better understanding BRCA1 functions at cellular and tissue levels.
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Affiliation(s)
- Jing Yang
- Department of Anatomy & Cell Biology, School of Medicine & Health Sciences, The George Washington University, Washington, DC, USA
| | - Leilei Qi
- Department of Anatomy & Cell Biology, School of Medicine & Health Sciences, The George Washington University, Washington, DC, USA
| | - Huai-Chin Chiang
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC, USA
| | - Bin Yuan
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC, USA
| | - Rong Li
- Department of Biochemistry & Molecular Medicine, School of Medicine & Health Sciences, The George Washington University, Washington, DC, USA
| | - Yanfen Hu
- Department of Anatomy & Cell Biology, School of Medicine & Health Sciences, The George Washington University, Washington, DC, USA
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28
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Ramberger E, Suarez-Artiles L, Perez-Hernandez D, Haji M, Popp O, Reimer U, Leutz A, Dittmar G, Mertins P. A universal peptide matrix interactomics approach to disclose motif dependent protein binding. Mol Cell Proteomics 2021; 20:100135. [PMID: 34391889 PMCID: PMC8453223 DOI: 10.1016/j.mcpro.2021.100135] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/22/2021] [Accepted: 08/10/2021] [Indexed: 12/02/2022] Open
Abstract
Protein–protein interactions mediated by intrinsically disordered regions are often based on short linear motifs (SLiMs). SLiMs are implicated in signal transduction and gene regulation yet remain technically laborious and notoriously challenging to study. Here, we present an optimized method for a protein interaction screen on a peptide matrix (PRISMA) in combination with quantitative MS. The protocol was benchmarked with previously described SLiM-based protein–protein interactions using peptides derived from EGFR, SOS1, GLUT1, and CEBPB and extended to map binding partners of kinase activation loops. The detailed protocol provides practical considerations for setting up a PRISMA screen and subsequently implementing PRISMA on a liquid-handling robotic platform as a cost-effective high-throughput method. Optimized PRISMA can be universally applied to systematically study SLiM-based interactions and associated post-translational modifications or mutations to advance our understanding of the largely uncharacterized interactomes of intrinsically disordered protein regions. Optimized protocol for analysis of peptide–protein interactions with peptide arrays. Detection of interactions affected by mutations or post-translational modifications. Mapping of interaction sites with overlapping peptide sequences. Implementation on a liquid-handling robotic platform.
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Affiliation(s)
- Evelyn Ramberger
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Lorena Suarez-Artiles
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | | | - Mohamad Haji
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Oliver Popp
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Ulf Reimer
- JPT Peptide Technologies GmbH, Berlin, Germany
| | - Achim Leutz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Institute of Biology, Humboldt University of Berlin, Berlin, Germany.
| | - Gunnar Dittmar
- Quantitative Biology Unit, Luxembourg Institute of Health, Luxembourg; Department of Life Sciences and Medicine, University of Luxembourg, L-4367 Belvaux, Luxembourg.
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Berlin Institute of Health (BIH), Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin; Deutsches Zentrum für Herz-Kreislauf-Forschung e. V. (DZHK), Berlin, Germany.
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29
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Population-wide diversity and stability of serum antibody epitope repertoires against human microbiota. Nat Med 2021; 27:1442-1450. [PMID: 34282338 DOI: 10.1038/s41591-021-01409-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/25/2021] [Indexed: 12/12/2022]
Abstract
Serum antibodies can recognize both pathogens and commensal gut microbiota. However, our current understanding of antibody repertoires is largely based on DNA sequencing of the corresponding B-cell receptor genes, and actual bacterial antigen targets remain incompletely characterized. Here we have profiled the serum antibody responses of 997 healthy individuals against 244,000 rationally selected peptide antigens derived from gut microbiota and pathogenic and probiotic bacteria. Leveraging phage immunoprecipitation sequencing (PhIP-Seq) based on phage-displayed synthetic oligo libraries, we detect a wide breadth of individual-specific as well as shared antibody responses against microbiota that associate with age and gender. We also demonstrate that these antibody epitope repertoires are more longitudinally stable than gut microbiome species abundances. Serum samples of more than 200 individuals collected five years apart could be accurately matched and could serve as an immunologic fingerprint. Overall, our results suggest that systemic antibody responses provide a non-redundant layer of information about microbiota beyond gut microbial species composition.
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30
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Epitope-directed monoclonal antibody production using a mixed antigen cocktail facilitates antibody characterization and validation. Commun Biol 2021; 4:441. [PMID: 33824395 PMCID: PMC8024308 DOI: 10.1038/s42003-021-01965-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 03/08/2021] [Indexed: 02/01/2023] Open
Abstract
High quality, well-validated antibodies are needed to mitigate irreproducibility and clarify conflicting data in science. We describe an epitope-directed monoclonal antibody (mAb) production method that addresses issues of antibody quality, validation and utility. The workflow is illustrated by generating mAbs against multiple in silico-predicted epitopes on human ankyrin repeat domain 1 (hANKRD1) in a single hybridoma production cycle. Antigenic peptides (13-24 residues long) presented as three-copy inserts on the surface exposed loop of a thioredoxin carrier produced high affinity mAbs that are reactive to native and denatured hANKRD1. ELISA assay miniaturization afforded by novel DEXT microplates allowed rapid hybridoma screening with concomitant epitope identification. Antibodies against spatially distant sites on hANKRD1 facilitated validation schemes applicable to two-site ELISA, western blotting and immunocytochemistry. The use of short antigenic peptides of known sequence facilitated direct epitope mapping crucial for antibody characterization. This robust method motivates its ready adoption for other protein targets.
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31
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Mazhar S, Leonard D, Sosa A, Schlatzer D, Thomas D, Narla G. Challenges and Reinterpretation of Antibody-Based Research on Phosphorylation of Tyr 307 on PP2Ac. Cell Rep 2021; 30:3164-3170.e3. [PMID: 32130915 DOI: 10.1016/j.celrep.2020.02.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 11/20/2019] [Accepted: 02/03/2020] [Indexed: 12/13/2022] Open
Abstract
Aberrant hyperphosphorylation of the protein phosphatase 2A catalytic subunit (PP2Ac) at Tyr307 has been associated with aggressive disease and poor clinical outcome in multiple cancers. However, the study of reversible phosphorylation at this site has relied entirely upon the use of antibodies-most prominently, the clone E155. Here, we provide evidence that the E155 and F-8 phospho-Tyr307 antibodies cannot differentiate between phosphorylated and unphosphorylated forms of PP2Ac. The form of PP2Ac bound by these antibodies in H358 cells is unphosphorylated at the C-terminal tail. Furthermore, these antibodies are sensitive to additional protein modifications that occur near Tyr307, including Thr304 phosphorylation and Leu309 methylation, when these post-translational modifications are present. Thus, studies that used these antibodies to report PP2Ac hyperphosphorylation require reinterpretation, as these antibodies cannot be reliably used as readouts for a single PP2Ac post-translational modification (PTM) change.
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Affiliation(s)
- Sahar Mazhar
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Daniel Leonard
- Department of Pathology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Alejandro Sosa
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Daniela Schlatzer
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Dafydd Thomas
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Goutham Narla
- Division of Genetic Medicine, Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI 48109, USA.
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32
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Abstract
Serodiagnosis of SARS-CoV-2 infection is impeded by immunological cross-reactivity among the human coronaviruses (HCoVs): SARS-CoV-2, SARS-CoV-1, MERS-CoV, OC43, 229E, HKU1, and NL63. Here we report the identification of humoral immune responses to SARS-CoV-2 peptides that may enable discrimination between exposure to SARS-CoV-2 and other HCoVs. We used a high-density peptide microarray and plasma samples collected at two time points from 50 subjects with SARS-CoV-2 infection confirmed by qPCR, samples collected in 2004–2005 from 11 subjects with IgG antibodies to SARS-CoV-1, 11 subjects with IgG antibodies to other seasonal human coronaviruses (HCoV), and 10 healthy human subjects. Through statistical modeling with linear regression and multidimensional scaling we identified specific peptides that were reassembled to identify 29 linear SARS-CoV-2 epitopes that were immunoreactive with plasma from individuals who had asymptomatic, mild or severe SARS-CoV-2 infections. Larger studies will be required to determine whether these peptides may be useful in serodiagnostics. Mishra, Huang et al. identify 29 linear SARS-CoV-2 epitopes that are immunoreactive with the plasma from individuals who had asymptomatic, mild, or severe SARS-CoV-2 infections. This study suggests the possibility of using these peptides to discriminate the exposure to SARS-CoV-2 and other human coronaviruses.
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Bolognesi MM, Mascadri F, Furia L, Faretta M, Bosisio FM, Cattoretti G. Antibodies validated for routinely processed tissues stain frozen sections unpredictably. Biotechniques 2021; 70:137-148. [PMID: 33541132 DOI: 10.2144/btn-2020-0149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background: Antibody validation for tissue staining is required for reproducibility; criteria to ensure validity have been published recently. The majority of these recommendations imply the use of routinely processed (formalin-fixed, paraffin-embedded) tissue. Materials & methods: We applied to lightly fixed frozen sections a panel of 126 antibodies validated for formalin-fixed, paraffin-embedded tissue with extended criteria. Results: Less than 30% of the antibodies performed as expected with all fixations. 35% preferred one fixation over another, 13% gave nonspecific staining and 23% did not stain at all. Conclusion: Individual antibody variability of the paratope's fitness for the fixed antigen may be the cause. Revalidation of established antibody panels is required when they are applied to sections whose fixation and processing are different from the tissue where they were initially validated.
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Affiliation(s)
- Maddalena M Bolognesi
- Pathology, Department of Medicine & Surgery, Università di Milano-Bicocca, Via Cadore 48, Monza 20900, Italy
| | - Francesco Mascadri
- Pathology, Department of Medicine & Surgery, Università di Milano-Bicocca, Via Cadore 48, Monza 20900, Italy
| | - Laura Furia
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Mario Faretta
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, Milan 20139, Italy
| | - Francesca M Bosisio
- Laboratory of Translational Cell & Tissue Research, KU Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Giorgio Cattoretti
- Pathology, Department of Medicine & Surgery, Università di Milano-Bicocca, Via Cadore 48, Monza 20900, Italy.,Department of Pathology, Ospedale San Gerardo, ASST-Monza, Via Pergolesi 33, Monza 20900, Italy
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Moreno-Yruela C, Bæk M, Vrsanova AE, Schulte C, Maric HM, Olsen CA. Hydroxamic acid-modified peptide microarrays for profiling isozyme-selective interactions and inhibition of histone deacetylases. Nat Commun 2021; 12:62. [PMID: 33397936 PMCID: PMC7782793 DOI: 10.1038/s41467-020-20250-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/19/2020] [Indexed: 02/07/2023] Open
Abstract
Histones control gene expression by regulating chromatin structure and function. The posttranslational modifications (PTMs) on the side chains of histones form the epigenetic landscape, which is tightly controlled by epigenetic modulator enzymes and further recognized by so-called reader domains. Histone microarrays have been widely applied to investigate histone-reader interactions, but not the transient interactions of Zn2+-dependent histone deacetylase (HDAC) eraser enzymes. Here, we synthesize hydroxamic acid-modified histone peptides and use them in femtomolar microarrays for the direct capture and detection of the four class I HDAC isozymes. Follow-up functional assays in solution provide insights into their suitability to discover HDAC substrates and inhibitors with nanomolar potency and activity in cellular assays. We conclude that similar hydroxamic acid-modified histone peptide microarrays and libraries could find broad application to identify class I HDAC isozyme-specific substrates and facilitate the development of isozyme-selective HDAC inhibitors and probes.
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Affiliation(s)
- Carlos Moreno-Yruela
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Michael Bæk
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Adela-Eugenie Vrsanova
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark.,Institute of Applied Biosciences & Department of Food Chemistry and Toxicology, Karlsruhe Institute of Technology, Adenauerring 20a, D-76131, Karlsruhe, Germany.,Division of Proteomics of Stem Cells and Cancer, DKFZ German Cancer Research Center, Im Neuenhemier Feld 581, D-69120, Heidelberg, Germany
| | - Clemens Schulte
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, D-97080, Würzburg, Germany
| | - Hans M Maric
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, D-97080, Würzburg, Germany.
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark.
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35
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Flego M, Colotti G, Ascione A, Dupuis ML, Petrucci E, Riccioni R, Andreotti M, Raggi C, Boe A, Barca S, Gellini M, Vella S, Mallano A. Isolation and preliminary characterization of a human 'phage display'-derived antibody against neural adhesion molecule-1 antigen interfering with fibroblast growth factor receptor-1 binding. Hum Antibodies 2021; 29:63-84. [PMID: 33164927 DOI: 10.3233/hab-200431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
BACKGROUND The NCAM or CD56 antigen is a cell surface glycoprotein belonging to the immunoglobulin super-family involved in cell-cell and cell-matrix adhesion. NCAM is also over-expressed in many tumour types and is considered a tumour associated antigen, even if its role and biological mechanisms implicated in tumour progression and metastasis have not yet to be elucidated. In particular, it is quite well documented the role of the interaction between the NCAM protein and the fibroblast growth factor receptor-1 in metastasis and invasion, especially in the ovarian cancer progression. OBJECTIVE Here we describe the isolation and preliminary characterization of a novel human anti-NCAM single chain Fragment variable antibody able to specifically bind NCAM-expressing cells, including epithelial ovarian cancer cells. METHODS The antibody was isolate by phage display selection and was characterized by ELISA, FACS analysis and SPR experiments. Interference in EOC migration was analyzed by scratch test. RESULTS It binds a partially linear epitope lying in the membrane proximal region of two fibronectin-like domains with a dissociation constant of 3.43 × 10-8 M. Interestingly, it was shown to interfere with the NCAM-FGFR1 binding and to partially decrease migration of EOC cells. CONCLUSIONS According to our knowledge, this is the first completely human antibody able to interfere with this newly individuated cancer mechanism.
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Affiliation(s)
- Michela Flego
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Gianni Colotti
- Institute of Molecular Biology and Pathology, Italian National Research Council, c/o Department Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Alessandro Ascione
- National Center for Control and Evaluation of Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Maria Luisa Dupuis
- Center for Gender Specific Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Eleonora Petrucci
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Roberta Riccioni
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Mauro Andreotti
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Carla Raggi
- National Center for Control and Evaluation of Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Alessandra Boe
- Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Stefano Barca
- National Center for Drug Research and Evaluation Unit of Preclinical and Clinical Evaluation of Medicinal Drugs, Istituto Superiore di Sanità, Rome, Italy
| | - Mara Gellini
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Stefano Vella
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Alessandra Mallano
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
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36
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Weinstain R, Slanina T, Kand D, Klán P. Visible-to-NIR-Light Activated Release: From Small Molecules to Nanomaterials. Chem Rev 2020; 120:13135-13272. [PMID: 33125209 PMCID: PMC7833475 DOI: 10.1021/acs.chemrev.0c00663] [Citation(s) in RCA: 337] [Impact Index Per Article: 67.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Indexed: 02/08/2023]
Abstract
Photoactivatable (alternatively, photoremovable, photoreleasable, or photocleavable) protecting groups (PPGs), also known as caged or photocaged compounds, are used to enable non-invasive spatiotemporal photochemical control over the release of species of interest. Recent years have seen the development of PPGs activatable by biologically and chemically benign visible and near-infrared (NIR) light. These long-wavelength-absorbing moieties expand the applicability of this powerful method and its accessibility to non-specialist users. This review comprehensively covers organic and transition metal-containing photoactivatable compounds (complexes) that absorb in the visible- and NIR-range to release various leaving groups and gasotransmitters (carbon monoxide, nitric oxide, and hydrogen sulfide). The text also covers visible- and NIR-light-induced photosensitized release using molecular sensitizers, quantum dots, and upconversion and second-harmonic nanoparticles, as well as release via photodynamic (photooxygenation by singlet oxygen) and photothermal effects. Release from photoactivatable polymers, micelles, vesicles, and photoswitches, along with the related emerging field of photopharmacology, is discussed at the end of the review.
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Affiliation(s)
- Roy Weinstain
- School
of Plant Sciences and Food Security, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Tomáš Slanina
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Dnyaneshwar Kand
- School
of Plant Sciences and Food Security, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Petr Klán
- Department
of Chemistry and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
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Sahlström P, Hansson M, Steen J, Amara K, Titcombe PJ, Forsström B, Stålesen R, Israelsson L, Piccoli L, Lundberg K, Klareskog L, Mueller DL, Catrina AI, Skriner K, Malmström V, Grönwall C. Different Hierarchies of Anti–Modified Protein Autoantibody Reactivities in Rheumatoid Arthritis. Arthritis Rheumatol 2020; 72:1643-1657. [DOI: 10.1002/art.41385] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 05/13/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Peter Sahlström
- Karolinska Institutet Karolinska University Hospital, Stockholm, Sweden, and Charité Universitätsmedizin Berlin Germany
| | - Monika Hansson
- Karolinska Institutet Karolinska University Hospital Stockholm Sweden
| | - Johanna Steen
- Karolinska Institutet Karolinska University Hospital Stockholm Sweden
| | - Khaled Amara
- Karolinska Institutet Karolinska University Hospital Stockholm Sweden
| | - Philip J. Titcombe
- Karolinska Institutet Karolinska University Hospital, Stockholm, Sweden, and University of Minnesota Medical School Minneapolis
| | | | - Ragnhild Stålesen
- Karolinska Institutet Karolinska University Hospital Stockholm Sweden
| | - Lena Israelsson
- Karolinska Institutet Karolinska University Hospital Stockholm Sweden
| | - Luca Piccoli
- Institute for Research in Biomedicine Università della Svizzera italiana Bellinzona Switzerland
| | - Karin Lundberg
- Karolinska Institutet Karolinska University Hospital Stockholm Sweden
| | - Lars Klareskog
- Karolinska Institutet Karolinska University Hospital Stockholm Sweden
| | | | - Anca I. Catrina
- Karolinska Institutet Karolinska University Hospital Stockholm Sweden
| | | | | | - Caroline Grönwall
- Karolinska Institutet Karolinska University Hospital Stockholm Sweden
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Haji Abdolvahab M, Venselaar H, Fazeli A, Arab SS, Behmanesh M. Point Mutation Approach to Reduce Antigenicity of Interferon Beta. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-019-09938-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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39
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Mikus M, Zandian A, Sjöberg R, Hamsten C, Forsström B, Andersson M, Greiff L, Uhlén M, Levin M, Nilsson P, van Hage M, Ohlin M. Allergome-wide peptide microarrays enable epitope deconvolution in allergen-specific immunotherapy. J Allergy Clin Immunol 2020; 147:1077-1086. [PMID: 32791163 DOI: 10.1016/j.jaci.2020.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 07/22/2020] [Accepted: 08/04/2020] [Indexed: 11/30/2022]
Abstract
BACKGROUND The interaction of allergens and allergen-specific IgE initiates the allergic cascade after crosslinking of receptors on effector cells. Antibodies of other isotypes may modulate such a reaction. Receptor crosslinking requires binding of antibodies to multiple epitopes on the allergen. Limited information is available on the complexity of the epitope structure of most allergens. OBJECTIVES We sought to allow description of the complexity of IgE, IgG4, and IgG epitope recognition at a global, allergome-wide level during allergen-specific immunotherapy (AIT). METHODS We generated an allergome-wide microarray comprising 731 allergens in the form of more than 172,000 overlapping 16-mer peptides. Allergen recognition by IgE, IgG4, and IgG was examined in serum samples collected from subjects undergoing AIT against pollen allergy. RESULTS Extensive induction of linear peptide-specific Phl p 1- and Bet v 1-specific humoral immunity was demonstrated in subjects undergoing a 3-year-long AIT against grass and birch pollen allergy, respectively. Epitope profiles differed between subjects but were largely established already after 1 year of AIT, suggesting that dominant allergen-specific antibody clones remained as important contributors to humoral immunity following their initial establishment during the early phase of AIT. Complex, subject-specific patterns of allergen isoform and group cross-reactivities in the repertoires were observed, patterns that may indicate different levels of protection against different allergen sources. CONCLUSIONS The study highlights the complexity and subject-specific nature of allergen epitopes recognized following AIT. We envisage that epitope deconvolution will be an important aspect of future efforts to describe and analyze the outcomes of AIT in a personalized manner.
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Affiliation(s)
- Maria Mikus
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden; Unit of Experimental Asthma and Allergy Research, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Arash Zandian
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden
| | - Ronald Sjöberg
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden
| | - Carl Hamsten
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Björn Forsström
- Division of Systems Biology, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden
| | - Morgan Andersson
- Department of Otorhinolaryngology, Head & Neck Surgery, Skåne University Hospital, Lund, Sweden
| | - Lennart Greiff
- Department of Otorhinolaryngology, Head & Neck Surgery, Skåne University Hospital, Lund, Sweden; Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Mathias Uhlén
- Division of Systems Biology, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden
| | - Mattias Levin
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Peter Nilsson
- Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology & SciLifeLab, Stockholm, Sweden
| | - Marianne van Hage
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Mats Ohlin
- Department of Immunotechnology, Lund University, Lund, Sweden.
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40
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Lindskog C, Backman M, Zieba A, Asplund A, Uhlén M, Landegren U, Pontén F. Proximity Ligation Assay as a Tool for Antibody Validation in Human Tissues. J Histochem Cytochem 2020; 68:515-529. [PMID: 32602410 DOI: 10.1369/0022155420936384] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Immunohistochemistry (IHC) is the accepted standard for spatial analysis of protein expression in tissues. IHC is widely used for cancer diagnostics and in basic research. The development of new antibodies to proteins with unknown expression patterns has created a demand for thorough validation. We have applied resources from the Human Protein Atlas project and the Antibody Portal at National Cancer Institute to generate protein expression data for 12 proteins across 39 cancer cell lines and 37 normal human tissue types. The outcome of IHC on consecutive sections from both cell and tissue microarrays using two independent antibodies for each protein was compared with in situ proximity ligation (isPLA), where binding by both antibodies is required to generate detection signals. Semi-quantitative scores from IHC and isPLA were compared with expression of the corresponding 12 transcripts across all cell lines and tissue types. Our results show a more consistent correlation between mRNA levels and isPLA as compared to IHC. The main benefits of isPLA include increased detection specificity and decreased unspecific staining compared to IHC. We conclude that implementing isPLA as a complement to IHC for analysis of protein expression and in antibody validation pipelines can lead to more accurate localization of proteins in tissue.
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Affiliation(s)
- Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Max Backman
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Agata Zieba
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Asplund
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Royal Institute of Technology, Stockholm, Sweden
| | - Ulf Landegren
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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Rowley AH, Baker SC, Arrollo D, Gruen LJ, Bodnar T, Innocentini N, Hackbart M, Cruz-Pulido YE, Wylie KM, Kim KYA, Shulman ST. A Protein Epitope Targeted by the Antibody Response to Kawasaki Disease. J Infect Dis 2020; 222:158-168. [PMID: 32052021 PMCID: PMC7296860 DOI: 10.1093/infdis/jiaa066] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 02/07/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Kawasaki disease (KD) is the leading cause of childhood acquired heart disease in developed nations and can result in coronary artery aneurysms and death. Clinical and epidemiologic features implicate an infectious cause but specific antigenic targets of the disease are unknown. Peripheral blood plasmablasts are normally highly clonally diverse but the antibodies they encode are approximately 70% antigen-specific 1-2 weeks after infection. METHODS We isolated single peripheral blood plasmablasts from children with KD 1-3 weeks after onset and prepared 60 monoclonal antibodies (mAbs). We used the mAbs to identify their target antigens and assessed serologic response among KD patients and controls to specific antigen. RESULTS Thirty-two mAbs from 9 of 11 patients recognize antigen within intracytoplasmic inclusion bodies in ciliated bronchial epithelial cells of fatal cases. Five of these mAbs, from 3 patients with coronary aneurysms, recognize a specific peptide, which blocks binding to inclusion bodies. Sera from 5/8 KD patients day ≥ 8 after illness onset, compared with 0/17 infant controls (P < .01), recognized the KD peptide antigen. CONCLUSIONS These results identify a protein epitope targeted by the antibody response to KD and provide a means to elucidate the pathogenesis of this important worldwide pediatric problem.
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Affiliation(s)
- Anne H Rowley
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Microbiology/Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Susan C Baker
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, Illinois, USA
| | - David Arrollo
- Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Leah J Gruen
- Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Tetyana Bodnar
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Nancy Innocentini
- Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Matthew Hackbart
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, Illinois, USA
| | - Yazmin E Cruz-Pulido
- Department of Microbiology and Immunology, Loyola University Chicago, Stritch School of Medicine, Maywood, Illinois, USA
| | - Kristine M Wylie
- Department of Pediatrics, Washington University School of Medicine, St Louis, Missouri, USA
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, Missouri, USA
| | - Kwang-Youn A Kim
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Stanford T Shulman
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
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Kula T, Dezfulian MH, Wang CI, Abdelfattah NS, Hartman ZC, Wucherpfennig KW, Lyerly HK, Elledge SJ. T-Scan: A Genome-wide Method for the Systematic Discovery of T Cell Epitopes. Cell 2020; 178:1016-1028.e13. [PMID: 31398327 PMCID: PMC6939866 DOI: 10.1016/j.cell.2019.07.009] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 04/20/2019] [Accepted: 07/09/2019] [Indexed: 12/20/2022]
Abstract
T cell recognition of specific antigens mediates protection from pathogens and controls neoplasias, but can also cause autoimmunity. Our knowledge of T cell antigens and their implications for human health is limited by the technical limitations of T cell profiling technologies. Here, we present T-Scan, a high-throughput platform for identification of antigens productively recognized by T cells. T-Scan uses lentiviral delivery of antigen libraries into cells for endogenous processing and presentation on major histocompatibility complex (MHC) molecules. Target cells functionally recognized by T cells are isolated using a reporter for granzyme B activity, and the antigens mediating recognition are identified by next-generation sequencing. We show T-Scan correctly identifies cognate antigens of T cell receptors (TCRs) from viral and human genome-wide libraries. We apply T-Scan to discover new viral antigens, perform high-resolution mapping of TCR specificity, and characterize the reactivity of a tumor-derived TCR. T-Scan is a powerful approach for studying T cell responses.
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Affiliation(s)
- Tomasz Kula
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard University Medical School, Boston, MA, USA
| | - Mohammad H Dezfulian
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard University Medical School, Boston, MA, USA
| | - Charlotte I Wang
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard University Medical School, Boston, MA, USA; Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Nouran S Abdelfattah
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard University Medical School, Boston, MA, USA
| | - Zachary C Hartman
- Departments of Surgery and Pathology, Duke University Medical Center, 571 Research Drive, Suite 433, Box 2606, Durham, NC 27710, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Department of Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Herbert Kim Lyerly
- Departments of Surgery, Immunology, and Pathology, Duke University Medical Center, 571 Research Drive, Suite 433, Box 2606, Durham, NC 27710, 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 University Medical School, Boston, MA, USA.
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Haj AK, Breitbach ME, Baker DA, Mohns MS, Moreno GK, Wilson NA, Lyamichev V, Patel J, Weisgrau KL, Dudley DM, O'Connor DH. High-Throughput Identification of MHC Class I Binding Peptides Using an Ultradense Peptide Array. THE JOURNAL OF IMMUNOLOGY 2020; 204:1689-1696. [PMID: 32060132 DOI: 10.4049/jimmunol.1900889] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/04/2020] [Indexed: 01/02/2023]
Abstract
Rational vaccine development and evaluation requires identifying and measuring the magnitude of epitope-specific CD8 T cell responses. However, conventional CD8 T cell epitope discovery methods are labor intensive and do not scale well. In this study, we accelerate this process by using an ultradense peptide array as a high-throughput tool for screening peptides to identify putative novel epitopes. In a single experiment, we directly assess the binding of four common Indian rhesus macaque MHC class I molecules (Mamu-A1*001, -A1*002, -B*008, and -B*017) to ∼61,000 8-mer, 9-mer, and 10-mer peptides derived from the full proteomes of 82 SIV and simian HIV isolates. Many epitope-specific CD8 T cell responses restricted by these four MHC molecules have already been identified in SIVmac239, providing an ideal dataset for validating the array; up to 64% of these known epitopes are found in the top 192 SIVmac239 peptides with the most intense MHC binding signals in our experiment. To assess whether the peptide array identified putative novel CD8 T cell epitopes, we validated the method by IFN-γ ELISPOT assay and found three novel peptides that induced CD8 T cell responses in at least two Mamu-A1*001-positive animals; two of these were validated by ex vivo tetramer staining. This high-throughput identification of peptides that bind class I MHC will enable more efficient CD8 T cell response profiling for vaccine development, particularly for pathogens with complex proteomes for which few epitope-specific responses have been defined.
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Affiliation(s)
- Amelia K Haj
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705
| | - Meghan E Breitbach
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705
| | - David A Baker
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705
| | - Mariel S Mohns
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705
| | - Gage K Moreno
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705
| | - Nancy A Wilson
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705
| | | | | | - Kim L Weisgrau
- Wisconsin National Primate Research Center, Madison, WI 53715
| | - Dawn M Dudley
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705; .,Wisconsin National Primate Research Center, Madison, WI 53715
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Campos-Pinto I, Méndez L, Schouten J, Wilkins J, Fedorova M, Pitt AR, Davis P, Spickett CM. Epitope mapping and characterization of 4-hydroxy-2-nonenal modified-human serum albumin using two different polyclonal antibodies. Free Radic Biol Med 2019; 144:234-244. [PMID: 31075498 DOI: 10.1016/j.freeradbiomed.2019.05.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/06/2019] [Accepted: 05/06/2019] [Indexed: 12/28/2022]
Abstract
Lipids are susceptible to damage by reactive oxygen species, and from lipid oxidation reactions many short chain lipid peroxidation products can be formed. 4-Hydroxy-2-nonenal (HNE) is one of the most abundant and cytotoxic lipid oxidation products and is known to form covalent adducts with nucleophilic amino acids of proteins. HNE-modified proteins have value as biomarkers and can be detected by antibody-based techniques, but most commercially available antibodies were raised against HNE-keyhole limpet hemocyanin. We used HNE-treated human serum albumin (HSA) to raise sheep antiserum and report for the first time the use of covalently modified peptide arrays to assess epitope binding of antibodies (Abs). Peptide arrays covering the sequence of HSA and treated post peptide synthesis with HNE were used to compare the different binding patterns of a commercial polyclonal antibody (pAb) raised against HNE-treated KLH and an in-house anti-HNE enriched pAb. The results were correlated with analysis of HNE-modified HSA by high-resolution tandem mass spectrometry. Both anti-HNE pAbs were found to bind strongly to eight common peptides on the HNE-treated HSA membranes, suggesting that HNE adducts per se induced an immune response in both cases even though different immunogens were used. Both antibodies bound with the highest affinity to the peptide 365DPHECYAKVFDEFKPLV381, which contains K378 and was also shown to be modified by the mass spectrometry analysis. Overall, the commercial anti-HNE pAb showed better specificity, recognizing nine out of the eleven adducts found by MS/MS, while the in-house enriched pAb only recognizes six. Nevertheless, the in-house pAb recognized specific peptides that were not recognized by the commercial pAb, which suggests the presence of clones uniquely specific to HNE adducts on HSA.
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Affiliation(s)
- Isabel Campos-Pinto
- Mologic, Ltd, Bedford Technology Park, Thurleigh, Bedfordshire, MK44 2YA, UK; School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - Lucía Méndez
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Germany; Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, 04103, Leipzig, Germany; Institute of Marine Research, Spanish Council for Scientific Resesarch, (IIM-CSIC), Vigo, Spain
| | - James Schouten
- Mologic, Ltd, Bedford Technology Park, Thurleigh, Bedfordshire, MK44 2YA, UK
| | - John Wilkins
- Mologic, Ltd, Bedford Technology Park, Thurleigh, Bedfordshire, MK44 2YA, UK
| | - Maria Fedorova
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, University of Leipzig, Germany; Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, 04103, Leipzig, Germany
| | - Andrew R Pitt
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Paul Davis
- Mologic, Ltd, Bedford Technology Park, Thurleigh, Bedfordshire, MK44 2YA, UK
| | - Corinne M Spickett
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
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45
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Karadag M, Arslan M, Kaleli NE, Kalyoncu S. Physicochemical determinants of antibody-protein interactions. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 121:85-114. [PMID: 32312427 DOI: 10.1016/bs.apcsb.2019.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Antibodies are specialized proteins generated by immune system for high specificity and affinity binding to target antigens. Because of their essential roles in immune system, antibodies have been successfully developed and engineered as biopharmaceuticals for treatment of various diseases. Analysis of antibody-protein interactions is always required to get detailed information on effectivity of such antibody-based therapeutics. Although physicochemical rules cannot be generalized for every antibody-protein interaction, there are some features which should be taken into account during antibody development and engineering efforts. In this chapter, physicochemical analysis of antibody paratope-protein epitope interactions will be discussed to highlight important characteristics. First, paratope and non-paratope regions of antibodies will be described and important roles of these regions on binding and biophysical features of antibodies will be discussed. Then, general features of epitope regions of protein antigens will be introduced along with several computational/experimental tools to identify them. Lastly, a rising star of antibody biopharmaceuticals, nanobodies, will be described to show importance of next-generation antibody fragment based biopharmaceuticals in drug development.
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Affiliation(s)
- Murat Karadag
- Izmir Biomedicine and Genome Center, İzmir, Turkey; Izmir Biomedicine and Genome Institute, Dokuz Eylul University, İzmir, Turkey
| | - Merve Arslan
- Izmir Biomedicine and Genome Center, İzmir, Turkey; Izmir Biomedicine and Genome Institute, Dokuz Eylul University, İzmir, Turkey
| | - Nazli Eda Kaleli
- Izmir Biomedicine and Genome Center, İzmir, Turkey; Izmir Biomedicine and Genome Institute, Dokuz Eylul University, İzmir, Turkey
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Steen J, Forsström B, Sahlström P, Odowd V, Israelsson L, Krishnamurthy A, Badreh S, Mathsson Alm L, Compson J, Ramsköld D, Ndlovu W, Rapecki S, Hansson M, Titcombe PJ, Bang H, Mueller DL, Catrina AI, Grönwall C, Skriner K, Nilsson P, Lightwood D, Klareskog L, Malmström V. Recognition of Amino Acid Motifs, Rather Than Specific Proteins, by Human Plasma Cell-Derived Monoclonal Antibodies to Posttranslationally Modified Proteins in Rheumatoid Arthritis. Arthritis Rheumatol 2019; 71:196-209. [PMID: 30152202 PMCID: PMC6563427 DOI: 10.1002/art.40699] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 08/23/2018] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Antibodies against posttranslationally modified proteins are a hallmark of rheumatoid arthritis (RA), but the emergence and pathogenicity of these autoantibodies are still incompletely understood. The aim of this study was to analyze the antigen specificities and mutation patterns of monoclonal antibodies (mAb) derived from RA synovial plasma cells and address the question of antigen cross-reactivity. METHODS IgG-secreting cells were isolated from RA synovial fluid, and the variable regions of the immunoglobulins were sequenced (n = 182) and expressed in full-length mAb (n = 93) and also as germline-reverted versions. The patterns of reactivity with 53,019 citrullinated peptides and 49,211 carbamylated peptides and the potential of the mAb to promote osteoclastogenesis were investigated. RESULTS Four unrelated anti-citrullinated protein autoantibodies (ACPAs), of which one was clonally expanded, were identified and found to be highly somatically mutated in the synovial fluid of a patient with RA. The ACPAs recognized >3,000 unique peptides modified by either citrullination or carbamylation. This highly multireactive autoantibody feature was replicated for Ig sequences derived from B cells from the peripheral blood of other RA patients. The plasma cell-derived mAb were found to target distinct amino acid motifs and partially overlapping protein targets. They also conveyed different effector functions as revealed in an osteoclast activation assay. CONCLUSION These findings suggest that the high level of cross-reactivity among RA autoreactive B cells is the result of different antigen encounters, possibly at different sites and at different time points. This is consistent with the notion that RA is initiated in one context, such as in the mucosal organs, and thereafter targets other sites, such as the joints.
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Affiliation(s)
- Johanna Steen
- Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | - Peter Sahlström
- Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden, and Charité Univeristätsmedizin, Berlin, Germany
| | | | - Lena Israelsson
- Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | - Sara Badreh
- Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | | | - Daniel Ramsköld
- Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | | | - Monika Hansson
- Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Philip J Titcombe
- Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden, and University of Minnesota Medical School, Minneapolis
| | | | | | - Anca I Catrina
- Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Caroline Grönwall
- Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | | | - Peter Nilsson
- KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Lars Klareskog
- Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Vivianne Malmström
- Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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Chen B, Khodadoust MS, Olsson N, Wagar LE, Fast E, Liu CL, Muftuoglu Y, Sworder BJ, Diehn M, Levy R, Davis MM, Elias JE, Altman RB, Alizadeh AA. Predicting HLA class II antigen presentation through integrated deep learning. Nat Biotechnol 2019; 37:1332-1343. [PMID: 31611695 PMCID: PMC7075463 DOI: 10.1038/s41587-019-0280-2] [Citation(s) in RCA: 205] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 09/09/2019] [Indexed: 12/21/2022]
Abstract
Accurate prediction of antigen presentation by human leukocyte antigen (HLA) class II molecules would be valuable for vaccine development and cancer immunotherapies. Current computational methods trained on in vitro binding data are limited by insufficient training data and algorithmic constraints. Here we describe MARIA (major histocompatibility complex analysis with recurrent integrated architecture; https://maria.stanford.edu/ ), a multimodal recurrent neural network for predicting the likelihood of antigen presentation from a gene of interest in the context of specific HLA class II alleles. In addition to in vitro binding measurements, MARIA is trained on peptide HLA ligand sequences identified by mass spectrometry, expression levels of antigen genes and protease cleavage signatures. Because it leverages these diverse training data and our improved machine learning framework, MARIA (area under the curve = 0.89-0.92) outperformed existing methods in validation datasets. Across independent cancer neoantigen studies, peptides with high MARIA scores are more likely to elicit strong CD4+ T cell responses. MARIA allows identification of immunogenic epitopes in diverse cancers and autoimmune disease.
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Affiliation(s)
- Binbin Chen
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Michael S Khodadoust
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Niclas Olsson
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Lisa E Wagar
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Ethan Fast
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Nash, Vaduz, Liechtenstein
| | - Chih Long Liu
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Yagmur Muftuoglu
- Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Brian J Sworder
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Ronald Levy
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, CA, USA
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Joshua E Elias
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub, Stanford University, Stanford, CA, USA
| | - Russ B Altman
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Ash A Alizadeh
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Center for Cancer Systems Biology, Stanford University, Stanford, CA, USA.
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48
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A spatial similarity of stereochemical environments formed by amino acid residues defines a common epitope of two non-homologous proteins. Sci Rep 2019; 9:14818. [PMID: 31616018 PMCID: PMC6794283 DOI: 10.1038/s41598-019-51350-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 07/19/2019] [Indexed: 01/02/2023] Open
Abstract
It is critical for development of high-quality antibodies in research and diagnostics to predict accurately their cross-reactivities with "off-target" molecules, which potentially induce false results. Herein, we report a good example of such a cross-reactivity for an off-target due to a stereochemical environment of epitopes, which does not simply depend on amino acid sequences. We found that significant subpopulation of a polyclonal peptide antibody against Bcnt (Bucentaur) (anti-BCNT-C antibody) cross-reacted with a completely different protein, glutamine synthetase (GS), and identified four amino acids, GYFE, in its C-terminal region as the core amino acids for the cross-reaction. Consistent with this finding, the anti-BCNT-C antibody strongly recognized endogenously and exogenously expressed GS in tissues and cultured cells by Western blotting and immunohistochemistry. Furthermore, we elucidated that the cross-reaction is caused by a spatial similarity between the stereochemical environments formed by amino acid residues, including the GYFE of GS and the GYIE of Bcnt, rather than by their primary sequences. These results suggest it is critical to comprehensively analyze antibody interactions with target molecules including off-targets with special attention to the physicochemical environments of epitope-paratope interfaces to decrease the risk of false interpretations of results using antibodies in science and clinical applications.
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49
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Shen L, Zhang J, Lee H, Batista MT, Johnston SA. RNA Transcription and Splicing Errors as a Source of Cancer Frameshift Neoantigens for Vaccines. Sci Rep 2019; 9:14184. [PMID: 31578439 PMCID: PMC6775166 DOI: 10.1038/s41598-019-50738-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 09/13/2019] [Indexed: 12/30/2022] Open
Abstract
The success of checkpoint inhibitors in cancer therapy is largely attributed to activating the patient's immune response to their tumor's neoantigens arising from DNA mutations. This realization has motivated the interest in personal cancer vaccines based on sequencing the patient's tumor DNA to discover neoantigens. Here we propose an additional, unrecognized source of tumor neoantigens. We show that errors in transcription of microsatellites (MS) and mis-splicing of exons create highly immunogenic frameshift (FS) neoantigens in tumors. The sequence of these FS neoantigens are predictable, allowing creation of a peptide array representing all possible neoantigen FS peptides. This array can be used to detect the antibody response in a patient to the FS peptides. A survey of 5 types of cancers reveals peptides that are personally reactive for each patient. This source of neoantigens and the method to discover them may be useful in developing cancer vaccines.
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Affiliation(s)
- Luhui Shen
- The Biodesign Institute Center for Innovations in Medicine, Arizona State University, Tempe, AZ, USA
| | - Jian Zhang
- The Biodesign Institute Center for Innovations in Medicine, Arizona State University, Tempe, AZ, USA
| | - HoJoon Lee
- The Biodesign Institute Center for Innovations in Medicine, Arizona State University, Tempe, AZ, USA.,Stanford University, Stanford, CA, USA
| | - Milene Tavares Batista
- The Biodesign Institute Center for Innovations in Medicine, Arizona State University, Tempe, AZ, USA
| | - Stephen Albert Johnston
- The Biodesign Institute Center for Innovations in Medicine, Arizona State University, Tempe, AZ, USA.
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50
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Nguyen HQ, Roy J, Harink B, Damle NP, Latorraca NR, Baxter BC, Brower K, Longwell SA, Kortemme T, Thorn KS, Cyert MS, Fordyce PM. Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads. eLife 2019; 8:e40499. [PMID: 31282865 PMCID: PMC6728138 DOI: 10.7554/elife.40499] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 07/03/2019] [Indexed: 12/22/2022] Open
Abstract
Transient, regulated binding of globular protein domains to Short Linear Motifs (SLiMs) in disordered regions of other proteins drives cellular signaling. Mapping the energy landscapes of these interactions is essential for deciphering and perturbing signaling networks but is challenging due to their weak affinities. We present a powerful technology (MRBLE-pep) that simultaneously quantifies protein binding to a library of peptides directly synthesized on beads containing unique spectral codes. Using MRBLE-pep, we systematically probe binding of calcineurin (CN), a conserved protein phosphatase essential for the immune response and target of immunosuppressants, to the PxIxIT SLiM. We discover that flanking residues and post-translational modifications critically contribute to PxIxIT-CN affinity and identify CN-binding peptides based on multiple scaffolds with a wide range of affinities. The quantitative biophysical data provided by this approach will improve computational modeling efforts, elucidate a broad range of weak protein-SLiM interactions, and revolutionize our understanding of signaling networks.
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Affiliation(s)
- Huy Quoc Nguyen
- Department of GeneticsStanford UniversityStanfordUnited States
| | - Jagoree Roy
- Department of BiologyStanford UniversityStanfordUnited States
| | - Björn Harink
- Department of GeneticsStanford UniversityStanfordUnited States
| | - Nikhil P Damle
- Department of BiologyStanford UniversityStanfordUnited States
| | | | - Brian C Baxter
- Department of Biochemistry and BiophysicsUniversity of California, San FranciscoSan FranciscoUnited States
| | - Kara Brower
- Department of BioengineeringStanford UniversityStanfordUnited States
| | - Scott A Longwell
- Department of BioengineeringStanford UniversityStanfordUnited States
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Kurt S Thorn
- Department of Biochemistry and BiophysicsUniversity of California, San FranciscoSan FranciscoUnited States
| | - Martha S Cyert
- Department of BiologyStanford UniversityStanfordUnited States
| | - Polly Morrell Fordyce
- Department of GeneticsStanford UniversityStanfordUnited States
- Department of BioengineeringStanford UniversityStanfordUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
- ChEM-H InstituteStanford UniversityStanfordUnited States
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