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Éliás S, Wrzodek C, Deane CM, Tissot AC, Klostermann S, Ros F. Prediction of polyspecificity from antibody sequence data by machine learning. FRONTIERS IN BIOINFORMATICS 2024; 3:1286883. [PMID: 38651055 PMCID: PMC11033685 DOI: 10.3389/fbinf.2023.1286883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/06/2023] [Indexed: 04/25/2024] Open
Abstract
Antibodies are generated with great diversity in nature resulting in a set of molecules, each optimized to bind a specific target. Taking advantage of their diversity and specificity, antibodies make up for a large part of recently developed biologic drugs. For therapeutic use antibodies need to fulfill several criteria to be safe and efficient. Polyspecific antibodies can bind structurally unrelated molecules in addition to their main target, which can lead to side effects and decreased efficacy in a therapeutic setting, for example via reduction of effective drug levels. Therefore, we created a neural-network-based model to predict polyspecificity of antibodies using the heavy chain variable region sequence as input. We devised a strategy for enriching antibodies from an immunization campaign either for antigen-specific or polyspecific binding properties, followed by generation of a large sequencing data set for training and cross-validation of the model. We identified important physico-chemical features influencing polyspecificity by investigating the behaviour of this model. This work is a machine-learning-based approach to polyspecificity prediction and, besides increasing our understanding of polyspecificity, it might contribute to therapeutic antibody development.
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Affiliation(s)
- Szabolcs Éliás
- Roche Pharma Research and Early Development Informatics, Roche Innovation Center Munich, Penzberg, Germany
| | - Clemens Wrzodek
- Roche Pharma Research and Early Development Informatics, Roche Innovation Center Munich, Penzberg, Germany
| | - Charlotte M. Deane
- Oxford Protein Informatics Group, Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Alain C. Tissot
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
| | - Stefan Klostermann
- Roche Pharma Research and Early Development Informatics, Roche Innovation Center Munich, Penzberg, Germany
| | - Francesca Ros
- Roche Pharmaceutical Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, Penzberg, Germany
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2
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Martinez BI, Mousa GA, Fleck K, MacCulloch T, Diehnelt CW, Stephanopoulos N, Stabenfeldt SE. Uncovering temporospatial sensitive TBI targeting strategies via in vivo phage display. SCIENCE ADVANCES 2022; 8:eabo5047. [PMID: 35867794 PMCID: PMC9307250 DOI: 10.1126/sciadv.abo5047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
The heterogeneous pathophysiology of traumatic brain injury (TBI) is a barrier to advancing diagnostics and therapeutics, including targeted drug delivery. We used a unique discovery pipeline to identify novel targeting motifs that recognize specific temporal phases of TBI pathology. This pipeline combined in vivo biopanning with domain antibody (dAb) phage display, next-generation sequencing analysis, and peptide synthesis. We identified targeting motifs based on the complementarity-determining region 3 structure of dAbs for acute (1 day post-injury) and subacute (7 days post-injury) post-injury time points in a preclinical TBI model (controlled cortical impact). Bioreactivity and temporal sensitivity of the targeting motifs were validated via immunohistochemistry. Immunoprecipitation-mass spectrometry indicated that the acute TBI targeting motif recognized targets associated with metabolic and mitochondrial dysfunction, whereas the subacute TBI motif was largely associated with neurodegenerative processes. This pipeline successfully discovered temporally specific TBI targeting motif/epitope pairs that will serve as the foundation for the next-generation targeted TBI therapeutics and diagnostics.
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Affiliation(s)
- Briana I. Martinez
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Gergey Alzaem Mousa
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Kiera Fleck
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - Tara MacCulloch
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Institute Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, USA
| | - Chris W. Diehnelt
- Biodesign Institute Center for Innovations in Medicine, Arizona State University, Tempe, AZ, USA
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- Biodesign Institute Center for Molecular Design and Biomimetics, Arizona State University, Tempe, AZ, USA
| | - Sarah E. Stabenfeldt
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
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Van Holsbeeck K, Martins JC, Ballet S. Downsizing antibodies: Towards complementarity-determining region (CDR)-based peptide mimetics. Bioorg Chem 2021; 119:105563. [PMID: 34942468 DOI: 10.1016/j.bioorg.2021.105563] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/20/2021] [Accepted: 12/12/2021] [Indexed: 12/27/2022]
Abstract
Monoclonal antibodies emerged as an important therapeutic drug class with remarkable specificity and binding affinity. Nonetheless, these heterotetrameric immunoglobulin proteins come with high manufacturing and therapeutic costs which can take extraordinary proportions, besides other limitations such as their limited in cellulo access imposed by their molecular size (ca. 150 kDa). These drawbacks stimulated the development of downsized functional antibody fragments (ca. 15-50 kDa), together with smaller synthetic peptides (ca. 1-3 kDa) derived from the antibodies' crucial complementarity-determining regions (CDR). Despite the general lack of success in the literal translation of CDR loops in peptide mimetics, rational structure-based and computational approaches have shown their potential for obtaining functional CDR-based peptide mimetics. In this review, we describe the efforts made in the development of antibody and nanobody paratope-derived peptide mimetics with particular focus on the used design strategies, in addition to highlighting the challenges associated with their development.
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Affiliation(s)
- Kevin Van Holsbeeck
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; NMR and Structure Analysis Unit, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium
| | - José C Martins
- NMR and Structure Analysis Unit, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
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4
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Martinez BI, Stabenfeldt SE. In Vivo Phage Display as a Biomarker Discovery Tool for the Complex Neural Injury Microenvironment. Curr Protoc 2021; 1:e67. [PMID: 33625787 DOI: 10.1002/cpz1.67] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The heterogeneous injury pathophysiology of traumatic brain injury (TBI) is a barrier to developing highly sensitive and specific diagnostic tools. Phage display, a protein-protein screening technique routinely used in drug development, has the potential to be a powerful biomarker discovery tool for TBI. However, analysis of these large and diverse phage libraries is a bottleneck to moving through the discovery pipeline in a timely and efficient manner. This article describes a unique discovery pipeline involving domain antibody (dAb) phage in vivo biopanning and next-generation sequencing (NGS) analysis to identify targeting motifs that recognize distinct aspects of TBI pathology. To demonstrate this process, we conduct in vivo biopanning on the controlled cortical impact mouse model of experimental TBI at 1 and 7 days postinjury. Phage accumulation in target tissues is quantified via titers before NGS preparation and analysis. This phage display biomarker discovery pipeline for TBI successfully achieves discovery of temporally specific TBI targeting motifs and may further TBI biomarker research for other characteristics of injury. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Phage production and purification Support Protocol: Controlled cortical impact model Basic Protocol 2: Injection and elution of phage Basic Protocol 3: Amplicon sequencing and sequence analysis.
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Affiliation(s)
- Briana I Martinez
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona.,School of Life Sciences, Arizona State University, Tempe, Arizona
| | - Sarah E Stabenfeldt
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona
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5
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White HN. B-Cell Memory Responses to Variant Viral Antigens. Viruses 2021; 13:565. [PMID: 33810456 PMCID: PMC8066974 DOI: 10.3390/v13040565] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/19/2021] [Accepted: 03/24/2021] [Indexed: 02/06/2023] Open
Abstract
A central feature of vertebrate immune systems is the ability to form antigen-specific immune memory in response to microbial challenge and so provide protection against future infection. In conflict with this process is the ability that many viruses have to mutate their antigens to escape infection- or vaccine-induced antibody memory responses. Mutable viruses such as dengue virus, influenza virus and of course coronavirus have a major global health impact, exacerbated by this ability to evade immune responses through mutation. There have been several outstanding recent studies on B-cell memory that also shed light on the potential and limitations of antibody memory to protect against viral antigen variation, and so promise to inform new strategies for vaccine design. For the purposes of this review, the current understanding of the different memory B-cell (MBC) populations, and their potential to recognize mutant antigens, will be described prior to some examples from antibody responses against the highly mutable RNA based flaviviruses, influenza virus and SARS-CoV-2.
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Affiliation(s)
- Harry N White
- Department of Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
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6
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Guthmiller JJ, Lan LYL, Fernández-Quintero ML, Han J, Utset HA, Bitar DJ, Hamel NJ, Stovicek O, Li L, Tepora M, Henry C, Neu KE, Dugan HL, Borowska MT, Chen YQ, Liu STH, Stamper CT, Zheng NY, Huang M, Palm AKE, García-Sastre A, Nachbagauer R, Palese P, Coughlan L, Krammer F, Ward AB, Liedl KR, Wilson PC. Polyreactive Broadly Neutralizing B cells Are Selected to Provide Defense against Pandemic Threat Influenza Viruses. Immunity 2020; 53:1230-1244.e5. [PMID: 33096040 PMCID: PMC7772752 DOI: 10.1016/j.immuni.2020.10.005] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/14/2020] [Accepted: 10/07/2020] [Indexed: 12/19/2022]
Abstract
Polyreactivity is the ability of a single antibody to bind to multiple molecularly distinct antigens and is a common feature of antibodies induced upon pathogen exposure. However, little is known about the role of polyreactivity during anti-influenza virus antibody responses. By analyzing more than 500 monoclonal antibodies (mAbs) derived from B cells induced by numerous influenza virus vaccines and infections, we found mAbs targeting conserved neutralizing influenza virus hemagglutinin epitopes were polyreactive. Polyreactive mAbs were preferentially induced by novel viral exposures due to their broad viral binding breadth. Polyreactivity augmented mAb viral binding strength by increasing antibody flexibility, allowing for adaption to imperfectly conserved epitopes. Lastly, we found affinity-matured polyreactive B cells were typically derived from germline polyreactive B cells that were preferentially selected to participate in B cell responses over time. Together, our data reveal that polyreactivity is a beneficial feature of antibodies targeting conserved epitopes.
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Affiliation(s)
- Jenna J Guthmiller
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Linda Yu-Ling Lan
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Monica L Fernández-Quintero
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Julianna Han
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Henry A Utset
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Dalia J Bitar
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Natalie J Hamel
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Olivia Stovicek
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Lei Li
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Micah Tepora
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Carole Henry
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Karlynn E Neu
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Haley L Dugan
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Marta T Borowska
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Yao-Qing Chen
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Sean T H Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Nai-Ying Zheng
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Min Huang
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Anna-Karin E Palm
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Tisch Cancer Center, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Raffael Nachbagauer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Peter Palese
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lynda Coughlan
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Microbiology and Immunology and Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Klaus R Liedl
- Center for Molecular Biosciences Innsbruck, Institute of General, Inorganic and Theoretical Chemistry, University of Innsbruck, 6020 Innsbruck, Austria
| | - Patrick C Wilson
- Department of Medicine, Section of Rheumatology, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA.
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7
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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: 0.6] [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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8
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Kaleli NE, Karadag M, Kalyoncu S. Phage display derived therapeutic antibodies have enriched aliphatic content: Insights for developability issues. Proteins 2019; 87:607-618. [DOI: 10.1002/prot.25685] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/07/2019] [Accepted: 03/13/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Nazlı Eda Kaleli
- Izmir Biomedicine and Genome Center Izmir Turkey
- Izmir Biomedicine and Genome Institute, Dokuz Eylül University Izmir Turkey
| | - Murat Karadag
- Izmir Biomedicine and Genome Center Izmir Turkey
- Izmir Biomedicine and Genome Institute, Dokuz Eylül University Izmir Turkey
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9
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Klinger M. A role for macromolecular crowding in off-target binding of therapeutic antibodies. Protein Eng Des Sel 2017; 30:489-494. [PMID: 28873984 DOI: 10.1093/protein/gzx035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 06/21/2017] [Indexed: 01/09/2023] Open
Abstract
The nonspecific binding of certain therapeutic antibodies to tissues or to soluble biomolecules can accelerate their clearance from the circulation and undermine their benefit to patients. This article proposes that tandem amino acid repeat sequences in antibody hypervariable segments, particularly the complementarity determining regions (CDRs), can enhance this off-target binding. This hypothesis is based on two sets of observations. First, in a limited number of cases, antibodies with clusters of amino acid repeats in their CDRs have significantly higher clearance rates in experimental animals than otherwise identical antibodies without the repeats. Second, tandem amino acid repeats are abundant in intracellular hub proteins where they appear to promote the promiscuous binding of these proteins to a wide variety of other molecules. These nonspecific hub protein interactions are highly favored by the intense macromolecular crowding that permeates the cytoplasm. A survey of the variable region sequences of 137 antibodies in various stages of development revealed that 26 have at least one CDR containing a cluster of three closely spaced amino acid repeats. If the overall hypothesis is valid, then it suggests strategies for site-directed mutagenesis to improve pharmacokinetic behavior and for the design of more reliable in vitro binding assays to predict off-target binding in vivo.
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Affiliation(s)
- Martin Klinger
- Hawk BioDiscovery, 7465 Highway 51, Sterrett, AL 35147, USA
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10
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Mannoor K, Xu Y, Chen C. Natural autoantibodies and associated B cells in immunity and autoimmunity. Autoimmunity 2013. [DOI: 10.3109/08916934.2012.748753] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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11
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Tschumper RC, Geyer SM, Campbell ME, Kay NE, Shanafelt TD, Zent CS, Nowakowski GS, Call TG, Dewald GW, Jelinek DF. Immunoglobulin diversity gene usage predicts unfavorable outcome in a subset of chronic lymphocytic leukemia patients. J Clin Invest 2008; 118:306-15. [PMID: 18064298 DOI: 10.1172/jci32625] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2007] [Accepted: 10/17/2007] [Indexed: 11/17/2022] Open
Abstract
Survival of patients with B cell chronic lymphocytic leukemia (B-CLL) can be predicted by analysis of mutations in the immunoglobulin heavy chain variable gene (IGHV). Patients without mutations (unmutated [UM]) are at greater risk for disease progression and death than patients with mutations (M). Despite this broad prognostic difference, there remains wide intragroup variation in the clinical outcome of UM patients, especially those with low/intermediate Rai risk disease. We evaluated UM B-CLL patients with low/intermediate Rai risk to determine the relationship between IGHV, IGH diversity (IGHD), and IGH joining (IGHJ) gene usage and time to treatment (TTT). Irrespective of IGHV usage, UM patients whose B-CLL cells expressed the IGHD3-3 gene had a significantly shorter TTT than other UM B-CLL patients, and specifically, use of the IGHD3-3 gene in reading frame 2 (RF2) predicted shorter TTT. As expected, Rai risk was the best single prognostic factor for TTT; however, IGHD usage was also a significant variable for TTT. Therefore, both IGHD gene and IGHD RF usage have prognostic relevance in UM B-CLL patients with low/intermediate Rai risk disease. In addition, these data support the concept that antigen-driven selection of specific Ig receptors plays a role in the clinical course of B-CLL.
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Affiliation(s)
- Renee C Tschumper
- Department of Immunology, Mayo Clinic College of Medicine, Mayo Clinic, Rochester, Minnesota 55905, USA
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12
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Tian Q, Beardall M, Xu Y, Li J, Parker DC, Casanova N, Bakke AC, Chen C. B Cells Expressing a Natural Polyreactive Autoantibody Have a Distinct Phenotype and Are Overrepresented in Immunoglobulin Heavy Chain Transgenic Mice. THE JOURNAL OF IMMUNOLOGY 2006; 177:2412-22. [PMID: 16888003 DOI: 10.4049/jimmunol.177.4.2412] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Despite stringent regulation of disease-associated autoantibodies, a substantial proportion of circulating Abs in sera of healthy individuals exhibit self-reactivity. These Abs are referred to as naturally occurring or natural autoantibodies (NAAs). To understand the origin and function of NAAs, we have generated a new site-directed transgenic mouse model in which a prerearranged VDJ gene coding for the H chain of a typical polyreactive NAA, ppc1-5, is inserted into the IgH locus. This H chain, when combined with its original L chain, the lambda1 L chain, yields a NAA that characteristically binds a variety of self and non-self Ags including ssDNA, actin, ubiquitin, and nitrophenyl phosphocholine. Despite their autoreactivity, B cells expressing ppc1-5H/lambda1 NAA are not negatively selected, but rather are overrepresented in the transgenic mice. The shift toward lambda1 expression mainly occurs during the transition of immature to mature B cells in the spleen, suggesting a BCR selection process. The ppc1-5H/lambda1 B cells exhibit a phenotype that is different from those of the known mature B cell populations, and they are located predominantly in the lymphoid follicles of the spleen and the lymph nodes. These B cells are functionally active, producing high levels of Abs in vivo and responding well to BCR stimulation in vitro. The findings indicate that the ppc1-5/lambda1 natural autoantibodies originate from a distinct B cell subset that may be positively selected by virtue of its poly/autoreactivity.
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Affiliation(s)
- Qi Tian
- Department of Pathology L113, Oregon Health and Science University, Portland, OR 97239, USA
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Marchalonis JJ, Adelman MK, Schluter SF, Ramsland PA. The antibody repertoire in evolution: chance, selection, and continuity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2006; 30:223-47. [PMID: 16083959 DOI: 10.1016/j.dci.2005.06.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
All jawed vertebrates contain the genetic elements essential for the function of the adaptive/combinatorial immune response, have diverse sets of natural antibodies resulting from segmental gene recombination, express comparable functional repertoires and can produce specific antibodies following appropriate immunization. Profound variability occurs in the third hypervariable (CDR3) segments of light and heavy chains even within antibodies of the same ostensible specificity. Germline VH and VL elements, as well as the joining (J) segments are highly conserved among the distinct vertebrate species. Conservation is particularly noted among the VH3-like sequences of all jawed vertebrates in the FR2 and FR3 segments, as well as in the FGXGT(R or K)L J-segment characteristic of light chains and TCRs and the WGXGT(uncharged)VT JH segments. Human VH3-53 and Vlambda6 family orthologs may be present over the entire range of vertebrates. Models of the three-dimensional structures of shark VH/VL combining sites indicate similarity in framework structure and comparable CDR usage to those of man. Although carcharhine shark VH regions show greater than 50% identity to the human VH germline prototype, searches of lower deuterostome and invertebrate databases fail to detect molecules with significant relatedness. Overall, antibodies of jawed vertebrates show tremendous individual diversity, but are constructed incorporating design features that arose with the evolutionary emergence of the jawed vertebrates and have been conserved through at least 450 million years of evolutionary time.
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Affiliation(s)
- John J Marchalonis
- Department of Microbiology and Immunology, College of Medicine, University of Arizona, 1501 N. Campbell Ave., Tucson, AZ 85724-5049, USA.
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Solem ST, Stenvik J. Antibody repertoire development in teleosts--a review with emphasis on salmonids and Gadus morhua L. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2006; 30:57-76. [PMID: 16084588 DOI: 10.1016/j.dci.2005.06.007] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The group of teleosts is highly diverse, comprising more than 23000 extant species. Studies of the teleost antibody repertoire have been conducted in many different species within different orders, though some species and families have been better characterised than others. The Atlantic cod (Gadus morhua L.) and several species within the Salmoninae (e.g. Salmo salar and Oncorynchus mykiss) are among the best-studied teleosts in terms of the antibody repertoire. The estimated size of the repertoire, the organisation of immunoglobulin (IG) gene segments, the expressed IG repertoire, the IgM serum concentration, and the serum antibody responses reveal some fundamental differences between these species. The serum IgM concentration of G. morhua is some ten times higher than that of S. salar, though G. morhua is characterised as a 'low' (or 'non') responder in terms of specific antibody production. In contrast, an antibody response is readily induced in S. salar, although the response is strongly regulated by antigen induced suppression. The IGHD gene of G. morhua has a unique structure, while the IGHM and IGHD genes of S. salar have a characteristic genomic organisation in two parallel loci. In addition, salmonids, express a broad repertoire of IGH and IGI V-region gene segments, while a single V gene family dominates the expressed heavy and light chain repertoire of G. morhua. Little is known about the developing antibody repertoire during ontogeny, in different stages of B-cell maturation, or in separate B-cell subsets. Information on the establishment of the preimmune repertoire, and the possible role of environmental antigens is also sparse.
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Affiliation(s)
- Stein Tore Solem
- Department of Marine Biotechnology, Norwegian College of Fishery Science, Breivika, N-9037 Tromsø, Norway.
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Adelman MK, Schluter SF, Marchalonis JJ. The natural antibody repertoire of sharks and humans recognizes the potential universe of antigens. Protein J 2004; 23:103-18. [PMID: 15106876 DOI: 10.1023/b:jopc.0000020077.73751.76] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In ancestral sharks, a rapid emergence in the evolution of the immune system occurred, giving jawed-vertebrates the necessary components for the combinatorial immune response (CIR). To compare the natural antibody (NAb) repertoires of the most divergent vertebrates with the capacity to produce antibodies, we isolated NAbs to the same set of antigens by affinity chromatography from two species of Carcharhine sharks and from human polyclonal IgG and IgM antibody preparations. The activities of the affinity-purified anti-T-cell receptor (anti-TCR) NAbs were compared with those of monoclonal anti-TCR NAbs that were generated from a systemic lupus erythematosus patient. We report that sharks and humans, representing the evolutionary extremes of vertebrate species sharing the CIR, have NAbs to human TCRs, Igs, the human senescent cell antigen, and to numerous retroviral antigens, indicating that essential features of the combinatorial repertoire and the capacity to recognize the potential universe of antigens is shared among all jawed-vertebrates.
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Affiliation(s)
- Miranda K Adelman
- Microbiology and Immunology, College of Medicine, University of Arizona, Tucson, AZ 85724, USA
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16
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Berezov A, Greene MI, Murali R. Structure-based approaches to inhibition of erbB receptors with peptide mimetics. Immunol Res 2004; 27:303-8. [PMID: 12857977 DOI: 10.1385/ir:27:2-3:303] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The epidermal growth factor (EGF) family of tyrosine kinase receptors (erbB receptors) are expressed at high levels in a wide variety of human cancers and have been associated with various features of advanced disease and poor prognosis. Therapeutic blockade of erbB signaling is a novel approach to the treatment of human tumors that could offer a noncytotoxic alternative to cancer treatment. A number of monoclonal antibodies (MAbs) directed against erbB receptors have been developed and demonstrated promising therapeutic results. We have designed small-molecule peptide mimetics of an anti-erbB rhu MAb 4D5 that can mimic structural and functional properties of the parental antibody. An alternative structure-based strategy of erbB receptor blockade with peptide mimetics by targeting receptor dimerization interfaces is also described.
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Affiliation(s)
- Alan Berezov
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, and the Abramson Family Cancer Research Institute, Philadelphia, PA 19104, USA
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17
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Collins AM, Sewell WA, Edwards MR. Immunoglobulin gene rearrangement, repertoire diversity, and the allergic response. Pharmacol Ther 2003; 100:157-70. [PMID: 14609718 DOI: 10.1016/j.pharmthera.2003.07.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The immunoglobulin repertoire arises as a consequence of combinatorial diversity, junctional diversity, and the process of somatic point mutation. Each of these processes involves biases that limit and shape the available immunoglobulin repertoire. The expressed repertoire is further shaped by selection, to the extent that biased gene usage can become apparent in many disease states. The study of rearranged immunoglobulin genes therefore may not only provide insights into the molecular processes involved in the generation of antibody diversity but also inform us of pathogenic processes and perhaps identify particular lymphocyte clones as therapeutic targets. Partly as a consequence of the low numbers of circulating IgE-committed B-cells, studies of rearranged IgE genes in allergic individuals have commenced relatively recently. In this review, recent advances in our understanding of the processes of immunoglobulin gene rearrangement and somatic point mutation are described, and biases inherent to these processes are discussed. The evidence that some diseases may be associated with particular gene rearrangements is then considered, with a particular focus on allergic disease. Reviewed data suggest that an important contribution to the IgE response may come from cells that use relatively rare heavy chain V (V(H)) segment genes, which display little somatic point mutation. Some IgE antibodies also seem to display polyreactive binding. In other contexts, these 3 characteristics have been associated with antibodies of the B-1 B-cell subset, and the possibility that B-1 B-cells contribute to the allergic response is therefore considered.
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Affiliation(s)
- A M Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, Sydney, Australia.
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18
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Edwards MR, Brouwer W, Choi CHY, Ruhno J, Ward RL, Collins AM. Analysis of IgE antibodies from a patient with atopic dermatitis: biased V gene usage and evidence for polyreactive IgE heavy chain complementarity-determining region 3. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2002; 168:6305-13. [PMID: 12055246 DOI: 10.4049/jimmunol.168.12.6305] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
To better understand V gene usage, specificity, and clonal origins of IgE Abs in allergic reactions, we have constructed a combinatorial Ab library from the mRNA of an adult patient with atopic dermatitis. Sequence analysis of random clones revealed that 33% of clones used the IGHV6-1 H chain V gene segment, the only member of the V(H)6 gene family. IGHV6-1 is rarely used in the expressed adult repertoire; however, it is associated with fetal derived Abs. Features of the V(H)6 rearrangements included short complementarity-determining region 3, frequent use of IGHD7-27 D gene, and little nucleotide addition at the D-J junction. There was also a low level of mutation compared with V(H)1, V(H)3, and V(H)4 rearrangements. The library was expressed as phage-Fab fusions, and specific phage selected by panning on the egg allergen ovomucoid. Upon expression as soluble IgE Fabs, 12 clones demonstrated binding to ovomucoid, skim milk, and BSA by ELISA. Nucleotide sequencing demonstrated that the IGHV6-1 V gene segment encoded each of the 12 multiply reactive IgE Fabs. A cyclic peptide was designed from the complementarity-determining region 3 of several of these clones. The cyclic peptide bound both self and nonself Ags, including ovomucoid, human IgG, tetanus toxoid, and human and bovine von Willebrand factor. These results suggest that some IgE Abs may bind more than one Ag, which would have important implications for understanding the multiple sensitivities seen in conditions such as atopic dermatitis.
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MESH Headings
- Adult
- Amino Acid Sequence
- Antibody Diversity/genetics
- Antibody Specificity/genetics
- Binding Sites, Antibody/genetics
- Binding, Competitive/genetics
- Binding, Competitive/immunology
- Cloning, Molecular
- Complementarity Determining Regions/analysis
- Complementarity Determining Regions/genetics
- Complementarity Determining Regions/metabolism
- DNA Mutational Analysis
- Dermatitis, Atopic/genetics
- Dermatitis, Atopic/immunology
- Female
- Gene Library
- Gene Rearrangement, B-Lymphocyte, Heavy Chain
- Humans
- Immunoglobulin E/analysis
- Immunoglobulin E/genetics
- Immunoglobulin E/metabolism
- Immunoglobulin Fab Fragments/biosynthesis
- Immunoglobulin Fragments/biosynthesis
- Immunoglobulin Fragments/genetics
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Heavy Chains/metabolism
- Immunoglobulin J-Chains/genetics
- Immunoglobulin Variable Region/genetics
- Immunoglobulin Variable Region/metabolism
- Molecular Sequence Data
- Nucleotides/metabolism
- Ovomucin/metabolism
- Peptides, Cyclic/chemical synthesis
- Peptides, Cyclic/metabolism
- Protein Binding/genetics
- Protein Binding/immunology
- Sequence Analysis, DNA
- Sequence Analysis, Protein
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Affiliation(s)
- Michael R Edwards
- School of Microbiology and Immunology, University of New South Wales, Kensington, Australia
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19
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Marchalonis JJ, Kaveri S, Lacroix-Desmazes S, Kazatchkine MD. Natural recognition repertoire and the evolutionary emergence of the combinatorial immune system. FASEB J 2002; 16:842-8. [PMID: 12039866 DOI: 10.1096/fj.01-0953hyp] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The primordial combinatorial immune recognition repertoire arose in the evolution of jawed vertebrates approximately 450 million years ago as a rapid genetic process independent of antigenic selection. We propose that it encompassed the entire repertoire of innate immunity involving molecules that had evolved over billions of years. The 'antigen-driven' compartment involving invasive pathogens operates in 'real time' showing inducibility and increases in affinity. Individuals within a species differ in their repertoires because of distinct antigenic challenges, genetics, or local environmental effects. The 'homeostatic' compartment that recognizes invariant cell and serum components should be conserved in all individuals of a species. The potential to recapitulate the entire recognition spectrum must be regenerated during the formation of new species. Evidence for the capacity of the combinatorial response to encompass the entire preexisting repertoire was obtained in studies of natural human IgG antibodies present in intravenous immunoglobulin. Since essential cellular recognition and regulatory elements are conserved throughout evolution, we propose that the natural antibodies of sharks, the most anciently emerged vertebrates to possess the combinatorial immune response, will resemble those of mammals in showing specificity for the conserved recognition/regulatory molecules. If verified, this hypothesis will establish the fundamental importance of natural antibodies not only in defense, but in regulation and functional homeostasis of the individual.
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20
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Robey IF, Edmundson AB, Schluter SF, Yocum DE, Marchalonis JJ. Specificity mapping of human anti-T cell receptor monoclonal natural antibodies: defining the properties of epitope recognition promiscuity. FASEB J 2002; 16:642-52. [PMID: 11978728 DOI: 10.1096/fj.01-0884com] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The classical concept of antibody binding is defined as an exclusive and high-affinity interaction with one epitope. The emerging reality about antibody combing sites, however, is that some can bind unrelated determinants. The studies presented here define this quality as epitope recognition promiscuity by analyzing the capacity of monoclonal human autoantibodies to bind sets of overlapping peptides duplicating the complete structures of T cell receptor (TCR) alpha and beta chains and immunoglobulin lambda chain. We assessed the binding of these monoclonal antibodies (mAbs) to a set of homologous peptides corresponding to the CDR1 segments of human Vbeta gene products, a major epitope used in the selection of the antibodies. We present data on the binding characteristics of four human mAbs selected for the ability to bind TCR epitopes. These mAbs are IgM molecules with VH and VL sequences in germline configuration, but have diverse VH CDR3 regions. These studies aim to characterize the property of epitope promiscuity and show that the relationship between the binding site and its epitope is a complex interaction and unpredictable from antigen sequence alone. Our results support the conclusion that epitope recognition promiscuity is a genuine feature of antibody and TCR recognition.
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Affiliation(s)
- Ian F Robey
- Department of Microbiology and Immunology, College of Medicine, University of Arizona, Tucson, Arizona 85724, USA
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21
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Berezov A, Zhang HT, Greene MI, Murali R. Disabling erbB receptors with rationally designed exocyclic mimetics of antibodies: structure-function analysis. J Med Chem 2001; 44:2565-74. [PMID: 11472210 DOI: 10.1021/jm000527m] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Overexpression of the HER2 receptor is observed in about 30% of breast and ovarian cancers and is often associated with an unfavorable prognosis. We have recently designed an anti-HER2 peptide (AHNP) based on the structure of the CDR-H3 loop of the anti-HER2 rhumAb 4D5 and showed that this peptide can mimic some functions of rhumAb 4D5. The peptide disabled HER2 tyrosine kinases in vitro and in vivo similar to the monoclonal antibody (Park, B.-W. et al. Nat. Biotechnol. 2000, 18, 194--198). AHNP has been shown to selectively bind to the extracellular domain of the HER2 receptor with a submicromolar affinity in Biacore assays. In the present paper, we demonstrate that in addition to being a structural and functional mimic of rhumAb 4D5, AHNP can also effectively compete with the antibody for binding to the HER2 receptor indicating a similar binding site for the peptide and the parental antibody. To further develop AHNP as an antitumor agent useful for preclinical trials and as a radiopharmaceutical to be used for tumor imaging, a number of derivatives of AHNP have been designed. Structure--function relationships have been studied using surface plasmon resonance technology. Some of the AHNP analogues have improved binding properties, solubility, and cytotoxic activity relative to AHNP. Residues in the exocyclic region of AHNP appear to be essential for high-affinity binding. Kinetic and equilibrium analysis of peptide-receptor binding for various AHNP analogues revealed a strong correlation between peptide binding characteristics and their biological activity. For AHNP analogues, dissociation rate constants have been shown to be better indicators of peptide biological activity than receptor-binding affinities. This study demonstrates a possibility of mimicking the well-documented antibody effects and its applications in tumor therapy by much smaller antibody-based cyclic peptides with potentially significant therapeutic advantages. Strategies used to improve binding properties of rationally designed AHNP analogues are discussed.
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MESH Headings
- Animals
- Antibodies, Monoclonal/chemistry
- Antineoplastic Agents/chemical synthesis
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/metabolism
- Antineoplastic Agents/pharmacology
- Binding, Competitive
- Cell Division/drug effects
- Drug Design
- Kinetics
- Mice
- Models, Molecular
- Molecular Mimicry
- Oligopeptides/chemical synthesis
- Oligopeptides/chemistry
- Oligopeptides/metabolism
- Oligopeptides/pharmacology
- Peptides, Cyclic/chemical synthesis
- Peptides, Cyclic/chemistry
- Peptides, Cyclic/metabolism
- Peptides, Cyclic/pharmacology
- Radiopharmaceuticals/chemical synthesis
- Radiopharmaceuticals/chemistry
- Receptor, ErbB-2/drug effects
- Receptor, ErbB-2/metabolism
- Solubility
- Structure-Activity Relationship
- Surface Plasmon Resonance
- Tumor Cells, Cultured
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Affiliation(s)
- A Berezov
- Department of Pathology and Laboratory Medicine, University of Pennsylvania School of Medicine, 36th and Hamilton Walk, Philadelphia, Pennsylvania 19104, USA
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22
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Notkins AL. Polyreactive antibodies and polyreactive antigen-binding B (PAB) Cells. Curr Top Microbiol Immunol 2001; 252:241-9. [PMID: 11125481 DOI: 10.1007/978-3-642-57284-5_25] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- A L Notkins
- Experimental Medicine Section, Oral Infection and Immunity Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, 30 Convent Drive, Bethesda, Maryland 20892, USA
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23
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Marchalonis JJ, Adelman MK, Robey IF, Schluter SF, Edmundson AB. Exquisite specificity and peptide epitope recognition promiscuity, properties shared by antibodies from sharks to humans. J Mol Recognit 2001; 14:110-21. [PMID: 11301481 DOI: 10.1002/jmr.527] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This review considers definitions of the specificity of antibodies including the development of recent concepts of recognition polyspecificity and epitope promiscuity. Using sets of homologous and unrelated peptides derived from the sequences of immunoglobulin and T cell receptor chains we offer operational definitions of cross-reactivity by investigating correlations of either identities in amino acid sequence, or in hydrophobicity/hydrophilicity profiles with degree of binding in enzyme-linked immunosorbent assays. Polyreactivity, or polyspecificity, are terms used to denote binding of a monoclonal antibody or purified antibody preparation to large complex molecules that are structurally unrelated, such as thyroglobulin and DNA. As a first approximation, there is a linear correlation between degree of sequence identity or hydrophobicity/hydrophilicity and antigenic cross-binding. However, catastrophic interchanges of amino acids can occur where changing of one amino acid out of 16 in a synthetic peptide essentially eliminates binding to certain antibodies. An operational definition of epitope promiscuity for peptides is the case where two peptides show little or no identity in amino acid sequence but bind strongly to the same antibody as shown by either direct binding or competitive inhibition. Analysis of antibodies of humans and sharks, the two most divergent species in evolution to express antibodies and the combinatorial immune response, indicates that the capacity for both exquisite specificity and epitope recognition promiscuity are essential conserved features of individual vertebrate antibodies.
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Affiliation(s)
- J J Marchalonis
- Microbiology and Immunology, College of Medicine, University of Arizona, Tucson, Arizona, USA.
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