51
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Bahmani B, Uehara M, Jiang L, Ordikhani F, Banouni N, Ichimura T, Solhjou Z, Furtmüller GJ, Brandacher G, Alvarez D, von Andrian UH, Uchimura K, Xu Q, Vohra I, Yilmam OA, Haik Y, Azzi J, Kasinath V, Bromberg JS, McGrath MM, Abdi R. Targeted delivery of immune therapeutics to lymph nodes prolongs cardiac allograft survival. J Clin Invest 2018; 128:4770-4786. [PMID: 30277476 PMCID: PMC6205374 DOI: 10.1172/jci120923] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 08/21/2018] [Indexed: 12/12/2022] Open
Abstract
The targeted delivery of therapeutic drugs to lymph nodes (LNs) provides an unprecedented opportunity to improve the outcomes of transplantation and immune-mediated diseases. The high endothelial venule is a specialized segment of LN vasculature that uniquely expresses peripheral node addressin (PNAd) molecules. PNAd is recognized by MECA79 mAb. We previously generated a MECA79 mAb-coated microparticle (MP) that carries tacrolimus. Although this MP trafficked to LNs, it demonstrated limited therapeutic efficacy in our transplant model. Here, we have synthesized a nanoparticle (NP) as a carrier of anti-CD3, and optimized the conjugation strategy to coat the NP surface with MECA79 mAb (MECA79-anti-CD3-NP) to enhance LN accumulation. As compared with nonconjugated NPs, a significantly higher quantity of MECA79-NPs accumulated in the draining lymph node (DLN). Many MECA79-NPs underwent internalization by T cells and dendritic cells within the LNs. Short-term treatment of murine cardiac allograft recipients with MECA79-anti-CD3-NP resulted in significantly prolonged allograft survival in comparison with the control groups. Prolonged graft survival following treatment with MECA79-anti-CD3-NP was characterized by a significant increase in intragraft and DLN Treg populations. Treg depletion abrogated the prolongation of heart allograft survival. We believe this targeted approach of drug delivery could redefine the methods of administering immune therapeutics in transplantation.
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Affiliation(s)
- Baharak Bahmani
- Transplantation Research Center and.,Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mayuko Uehara
- Transplantation Research Center and.,Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Liwei Jiang
- Transplantation Research Center and.,Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Farideh Ordikhani
- Transplantation Research Center and.,Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Naima Banouni
- Transplantation Research Center and.,Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Takaharu Ichimura
- Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Zhabiz Solhjou
- Transplantation Research Center and.,Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Georg J Furtmüller
- Department of Plastic and Reconstructive Surgery, Vascularized Composite Allotransplantation Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Gerald Brandacher
- Department of Plastic and Reconstructive Surgery, Vascularized Composite Allotransplantation Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - David Alvarez
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Ulrich H von Andrian
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Kenji Uchimura
- Unite de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS, Universite de Lille 1, Villeneuve d'Ascq, France
| | - Qiaobing Xu
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts, USA
| | - Ishaan Vohra
- Transplantation Research Center and.,Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Osman A Yilmam
- Transplantation Research Center and.,Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Yousef Haik
- College of Science and Engineering, Hamad bin Khalifa University, Doha, Qatar
| | - Jamil Azzi
- Transplantation Research Center and.,Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Vivek Kasinath
- Transplantation Research Center and.,Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jonathan S Bromberg
- Department of Surgery and Microbiology and Immunobiology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Martina M McGrath
- Transplantation Research Center and.,Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Reza Abdi
- Transplantation Research Center and.,Renal Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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52
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Nowak C, Tiwari A, Liu H. Asparagine Deamidation in a Complementarity Determining Region of a Recombinant Monoclonal Antibody in Complex with Antigen. Anal Chem 2018; 90:6998-7003. [DOI: 10.1021/acs.analchem.8b01322] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Christine Nowak
- Product Characterization, Alexion Pharmaceuticals, 100 College Street, New Haven, Connecticut 06510, United States
| | - Ashish Tiwari
- Product Characterization, Alexion Pharmaceuticals, 100 College Street, New Haven, Connecticut 06510, United States
| | - Hongcheng Liu
- Product Characterization, Alexion Pharmaceuticals, 100 College Street, New Haven, Connecticut 06510, United States
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53
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Compositional characteristics of human peripheral TRBV pseudogene rearrangements. Sci Rep 2018; 8:5926. [PMID: 29651132 PMCID: PMC5897323 DOI: 10.1038/s41598-018-24367-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 04/03/2018] [Indexed: 11/08/2022] Open
Abstract
The diversity of the T cell receptor (TCR) complementarity determining region 3 (CDR3) repertoire is the result of random combinations, insertions and deletions during recombination of the germline V, D and J gene fragments. During evolution, some human TCR beta chain variable (TRBV) pseudogenes have been retained. Many previous studies have focused on functional TRBV genes, while little attention has been given to TRBV pseudogenes. To describe the compositional characteristics of TRBV pseudogene rearrangements, we compared and analysed TRBV pseudogenes, TRBV open reading frames (ORFs) and functional TRBV genes via high-throughput sequencing of DNA obtained from the peripheral blood of 4 healthy volunteers and 4 patients. Our results revealed several differences in J and D gene usage. The V deletion distribution profile of the pseudogenes was significantly different from that of the ORFs and functional genes. In addition, arginine, lysine and cysteine were more frequently used in putative CDR3 pseudogene rearrangements, while functional rearrangements used more leucine. This study presents a comprehensive description of the compositional characteristics of peripheral TRBV pseudogene rearrangements, which will provide a reference for further research on TRBV pseudogenes.
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54
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Abstract
Disulfide linkage is critical to protein folding and structural stability. The location of disulfide linkages for antibodies is routinely discovered by comparing the chromatograms of the reduced and non-reduced peptide mapping with location identification confirmed by collision-induced dissociation (CID) mass spectrometry (MS)/MS. However, CID product spectra of disulfide-linked peptides can be difficult to interpret, and provide limited information on the backbone region within the disulfide loop. Here, we applied an electron-transfer dissociation (ETD)/CID combined fragmentation method that identifies the disulfide linkage without intensive LC comparison, and yet maps the disulfide location accurately. The native protein samples were digested using trypsin for proteolysis. The method uses RapiGest SF Surfactant and obviates the need for reduction/alkylation and extensive sample manipulation. An aliquot of the digest was loaded onto a C4 analytical column. Peptides were gradient-eluted and analyzed using a Thermo Scientific LTQ Orbitrap Elite mass spectrometer for the ETD-triggered CID MS3 experiment. Survey MS scans were followed by data-dependent scans consisting of ETD MS2 scans on the most intense ion in the survey scan, followed by 5 MS3 CID scans on the 5 most intense ions in the ETD MS2 scan. We were able to identify the disulfide-mediated structural variants A and A/B forms and their corresponding disulfide linkages in an immunoglobulin G2 monoclonal antibody with λ light chain (IgG2λ), where the location of cysteine linkages were unambiguously determined.
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Affiliation(s)
- Xiaoyan Guan
- a Process Development, Amgen Inc. , Thousand Oaks , CA , United States
| | - Le Zhang
- a Process Development, Amgen Inc. , Thousand Oaks , CA , United States
| | - Jette Wypych
- a Process Development, Amgen Inc. , Thousand Oaks , CA , United States
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55
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Baharlou R, Tajik N, Habibi-Anbouhi M, Shokrgozar MA, Zarnani AH, Shahhosseini F, Behdani M. Generation and characterization of an anti-delta like ligand-4 Nanobody to induce non-productive angiogenesis. Anal Biochem 2018; 544:34-41. [DOI: 10.1016/j.ab.2017.12.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 10/23/2017] [Accepted: 12/11/2017] [Indexed: 12/25/2022]
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56
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Rout ED, Burnett RC, Labadie JD, Yoshimoto JA, Avery AC. Preferential use of unmutated immunoglobulin heavy variable region genes in Boxer dogs with chronic lymphocytic leukemia. PLoS One 2018; 13:e0191205. [PMID: 29385200 PMCID: PMC5791963 DOI: 10.1371/journal.pone.0191205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/30/2017] [Indexed: 01/25/2023] Open
Abstract
Human chronic lymphocytic leukemia (CLL) is a clinically heterogeneous disease, and immunoglobulin heavy variable region (IGHV) gene mutational status is an important prognostic marker. IGHV mutational status has not been previously examined in canine CLL. We sequenced the IGHV-D-J rearrangements from 55 canine patients with CLL, including 36 non-Boxer and 19 Boxer dogs. The majority of non-Boxers (75%) had mutated IGHV genes, whereas the majority of Boxers (79%) had unmutated IGHV genes. IGHV3-41 and IGHV3-67 gene usage was significantly higher in Boxers with CLL compared to non-Boxers. Additionally, 11 Boxers with large B-cell lymphoma and the normal IGHV repertoire of six control dogs (three Boxers and three non-Boxers) were sequenced. IGHV3-41 was preferentially used in Boxers with other forms of lymphoma and without lymphoproliferative disease. However, preferential use of unmutated IGHV genes was unique to Boxers with CLL, suggesting Boxers may be a valuable model to investigate unmutated CLL.
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MESH Headings
- Animals
- Base Sequence
- Case-Control Studies
- DNA Mutational Analysis
- DNA, Neoplasm/genetics
- Dog Diseases/genetics
- Dog Diseases/immunology
- Dogs
- Female
- Gene Rearrangement, B-Lymphocyte, Heavy Chain
- Genes, Immunoglobulin Heavy Chain
- Immunoglobulin Variable Region/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Leukemia, Lymphocytic, Chronic, B-Cell/veterinary
- Male
- Mutation
- Sequence Homology, Nucleic Acid
- Species Specificity
- VDJ Exons
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Affiliation(s)
- Emily D. Rout
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
| | - Robert C. Burnett
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Julia D. Labadie
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Janna A. Yoshimoto
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Anne C. Avery
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
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57
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Abstract
IMGT®, the international ImMunoGeneTics information system® ( http://www.imgt.org ), was created in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS) to manage the huge diversity of the antigen receptors, immunoglobulins (IG) or antibodies, and T cell receptors (TR). The founding of IMGT® marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. Standardized sequence and structure analysis of antibody using IMGT® databases and tools allow one to bridge, for the first time, the gap between antibody sequences and three-dimensional (3D) structures. This is achieved through the IMGT Scientific chart rules, based on the IMGT-ONTOLOGY concepts of classification (IMGT gene and allele nomenclature), description (IMGT standardized labels), and numerotation (IMGT unique numbering and IMGT Collier de Perles). IMGT® is acknowledged as the global reference for immunogenetics and immunoinformatics, and its standards are particularly useful for antibody engineering and humanization. IMGT® databases for antibody nucleotide sequences and genes include IMGT/LIGM-DB and IMGT/GENE-DB, respectively, and nucleotide sequence analysis is performed by the IMGT/V-QUEST and IMGT/JunctionAnalysis tools and for NGS by IMGT/HighV-QUEST. In this chapter, we focus on IMGT® databases and tools for amino acid sequences, two-dimensional (2D) and three-dimensional (3D) structures: the IMGT/DomainGapAlign and IMGT Collier de Perles tools and the IMGT/2Dstructure-DB and IMGT/3Dstructure-DB database. IMGT/mAb-DB provides the query interface for monoclonal antibodies (mAb), fusion proteins for immune applications (FPIA), and composite proteins for clinical applications (CPCA) and related proteins of interest (RPI) and links to the proposed and recommended lists of the World Health Organization International Nonproprietary Name (WHO INN) programme, to IMGT/2Dstructure-DB for amino acid sequences, and to IMGT/3Dstructure-DB and its associated tools (IMGT/StructuralQuery, IMGT/DomainSuperimpose) for crystallized antibodies.
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58
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Abstract
Efforts to develop effective antibody therapeutics are frequently hampered by issues such as aggregation and nonspecificity, often only detected in late stages of the development process. In this study, we used a high throughput cross-reactivity assay to select nonspecific clones from a naïve human repertoire scFv library displayed on the surface of yeast. Most antibody families were de-enriched; however, the rarely expressed VH6 family was highly enriched among nonspecific clones, representing almost 90% of isolated clones. Mutational analysis of this family reveals a dominant role of CDRH2 in driving nonspecific binding. Homology modeling of a panel of VH6 antibodies shows a constrained β-sheet structure in CDRH2 that is not present in other families, potentially contributing to nonspecificity of the family. These findings confirm the common decision to exclude VH6 from synthetic antibody libraries, and support VH6 polyreactivity as a possible important role for the family in early ontogeny and cause for its overabundance in cases of some forms of autoimmunity.
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Affiliation(s)
- Ryan L Kelly
- a Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , Cambridge , MA , U.S.A
| | - Jessie Zhao
- b Department of Chemical Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , Cambridge , MA , U.S.A
| | - Doris Le
- b Department of Chemical Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , Cambridge , MA , U.S.A
| | - K Dane Wittrup
- a Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , Cambridge , MA , U.S.A.,b Department of Chemical Engineering, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , Cambridge , MA , U.S.A
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59
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Jain T, Boland T, Lilov A, Burnina I, Brown M, Xu Y, Vásquez M. Prediction of delayed retention of antibodies in hydrophobic interaction chromatography from sequence using machine learning. Bioinformatics 2017; 33:3758-3766. [DOI: 10.1093/bioinformatics/btx519] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/11/2017] [Indexed: 12/16/2022] Open
Affiliation(s)
- Tushar Jain
- Computational Biology, Adimab, Palo Alto, CA, USA
| | - Todd Boland
- Computational Biology, Adimab, Palo Alto, CA, USA
| | | | | | | | - Yingda Xu
- Protein Analytics, Adimab, Lebanon, NH, USA
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60
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Antonacci R, Bellini M, Castelli V, Ciccarese S, Massari S. Data characterizing the genomic structure of the T cell receptor (TRB) locus in Camelus dromedarius. Data Brief 2017; 14:507-514. [PMID: 28856181 PMCID: PMC5562110 DOI: 10.1016/j.dib.2017.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/21/2017] [Accepted: 08/01/2017] [Indexed: 11/18/2022] Open
Abstract
These data are presented in support of structural and evolutionary analysis of the published article entitled “The occurrence of three D-J-C clusters within the dromedary TRB locus highlights a shared evolution in Tylopoda, Ruminantia and Suina” (Antonacci et al., 2017) [1]. Here we describe the genomic structure and the gene content of the T cell receptor beta chain (TRB) locus in Camelus dromedarius. As in the other species of mammals, the general genomic organization of the dromedary TRB locus consists of a pool of TRBV genes located upstream of in tandem TRBD-J-C clusters, followed by a TRBV gene with an inverted transcriptional orientation. A peculiarity of the dromedary TRB locus structure is the presence of three TRBD-J-C clusters, which is a common feature of sheep, cattle and pig sequences.
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Affiliation(s)
- Rachele Antonacci
- Department of Biology, University “Aldo Moro” of Bari, Bari, Italy
- Correspondence to: Dept. of Biology, University of Bari, Via Orabona, 4, 70126 Bari, Italy.Dept. of Biology, University of BariVia Orabona, 4Bari70126Italy
| | | | - Vito Castelli
- Department of Biology, University “Aldo Moro” of Bari, Bari, Italy
| | | | - Serafina Massari
- Department of Biological and Environmental Science e Technologies, University of Salento, Lecce, Italy
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61
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Regl C, Wohlschlager T, Holzmann J, Huber CG. A Generic HPLC Method for Absolute Quantification of Oxidation in Monoclonal Antibodies and Fc-Fusion Proteins Using UV and MS Detection. Anal Chem 2017; 89:8391-8398. [DOI: 10.1021/acs.analchem.7b01755] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Christof Regl
- Department
of Molecular Biology, Division of Chemistry and Bioanalytics, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria
- Christian
Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria
| | - Therese Wohlschlager
- Department
of Molecular Biology, Division of Chemistry and Bioanalytics, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria
- Christian
Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria
| | - Johann Holzmann
- Christian
Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria
- Technical
Development
Biosimilars, Physicochemical Characterization Kundl, Novartis BTDM,
Sandoz GmbH, Biochemiestrasse 10, 6250 Kundl, Austria
| | - Christian G. Huber
- Department
of Molecular Biology, Division of Chemistry and Bioanalytics, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria
- Christian
Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria
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62
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Giudicelli V, Duroux P, Kossida S, Lefranc MP. IG and TR single chain fragment variable (scFv) sequence analysis: a new advanced functionality of IMGT/V-QUEST and IMGT/HighV-QUEST. BMC Immunol 2017; 18:35. [PMID: 28651553 PMCID: PMC5485737 DOI: 10.1186/s12865-017-0218-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/16/2017] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND IMGT®, the international ImMunoGeneTics information system® ( http://www.imgt.org ), was created in 1989 in Montpellier, France (CNRS and Montpellier University) to manage the huge and complex diversity of the antigen receptors, and is at the origin of immunoinformatics, a science at the interface between immunogenetics and bioinformatics. Immunoglobulins (IG) or antibodies and T cell receptors (TR) are managed and described in the IMGT® databases and tools at the level of receptor, chain and domain. The analysis of the IG and TR variable (V) domain rearranged nucleotide sequences is performed by IMGT/V-QUEST (online since 1997, 50 sequences per batch) and, for next generation sequencing (NGS), by IMGT/HighV-QUEST, the high throughput version of IMGT/V-QUEST (portal begun in 2010, 500,000 sequences per batch). In vitro combinatorial libraries of engineered antibody single chain Fragment variable (scFv) which mimic the in vivo natural diversity of the immune adaptive responses are extensively screened for the discovery of novel antigen binding specificities. However the analysis of NGS full length scFv (~850 bp) represents a challenge as they contain two V domains connected by a linker and there is no tool for the analysis of two V domains in a single chain. METHODS The functionality "Analyis of single chain Fragment variable (scFv)" has been implemented in IMGT/V-QUEST and, for NGS, in IMGT/HighV-QUEST for the analysis of the two V domains of IG and TR scFv. It proceeds in five steps: search for a first closest V-REGION, full characterization of the first V-(D)-J-REGION, then search for a second V-REGION and full characterization of the second V-(D)-J-REGION, and finally linker delimitation. RESULTS For each sequence or NGS read, positions of the 5'V-DOMAIN, linker and 3'V-DOMAIN in the scFv are provided in the 'V-orientated' sense. Each V-DOMAIN is fully characterized (gene identification, sequence description, junction analysis, characterization of mutations and amino changes). The functionality is generic and can analyse any IG or TR single chain nucleotide sequence containing two V domains, provided that the corresponding species IMGT reference directory is available. CONCLUSION The "Analysis of single chain Fragment variable (scFv)" implemented in IMGT/V-QUEST and, for NGS, in IMGT/HighV-QUEST provides the identification and full characterization of the two V domains of full-length scFv (~850 bp) nucleotide sequences from combinatorial libraries. The analysis can also be performed on concatenated paired chains of expressed antigen receptor IG or TR repertoires.
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Affiliation(s)
- Véronique Giudicelli
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002, CNRS, Montpellier University, Montpellier, France.
| | - Patrice Duroux
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002, CNRS, Montpellier University, Montpellier, France.
| | - Sofia Kossida
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002, CNRS, Montpellier University, Montpellier, France.
| | - Marie-Paule Lefranc
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002, CNRS, Montpellier University, Montpellier, France.
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63
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Rouet R, Langley DB, Schofield P, Christie M, Roome B, Porebski BT, Buckle AM, Clifton BE, Jackson CJ, Stock D, Christ D. Structural reconstruction of protein ancestry. Proc Natl Acad Sci U S A 2017; 114:3897-3902. [PMID: 28356519 PMCID: PMC5393204 DOI: 10.1073/pnas.1613477114] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ancestral protein reconstruction allows the resurrection and characterization of ancient proteins based on computational analyses of sequences of modern-day proteins. Unfortunately, many protein families are highly divergent and not suitable for sequence-based reconstruction approaches. This limitation is exemplified by the antigen receptors of jawed vertebrates (B- and T-cell receptors), heterodimers formed by pairs of Ig domains. These receptors are believed to have evolved from an extinct homodimeric ancestor through a process of gene duplication and diversification; however molecular evidence has so far remained elusive. Here, we use a structural approach and laboratory evolution to reconstruct such molecules and characterize their interaction with antigen. High-resolution crystal structures of reconstructed homodimeric receptors in complex with hen-egg white lysozyme demonstrate how nanomolar affinity binding of asymmetrical antigen is enabled through selective recruitment and structural plasticity within the receptor-binding site. Our results provide structural evidence in support of long-held theories concerning the evolution of antigen receptors, and provide a blueprint for the experimental reconstruction of protein ancestry in the absence of phylogenetic evidence.
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Affiliation(s)
- Romain Rouet
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, NSW 2010, Australia
| | - David B Langley
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, NSW 2010, Australia
| | - Peter Schofield
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, NSW 2010, Australia
| | - Mary Christie
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, NSW 2010, Australia
| | - Brendan Roome
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, NSW 2010, Australia
| | - Benjamin T Porebski
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Ashley M Buckle
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Ben E Clifton
- Research School of Chemistry, Australian National University, Acton, ACT 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Acton, ACT 2601, Australia
| | - Daniela Stock
- Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, NSW 2010, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Sydney, NSW 2010, Australia
| | - Daniel Christ
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia;
- Faculty of Medicine, St. Vincent's Clinical School, University of New South Wales, Darlinghurst, Sydney, NSW 2010, Australia
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64
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Reshetova P, van Schaik BDC, Klarenbeek PL, Doorenspleet ME, Esveldt REE, Tak PP, Guikema JEJ, de Vries N, van Kampen AHC. Computational Model Reveals Limited Correlation between Germinal Center B-Cell Subclone Abundancy and Affinity: Implications for Repertoire Sequencing. Front Immunol 2017; 8:221. [PMID: 28321219 PMCID: PMC5337809 DOI: 10.3389/fimmu.2017.00221] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/16/2017] [Indexed: 12/18/2022] Open
Abstract
Immunoglobulin repertoire sequencing has successfully been applied to identify expanded antigen-activated B-cell clones that play a role in the pathogenesis of immune disorders. One challenge is the selection of the Ag-specific B cells from the measured repertoire for downstream analyses. A general feature of an immune response is the expansion of specific clones resulting in a set of subclones with common ancestry varying in abundance and in the number of acquired somatic mutations. The expanded subclones are expected to have BCR affinities for the Ag higher than the affinities of the naive B cells in the background population. For these reasons, several groups successfully proceeded or suggested selecting highly abundant subclones from the repertoire to obtain the Ag-specific B cells. Given the nature of affinity maturation one would expect that abundant subclones are of high affinity but since repertoire sequencing only provides information about abundancies, this can only be verified with additional experiments, which are very labor intensive. Moreover, this would also require knowledge of the Ag, which is often not available for clinical samples. Consequently, in general we do not know if the selected highly abundant subclone(s) are also the high(est) affinity subclones. Such knowledge would likely improve the selection of relevant subclones for further characterization and Ag screening. Therefore, to gain insight in the relation between subclone abundancy and affinity, we developed a computational model that simulates affinity maturation in a single GC while tracking individual subclones in terms of abundancy and affinity. We show that the model correctly captures the overall GC dynamics, and that the amount of expansion is qualitatively comparable to expansion observed from B cells isolated from human lymph nodes. Analysis of the fraction of high- and low-affinity subclones among the unexpanded and expanded subclones reveals a limited correlation between abundancy and affinity and shows that the low abundant subclones are of highest affinity. Thus, our model suggests that selecting highly abundant subclones from repertoire sequencing experiments would not always lead to the high(est) affinity B cells. Consequently, additional or alternative selection approaches need to be applied.
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Affiliation(s)
- Polina Reshetova
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands; Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Barbera D C van Schaik
- Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam , Amsterdam , Netherlands
| | - Paul L Klarenbeek
- Amsterdam Rheumatology and Immunology Center, Academic Medical Center , Amsterdam , Netherlands
| | - Marieke E Doorenspleet
- Amsterdam Rheumatology and Immunology Center, Academic Medical Center , Amsterdam , Netherlands
| | - Rebecca E E Esveldt
- Amsterdam Rheumatology and Immunology Center, Academic Medical Center , Amsterdam , Netherlands
| | - Paul-Peter Tak
- Department of Clinical Immunology and Rheumatology, Academic Medical Center, University of Amsterdam , Amsterdam , Netherlands
| | - Jeroen E J Guikema
- Department of Pathology, Academic Medical Center, University of Amsterdam , Amsterdam , Netherlands
| | - Niek de Vries
- Amsterdam Rheumatology and Immunology Center, Academic Medical Center , Amsterdam , Netherlands
| | - Antoine H C van Kampen
- Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands; Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
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Dambrun M, Dechavanne C, Emmanuel A, Aussenac F, Leduc M, Giangrande C, Vinh J, Dugoujon JM, Lefranc MP, Guillonneau F, Migot-Nabias F. Human Immunoglobulin Heavy Gamma Chain Polymorphisms: Molecular Confirmation Of Proteomic Assessment. Mol Cell Proteomics 2017; 16:824-839. [PMID: 28265047 DOI: 10.1074/mcp.m116.064733] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 02/01/2017] [Indexed: 11/06/2022] Open
Abstract
Immunoglobulin G (IgG) proteins are known for the huge diversity of the variable domains of their heavy and light chains, aimed at protecting each individual against foreign antigens. The IgG also harbor specific polymorphism concentrated in the CH2 and CH3-CHS constant regions located on the Fc fragment of their heavy chains. But this individual particularity relies only on a few amino acids among which some could make accurate sequence determination a challenge for mass spectrometry-based techniques.The purpose of the study was to bring a molecular validation of proteomic results by the sequencing of encoding DNA fragments. It was performed using ten individual samples (DNA and sera) selected on the basis of their Gm (gamma marker) allotype polymorphism in order to cover the main immunoglobulin heavy gamma (IGHG) gene diversity. Gm allotypes, reflecting part of this diversity, were determined by a serological method. On its side, the IGH locus comprises four functional IGHG genes totalizing 34 alleles and encoding the four IgG subclasses. The genomic study focused on the nucleotide polymorphism of the CH2 and CH3-CHS exons and of the intron. Despite strong sequence identity, four pairs of specific gene amplification primers could be designed. Additional primers were identified to perform the subsequent sequencing. The nucleotide sequences obtained were first assigned to a specific IGHG gene, and then IGHG alleles were deduced using a home-made decision tree reading of the nucleotide sequences. IGHG amino acid (AA) alleles were determined by mass spectrometry. Identical results were found at 95% between alleles identified by proteomics and those deduced from genomics. These results validate the proteomic approach which could be used for diagnostic purposes, namely for a mother-and-child differential IGHG detection in a context of suspicion of congenital infection.
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Affiliation(s)
- Magalie Dambrun
- From the ‡Institut de Recherche pour le Développement, UMR 216 Mère et enfant face aux infections tropicales, Paris, France.,§COMUE Sorbonne Paris Cité, Faculté de Pharmacie, Université Paris Descartes, Paris, France.,¶¶Magalie Dambrun, Célia Dechavanne and Alexandra Emmanuel contributed equally to this work
| | - Célia Dechavanne
- From the ‡Institut de Recherche pour le Développement, UMR 216 Mère et enfant face aux infections tropicales, Paris, France.,§COMUE Sorbonne Paris Cité, Faculté de Pharmacie, Université Paris Descartes, Paris, France.,¶¶Magalie Dambrun, Célia Dechavanne and Alexandra Emmanuel contributed equally to this work
| | - Alexandra Emmanuel
- From the ‡Institut de Recherche pour le Développement, UMR 216 Mère et enfant face aux infections tropicales, Paris, France.,§COMUE Sorbonne Paris Cité, Faculté de Pharmacie, Université Paris Descartes, Paris, France.,¶ESPCI Paris, PSL Research University, Spectrométrie de Masse Biologique et Protéomique (SMBP), CNRS USR 3149, Paris, France.,¶¶Magalie Dambrun, Célia Dechavanne and Alexandra Emmanuel contributed equally to this work
| | - Florentin Aussenac
- From the ‡Institut de Recherche pour le Développement, UMR 216 Mère et enfant face aux infections tropicales, Paris, France.,§COMUE Sorbonne Paris Cité, Faculté de Pharmacie, Université Paris Descartes, Paris, France
| | - Marjorie Leduc
- ‖Plate-forme protéomique de l'Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Chiara Giangrande
- ¶ESPCI Paris, PSL Research University, Spectrométrie de Masse Biologique et Protéomique (SMBP), CNRS USR 3149, Paris, France
| | - Joëlle Vinh
- ¶ESPCI Paris, PSL Research University, Spectrométrie de Masse Biologique et Protéomique (SMBP), CNRS USR 3149, Paris, France
| | - Jean-Michel Dugoujon
- **Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse, UMR 5288, CNRS et Université Paul Sabatier Toulouse III, Toulouse, France
| | - Marie-Paule Lefranc
- ‡‡IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire, LIGM, Institut de Génétique Humaine, IGH, UMR 9002, CNRS et Université de Montpellier, Montpellier, France.,§§Institut Universitaire de France, Paris, France
| | - François Guillonneau
- ‖Plate-forme protéomique de l'Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,‖‖François Guillonneau and Florence Migot-Nabias contributed equally to this work
| | - Florence Migot-Nabias
- From the ‡Institut de Recherche pour le Développement, UMR 216 Mère et enfant face aux infections tropicales, Paris, France; .,§COMUE Sorbonne Paris Cité, Faculté de Pharmacie, Université Paris Descartes, Paris, France.,‖‖François Guillonneau and Florence Migot-Nabias contributed equally to this work
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66
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Nowak C, Ponniah G, Neill A, Liu H. Characterization of succinimide stability during trypsin digestion for LC-MS analysis. Anal Biochem 2017; 526:1-8. [PMID: 28274724 DOI: 10.1016/j.ab.2017.03.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 03/02/2017] [Accepted: 03/03/2017] [Indexed: 12/13/2022]
Abstract
LC-MS peptide mapping is the most commonly used method to analyze protein modifications. The proteins are generally digested using trypsin at a slightly basic pH at 37 °C from several hours to overnight. Assay-induced artifacts can be generated during this procedure, potentially causing false-positive or false-negative results for a given modification. Unfortunately, for the analysis of succinimide, both false-negative and false-positive results can be generated within the same procedure. This study evaluates the stability of succinimide during the peptide mapping procedure and has demonstrated that up to 13% of pre-existing succinimide was lost during a 4 h trypsin digestion at pH 5.0 which was previously determined to be optimal for the detection of succinimide. The same procedure was able to simultaneously generate approximately 3% succinimide. Using the optimized procedure, it was also found that two aspartate residues that are followed by glycine residues in the conserved Fc region of a recombinant monoclonal antibody were not prone to isomerization. On the other hand, an aspartate residue followed by a glycine in the heavy chain variable domain was highly susceptible to isomerization. Interestingly, the antibody containing the succinimide eluted from an SEC column after the monomer peak.
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Affiliation(s)
- Christine Nowak
- Product Characterization, Alexion Pharmaceuticals, 100 College Street, New Haven, CT 06510, United States
| | - Gomathinayagam Ponniah
- Product Characterization, Alexion Pharmaceuticals, 100 College Street, New Haven, CT 06510, United States
| | - Alyssa Neill
- Product Characterization, Alexion Pharmaceuticals, 100 College Street, New Haven, CT 06510, United States
| | - Hongcheng Liu
- Product Characterization, Alexion Pharmaceuticals, 100 College Street, New Haven, CT 06510, United States.
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67
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Jeong S, Park JY, Cha MG, Chang H, Kim YI, Kim HM, Jun BH, Lee DS, Lee YS, Jeong JM, Lee YS, Jeong DH. Highly robust and optimized conjugation of antibodies to nanoparticles using quantitatively validated protocols. NANOSCALE 2017; 9:2548-2555. [PMID: 28150822 DOI: 10.1039/c6nr04683e] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Antibody-conjugated nanoparticles (NPs) have attracted great attention in diagnostic and therapeutic applications due to their high sensitivity and specificity for biotargets, as well as their wide applicability. Unfortunately, these features are significantly affected by antibody conjugation methods in terms of conjugation efficiency, orientation of the target binding site in the antibody, and denaturation during chemical conjugation reactions. Furthermore, the number of conjugated antibodies on each NP and the overall targeting efficacy are critical factors for a quantitative bioassay with antibody-conjugated NPs. Herein, we report a versatile and oriented antibody conjugation method using copper-free click chemistry. Moreover, the number of conjugated antibodies and their binding capacity were quantitatively and experimentally evaluated using fluorescently-labeled antibodies and antigens. The strong binding capability of antibody-conjugated NPs prepared using the copper-free click chemistry-based conjugation strategy was 8 times superior to the binding capability seen following the use of the EDC/NHS-coupling method. Additionally, the versatility of the developed antibody conjugation method was also demonstrated by conjugation of the antibody to three kinds of silica-encapsulated NPs.
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Affiliation(s)
- Sinyoung Jeong
- Department of Chemistry Education, Seoul National University, Seoul 08826, Korea.
| | - Ji Yong Park
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Korea. and Major in Biomedical Sciences, Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 08826, Korea
| | - Myeong Geun Cha
- Department of Chemistry Education, Seoul National University, Seoul 08826, Korea.
| | - Hyejin Chang
- Department of Chemistry Education, Seoul National University, Seoul 08826, Korea.
| | - Yong-Il Kim
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Korea.
| | - Hyung-Mo Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Bong-Hyun Jun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea
| | - Dong Soo Lee
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Korea. and Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine or College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Yoon-Sik Lee
- School of Chemical and Biological Engineering, Seoul National University, Seoul 08826, Korea
| | - Jae Min Jeong
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Korea.
| | - Yun-Sang Lee
- Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Korea. and Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine or College of Pharmacy, Seoul National University, Seoul 08826, Korea
| | - Dae Hong Jeong
- Department of Chemistry Education, Seoul National University, Seoul 08826, Korea.
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68
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Yang R, Jain T, Lynaugh H, Nobrega RP, Lu X, Boland T, Burnina I, Sun T, Caffry I, Brown M, Zhi X, Lilov A, Xu Y. Rapid assessment of oxidation via middle-down LCMS correlates with methionine side-chain solvent-accessible surface area for 121 clinical stage monoclonal antibodies. MAbs 2017; 9:646-653. [PMID: 28281887 DOI: 10.1080/19420862.2017.1290753] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Susceptibility of methionine to oxidation is an important concern for chemical stability during the development of a monoclonal antibody (mAb) therapeutic. To minimize downstream risks, leading candidates are usually screened under forced oxidation conditions to identify oxidation-labile molecules. Here we report results of forced oxidation on a large set of in-house expressed and purified mAbs with variable region sequences corresponding to 121 clinical stage mAbs. These mAb samples were treated with 0.1% H2O2 for 24 hours before enzymatic cleavage below the hinge, followed by reduction of inter-chain disulfide bonds for the detection of the light chain, Fab portion of heavy chain (Fd) and Fc by liquid chromatography-mass spectrometry. This high-throughput, middle-down approach allows detection of oxidation site(s) at the resolution of 3 distinct segments. The experimental oxidation data correlates well with theoretical predictions based on the solvent-accessible surface area of the methionine side-chains within these segments. These results validate the use of upstream computational modeling to predict mAb oxidation susceptibility at the sequence level.
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Affiliation(s)
- Rong Yang
- a Protein Analytics, Adimab , Lebanon , NH , USA
| | - Tushar Jain
- b Computational Biology, Adimab , Palo Alto , CA , USA
| | | | | | - Xiaojun Lu
- a Protein Analytics, Adimab , Lebanon , NH , USA
| | - Todd Boland
- b Computational Biology, Adimab , Palo Alto , CA , USA
| | | | - Tingwan Sun
- a Protein Analytics, Adimab , Lebanon , NH , USA
| | | | | | - Xiaoyong Zhi
- a Protein Analytics, Adimab , Lebanon , NH , USA
| | | | - Yingda Xu
- a Protein Analytics, Adimab , Lebanon , NH , USA
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69
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Immunoglobulin light chain (IGL) genes in torafugu: Genomic organization and identification of a third teleost IGL isotype. Sci Rep 2017; 7:40416. [PMID: 28098239 PMCID: PMC5241823 DOI: 10.1038/srep40416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 12/06/2016] [Indexed: 02/05/2023] Open
Abstract
Here, we report a genome-wide survey of immunoglobulin light chain (IGL) genes of torafugu (Takifugu rubripes) revealing multi-clusters spanning three separate chromosomes (v5 assembly) and 45 scaffolds (v4 assembly). Conventional sequence similarity searches and motif scanning approaches based on recombination signal sequence (RSS) motifs were used. We found that three IGL isotypes (L1, L2, and L3) exist in torafugu and that several loci for each isotype are present. The transcriptional orientations of the variable IGL (VL) segments were found to be either the same (in the L2 isotype) or opposite (in the L1 and L3 isotypes) to the IGL joining (JL) and constant (CL) segments, suggesting they can undergo rearrangement by deletion or inversion when expressed. Alignments of expressed sequence tags (ESTs) to corresponding germline gene segments revealed expression of the three IGL isotypes in torafugu. Taken together, our findings provide a genomic framework for torafugu IGL genes and show that the IG diversity of this species could be attributed to at least three distinct chromosomal regions.
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70
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Andrich K, Hegenbart U, Kimmich C, Kedia N, Bergen HR, Schönland S, Wanker E, Bieschke J. Aggregation of Full-length Immunoglobulin Light Chains from Systemic Light Chain Amyloidosis (AL) Patients Is Remodeled by Epigallocatechin-3-gallate. J Biol Chem 2016; 292:2328-2344. [PMID: 28031465 DOI: 10.1074/jbc.m116.750323] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 12/22/2016] [Indexed: 11/06/2022] Open
Abstract
Intervention into amyloid deposition with anti-amyloid agents like the polyphenol epigallocatechin-3-gallate (EGCG) is emerging as an experimental secondary treatment strategy in systemic light chain amyloidosis (AL). In both AL and multiple myeloma (MM), soluble immunoglobulin light chains (LC) are produced by clonal plasma cells, but only in AL do they form amyloid deposits in vivo We investigated the amyloid formation of patient-derived LC and their susceptibility to EGCG in vitro to probe commonalities and systematic differences in their assembly mechanisms. We isolated nine LC from the urine of AL and MM patients. We quantified their thermodynamic stabilities and monitored their aggregation under physiological conditions by thioflavin T fluorescence, light scattering, SDS stability, and atomic force microscopy. LC from all patients formed amyloid-like aggregates, albeit with individually different kinetics. LC existed as dimers, ∼50% of which were linked by disulfide bridges. Our results suggest that cleavage into LC monomers is required for efficient amyloid formation. The kinetics of AL LC displayed a transition point in concentration dependence, which MM LC lacked. The lack of concentration dependence of MM LC aggregation kinetics suggests that conformational change of the light chain is rate-limiting for these proteins. Aggregation kinetics displayed two distinct phases, which corresponded to the formation of oligomers and amyloid fibrils, respectively. EGCG specifically inhibited the second aggregation phase and induced the formation of SDS-stable, non-amyloid LC aggregates. Our data suggest that EGCG intervention does not depend on the individual LC sequence and is similar to the mechanism observed for amyloid-β and α-synuclein.
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Affiliation(s)
- Kathrin Andrich
- From the Department of Biomedical Engineering, Washington University, St. Louis, Missouri 63130-4899.,the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Ute Hegenbart
- the Department of Internal Medicine V (Hematology/Amyloidosis Center), University Hospital Heidelberg, 69120 Heidelberg, Germany, and
| | - Christoph Kimmich
- the Department of Internal Medicine V (Hematology/Amyloidosis Center), University Hospital Heidelberg, 69120 Heidelberg, Germany, and
| | - Niraja Kedia
- From the Department of Biomedical Engineering, Washington University, St. Louis, Missouri 63130-4899
| | - H Robert Bergen
- the Translational PKD Center, Mayo Clinic, Rochester, Minnesota 55905
| | - Stefan Schönland
- the Department of Internal Medicine V (Hematology/Amyloidosis Center), University Hospital Heidelberg, 69120 Heidelberg, Germany, and
| | - Erich Wanker
- the Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Jan Bieschke
- From the Department of Biomedical Engineering, Washington University, St. Louis, Missouri 63130-4899,
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71
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Ayad LAK, Pissis SPP, Retha A. libFLASM: a software library for fixed-length approximate string matching. BMC Bioinformatics 2016; 17:454. [PMID: 27832739 PMCID: PMC5103500 DOI: 10.1186/s12859-016-1320-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/03/2016] [Indexed: 01/06/2023] Open
Abstract
Background Approximate string matching is the problem of finding all factors of a given text that are at a distance at most k from a given pattern. Fixed-length approximate string matching is the problem of finding all factors of a text of length n that are at a distance at most k from any factor of length ℓ of a pattern of length m. There exist bit-vector techniques to solve the fixed-length approximate string matching problem in time \documentclass[12pt]{minimal}
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\begin{document}$\mathcal {O}(m\lceil \ell /w \rceil n)$\end{document}O(m⌈ℓ/w⌉n) and space \documentclass[12pt]{minimal}
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\begin{document}$\mathcal {O}(m\lceil \ell /w\rceil)$\end{document}O(m⌈ℓ/w⌉) under the edit and Hamming distance models, where w is the size of the computer word; as such these techniques are independent of the distance threshold k or the alphabet size. Fixed-length approximate string matching is a generalisation of approximate string matching and, hence, has numerous direct applications in computational molecular biology and elsewhere. Results We present and make available libFLASM, a free open-source C++ software library for solving fixed-length approximate string matching under both the edit and the Hamming distance models. Moreover we describe how fixed-length approximate string matching is applied to solve real problems by incorporating libFLASM into established applications for multiple circular sequence alignment as well as single and structured motif extraction. Specifically, we describe how it can be used to improve the accuracy of multiple circular sequence alignment in terms of the inferred likelihood-based phylogenies; and we also describe how it is used to efficiently find motifs in molecular sequences representing regulatory or functional regions. The comparison of the performance of the library to other algorithms show how it is competitive, especially with increasing distance thresholds. Conclusions Fixed-length approximate string matching is a generalisation of the classic approximate string matching problem. We present libFLASM, a free open-source C++ software library for solving fixed-length approximate string matching. The extensive experimental results presented here suggest that other applications could benefit from using libFLASM, and thus further maintenance and development of libFLASM is desirable.
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Affiliation(s)
- Lorraine A K Ayad
- Department of Informatics, King's College London, The Strand, London, WC2R 2LS, UK
| | - Solon P P Pissis
- Department of Informatics, King's College London, The Strand, London, WC2R 2LS, UK.
| | - Ahmad Retha
- Department of Informatics, King's College London, The Strand, London, WC2R 2LS, UK
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72
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Linguiti G, Antonacci R, Tasco G, Grande F, Casadio R, Massari S, Castelli V, Consiglio A, Lefranc MP, Ciccarese S. Genomic and expression analyses of Tursiops truncatus T cell receptor gamma (TRG) and alpha/delta (TRA/TRD) loci reveal a similar basic public γδ repertoire in dolphin and human. BMC Genomics 2016; 17:634. [PMID: 27528257 PMCID: PMC4986337 DOI: 10.1186/s12864-016-2841-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 06/15/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The bottlenose dolphin (Tursiops truncatus) is a mammal that belongs to the Cetartiodactyla and have lived in marine ecosystems for nearly 60 millions years. Despite its popularity, our knowledge about its adaptive immunity and evolution is very limited. Furthermore, nothing is known about the genomics and evolution of dolphin antigen receptor immunity. RESULTS Here we report a evolutionary and expression study of Tursiops truncatus T cell receptor gamma (TRG) and alpha/delta (TRA/TRD) genes. We have identified in silico the TRG and TRA/TRD genes and analyzed the relevant mature transcripts in blood and in skin from four subjects. The dolphin TRG locus is the smallest and simplest of all mammalian loci as yet studied. It shows a genomic organization comprising two variable (V1 and V2), three joining (J1, J2 and J3) and a single constant (C), genes. Despite the fragmented nature of the genome assemblies, we deduced the TRA/TRD locus organization, with the recent TRDV1 subgroup genes duplications, as it is expected in artiodactyls. Expression analysis from blood of a subject allowed us to assign unambiguously eight TRAV genes to those annotated in the genomic sequence and to twelve new genes, belonging to five different subgroups. All transcripts were productive and no relevant biases towards TRAV-J rearrangements are observed. Blood and skin from four unrelated subjects expression data provide evidence for an unusual ratio of productive/unproductive transcripts which arise from the TRG V-J gene rearrangement and for a "public" gamma delta TR repertoire. The productive cDNA sequences, shared both in the same and in different individuals, include biases of the TRGV1 and TRGJ2 genes. The high frequency of TRGV1-J2/TRDV1- D1-J4 productive rearrangements in dolphins may represent an interesting oligo-clonal population comparable to that found in human with the TRGV9- JP/TRDV2-D-J T cells and in primates. CONCLUSIONS Although the features of the TRG and TRA/TRD loci organization reflect those of the so far examined artiodactyls, genomic results highlight in dolphin an unusually simple TRG locus. The cDNA analysis reveal productive TRA/TRD transcripts and unusual ratios of productive/unproductive TRG transcripts. Comparing multiple different individuals, evidence is found for a "public" gamma delta TCR repertoire thus suggesting that in dolphins as in human the gamma delta TCR repertoire is accompanied by selection for public gamma chain.
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MESH Headings
- Amino Acid Sequence
- Animals
- Bottle-Nosed Dolphin/genetics
- Bottle-Nosed Dolphin/metabolism
- Gene Expression Profiling
- Gene Expression Regulation
- Genetic Loci
- Humans
- Molecular Sequence Data
- Phylogeny
- Protein Structure, Secondary
- RNA/blood
- RNA/isolation & purification
- RNA/metabolism
- Receptors, Antigen, T-Cell, alpha-beta/classification
- Receptors, Antigen, T-Cell, alpha-beta/genetics
- Receptors, Antigen, T-Cell, alpha-beta/metabolism
- Receptors, Antigen, T-Cell, gamma-delta/classification
- Receptors, Antigen, T-Cell, gamma-delta/genetics
- Receptors, Antigen, T-Cell, gamma-delta/metabolism
- Sequence Alignment
- Skin/metabolism
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Affiliation(s)
- Giovanna Linguiti
- Department of Biology, University of Bari, via E. Orabona 4, 70125 Bari, Italy
| | - Rachele Antonacci
- Department of Biology, University of Bari, via E. Orabona 4, 70125 Bari, Italy
| | - Gianluca Tasco
- Biocomputing Group, CIRI-Health Science and Technologies/Department of Biology, University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Francesco Grande
- Zoomarine Italia SpA, via Casablanca 61, 00071 Pomezia, RM Italy
| | - Rita Casadio
- Biocomputing Group, CIRI-Health Science and Technologies/Department of Biology, University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Serafina Massari
- Department of Biological and Environmental Science e Technologies, University of Salento, via per Monteroni, 73100 Lecce, Italy
| | - Vito Castelli
- Department of Biology, University of Bari, via E. Orabona 4, 70125 Bari, Italy
| | - Arianna Consiglio
- CNR, Institute for Biomedical Technologies of Bari, via Amendola, 70125 Bari, Italy
| | - Marie-Paule Lefranc
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d’ImmunoGénétique Moléculaire, Institut de Génétique Humaine, UPR CNRS 1142, University of Montpellier, 34396 Montpellier Cedex 5, France
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73
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Agostino M, Mancera RL, Ramsland PA, Fernández-Recio J. Optimization of protein-protein docking for predicting Fc-protein interactions. J Mol Recognit 2016; 29:555-568. [PMID: 27445195 DOI: 10.1002/jmr.2555] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 06/12/2016] [Accepted: 06/14/2016] [Indexed: 01/08/2023]
Abstract
The antibody crystallizable fragment (Fc) is recognized by effector proteins as part of the immune system. Pathogens produce proteins that bind Fc in order to subvert or evade the immune response. The structural characterization of the determinants of Fc-protein association is essential to improve our understanding of the immune system at the molecular level and to develop new therapeutic agents. Furthermore, Fc-binding peptides and proteins are frequently used to purify therapeutic antibodies. Although several structures of Fc-protein complexes are available, numerous others have not yet been determined. Protein-protein docking could be used to investigate Fc-protein complexes; however, improved approaches are necessary to efficiently model such cases. In this study, a docking-based structural bioinformatics approach is developed for predicting the structures of Fc-protein complexes. Based on the available set of X-ray structures of Fc-protein complexes, three regions of the Fc, loosely corresponding to three turns within the structure, were defined as containing the essential features for protein recognition and used as restraints to filter the initial docking search. Rescoring the filtered poses with an optimal scoring strategy provided a success rate of approximately 80% of the test cases examined within the top ranked 20 poses, compared to approximately 20% by the initial unrestrained docking. The developed docking protocol provides a significant improvement over the initial unrestrained docking and will be valuable for predicting the structures of currently undetermined Fc-protein complexes, as well as in the design of peptides and proteins that target Fc.
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Affiliation(s)
- Mark Agostino
- School of Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, Australia.,Joint BSC-CRG-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain.,Centre for Biomedical Research, Burnet Institute, Melbourne, Australia
| | - Ricardo L Mancera
- School of Biomedical Sciences, Curtin Health Innovation Research Institute and Curtin Institute for Computation, Curtin University, Perth, Australia
| | - Paul A Ramsland
- Centre for Biomedical Research, Burnet Institute, Melbourne, Australia. .,School of Science, RMIT University, Bundoora, Australia. .,Department of Surgery Austin Health, University of Melbourne, Heidelberg, Australia. .,Department of Immunology, Monash University, Alfred Medical Research and Education Precinct, Melbourne, Australia.
| | - Juan Fernández-Recio
- Joint BSC-CRG-IRB Research Program in Computational Biology, Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain.
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74
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Webster CI, Bryson CJ, Cloake EA, Jones TD, Austin MJ, Karle AC, Spindeldreher S, Lowe DC, Baker MP. A comparison of the ability of the human IgG1 allotypes G1m3 and G1m1,17 to stimulate T-cell responses from allotype matched and mismatched donors. MAbs 2016; 8:253-63. [PMID: 26821574 PMCID: PMC4966604 DOI: 10.1080/19420862.2015.1128605] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The immunogenicity of clinically administered antibodies has clinical implications for the patients receiving them, ranging from mild consequences, such as increased clearance of the drug from the circulation, to life-threatening effects. The emergence of methods to engineer variable regions resulting in the generation of humanised and fully human antibodies as therapeutics has reduced the potential for adverse immunogenicity. However, due to differences in sequence referred to as allotypic variation, antibody constant regions are not homogeneous within the human population, even within sub-classes of the same immunoglobulin isotype. For therapeutically administered antibodies, the potential exists for an immune response from the patient to the antibody if the allotype of patient and antibody do not match. Allotypic distribution in the human population varies within and across ethnic groups making the choice of allotype for a therapeutic antibody difficult. This study investigated the potential of human IgG1 allotypes to stimulate responses in human CD4(+) T cells from donors matched for homologous and heterologous IgG1 allotypes. Allotypic variants of the therapeutic monoclonal antibody trastuzumab were administered to genetically defined allotypic matched and mismatched donor T cells. No significant responses were observed in the mismatched T cells. To investigate the lack of T-cell responses in relation to mismatched allotypes, HLA-DR agretopes were identified via MHC associated peptide proteomics (MAPPs). As expected, many HLA-DR restricted peptides were presented. However, there were no peptides presented from the sequence regions containing the allotypic variations. Taken together, the results from the T-cell assay and MAPPs assay indicate that the allotypic differences in human IgG1 do not represent a significant risk for induction of immunogenicity.
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Affiliation(s)
- Carl I Webster
- a MedImmune Ltd, Milstein Building , Granta Park, Cambridge , CB21 6GH , United Kingdom
| | - Christine J Bryson
- b Antitope Ltd (An Abzena company), Babraham Research Campus , Babraham, Cambridge , CB22 3AT , United Kingdom
| | - Edward A Cloake
- b Antitope Ltd (An Abzena company), Babraham Research Campus , Babraham, Cambridge , CB22 3AT , United Kingdom
| | - Tim D Jones
- b Antitope Ltd (An Abzena company), Babraham Research Campus , Babraham, Cambridge , CB22 3AT , United Kingdom
| | - Mark J Austin
- a MedImmune Ltd, Milstein Building , Granta Park, Cambridge , CB21 6GH , United Kingdom
| | - Anette C Karle
- c Novartis Pharma AG , Klybeckstrasse 141, CH-4057 Basel , Switzerland
| | | | - David C Lowe
- a MedImmune Ltd, Milstein Building , Granta Park, Cambridge , CB21 6GH , United Kingdom
| | - Matthew P Baker
- b Antitope Ltd (An Abzena company), Babraham Research Campus , Babraham, Cambridge , CB22 3AT , United Kingdom
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75
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Pinheiro A, Neves F, Lemos de Matos A, Abrantes J, van der Loo W, Mage R, Esteves PJ. An overview of the lagomorph immune system and its genetic diversity. Immunogenetics 2015; 68:83-107. [PMID: 26399242 DOI: 10.1007/s00251-015-0868-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 08/31/2015] [Indexed: 01/11/2023]
Abstract
Our knowledge of the lagomorph immune system remains largely based upon studies of the European rabbit (Oryctolagus cuniculus), a major model for studies of immunology. Two important and devastating viral diseases, rabbit hemorrhagic disease and myxomatosis, are affecting European rabbit populations. In this context, we discuss the genetic diversity of the European rabbit immune system and extend to available information about other lagomorphs. Regarding innate immunity, we review the most recent advances in identifying interleukins, chemokines and chemokine receptors, Toll-like receptors, antiviral proteins (RIG-I and Trim5), and the genes encoding fucosyltransferases that are utilized by rabbit hemorrhagic disease virus as a portal for invading host respiratory and gut epithelial cells. Evolutionary studies showed that several genes of innate immunity are evolving by strong natural selection. Studies of the leporid CCR5 gene revealed a very dramatic change unique in mammals at the second extracellular loop of CCR5 resulting from a gene conversion event with the paralogous CCR2. For the adaptive immune system, we review genetic diversity at the loci encoding antibody variable and constant regions, the major histocompatibility complex (RLA) and T cells. Studies of IGHV and IGKC genes expressed in leporids are two of the few examples of trans-species polymorphism observed outside of the major histocompatibility complex. In addition, we review some endogenous viruses of lagomorph genomes, the importance of the European rabbit as a model for human disease studies, and the anticipated role of next-generation sequencing in extending knowledge of lagomorph immune systems and their evolution.
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Affiliation(s)
- Ana Pinheiro
- InBIO-Research Network in Biodiversity and Evolutionary Biology, CIBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr. 7, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal
- SaBio-IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain
| | - Fabiana Neves
- InBIO-Research Network in Biodiversity and Evolutionary Biology, CIBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr. 7, 4485-661, Vairão, Portugal
- UMIB/UP-Unidade Multidisciplinar de Investigação Biomédica, Universidade do Porto, Porto, Portugal
| | - Ana Lemos de Matos
- Department of Molecular Genetics & Microbiology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Joana Abrantes
- InBIO-Research Network in Biodiversity and Evolutionary Biology, CIBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr. 7, 4485-661, Vairão, Portugal
| | - Wessel van der Loo
- InBIO-Research Network in Biodiversity and Evolutionary Biology, CIBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr. 7, 4485-661, Vairão, Portugal
| | - Rose Mage
- NIAID, NIH, Bethesda, MD, 20892, USA
| | - Pedro José Esteves
- InBIO-Research Network in Biodiversity and Evolutionary Biology, CIBIO, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, nr. 7, 4485-661, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007, Porto, Portugal.
- CITS-Centro de Investigação em Tecnologias de Saúde, CESPU, Gandra, Portugal.
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Piccinni B, Massari S, Caputi Jambrenghi A, Giannico F, Lefranc MP, Ciccarese S, Antonacci R. Sheep (Ovis aries) T cell receptor alpha (TRA) and delta (TRD) genes and genomic organization of the TRA/TRD locus. BMC Genomics 2015; 16:709. [PMID: 26383271 PMCID: PMC4574546 DOI: 10.1186/s12864-015-1790-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 07/22/2015] [Indexed: 11/30/2022] Open
Abstract
Background In mammals, T cells develop along two discrete pathways characterized by expression of either the αβ or the γδ T cell receptors. Human and mouse display a low peripheral blood γδ T cell percentage ("γδ low species") while sheep, bovine and pig accounts for a high proportion of γδ T lymphocytes ("γδ high species"). While the T cell receptor alpha (TRA) and delta (TRD) genes and the genomic organization of the TRA/TRD locus has been determined in human and mouse, this information is still poorly known in artiodactyl species, such as sheep. Results The analysis of the current Ovis aries whole genome assembly, Oar_v3.1, revealed that, as in the other mammalian species, the sheep TRD locus is nested within the TRA locus. In the most 5’ part the TRA/TRD locus contains TRAV genes which are intermingled with TRDV genes, then TRD genes which include seven TRDD, four TRDJ genes, one TRDC and a single TRDV gene with an inverted transcriptional orientation, and finally in the most 3’ part, the TRA locus is completed by 61 TRAJ genes and one TRAC gene. Comparative sequence and analysis and annotation led to the identification of 66 TRAV genes assigned to 34 TRAV subgroups and 25 TRDV genes belonging to the TRDV1 subgroup, while one gene was found for each TRDV2, TRDV3 and TRDV4 subgroups. Multiple duplication events within several TRAV subgroups have generated the sheep TRAV germline repertoire, which is substantially larger than the human one. A significant proportion of these TRAV gene duplications seems to have occurred simultaneously with the amplification of the TRDV1 subgroup genes. This dynamic of expansion has also generated novel multigene subgroups, which are species-specific. Ovis aries TRA and TRD genes identified in this study were assigned IMGT definitive or temporary names and were approved by the IMGT/WHO-IUIS nomenclature committee. The completeness of the genome assembly in the 3' part of the locus has allowed us to interpret rearranged CDR3 of cDNA from both TRA and TRD chain repertoires. The involvement of one up to four TRDD genes into a single transcript makes the potential sheep TRD chain much larger than any known TR chain repertoire. Conclusions The sheep genome, as the bovine genome, contains a large and diverse repertoire of TRA and TRD genes when compared to the “γδ T cell low” species genomes. The composition and length of the rearranged CDR3 in TRD V-delta domains influence the three-dimensional configuration of the antigen-combining site thus suggesting that in ruminants, γδ T cells play a more important and specific role in immune recognition. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1790-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Barbara Piccinni
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Universita' del Salento, Lecce, Italy. .,Dipartimento di Biologia, Universita' degli Studi di Bari Aldo Moro, Bari, Italy.
| | - Serafina Massari
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Universita' del Salento, Lecce, Italy.
| | - Anna Caputi Jambrenghi
- Dipartimento di Scienze Agro-Ambientali e Territoriali, Universita' degli Studi di Bari Aldo Moro, Bari, Italy.
| | - Francesco Giannico
- Dipartimento di Scienze Agro-Ambientali e Territoriali, Universita' degli Studi di Bari Aldo Moro, Bari, Italy.
| | - Marie-Paule Lefranc
- IMGT, Laboratoire d'ImmunoGénétique Moléculaire, Institut de Génétique Humaine, UPR CNRS 1142, Université Montpellier 2, 34396, Montpellier, Cedex 5, France.
| | - Salvatrice Ciccarese
- Dipartimento di Biologia, Universita' degli Studi di Bari Aldo Moro, Bari, Italy.
| | - Rachele Antonacci
- Dipartimento di Biologia, Universita' degli Studi di Bari Aldo Moro, Bari, Italy.
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77
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Pinheiro A, Almeida T, Esteves PJ. Survey of genetic diversity of IgG in wild and domestic rabbits. Int J Immunogenet 2015. [DOI: 10.1111/iji.12222] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- A. Pinheiro
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology; Universidade do Porto; Campus de Vairão; Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências da Universidade do Porto; Porto; Portugal
- SaBio IREC (CSIC-UCLM-JCCM); Ciudad Real; Spain
| | - T. Almeida
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology; Universidade do Porto; Campus de Vairão; Vairão Portugal
| | - P. J. Esteves
- CIBIO, InBIO - Research Network in Biodiversity and Evolutionary Biology; Universidade do Porto; Campus de Vairão; Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências da Universidade do Porto; Porto; Portugal
- CESPU; Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde; Gandra PRD; Portugal
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Pinheiro A, Woof JM, Almeida T, Abrantes J, Alves PC, Gortázar C, Esteves PJ. Leporid immunoglobulin G shows evidence of strong selective pressure on the hinge and CH3 domains. Open Biol 2015; 4:140088. [PMID: 25185680 PMCID: PMC4185434 DOI: 10.1098/rsob.140088] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Immunoglobulin G (IgG) is the predominant serum immunoglobulin and has the longest serum half-life of all the antibody classes. The European rabbit IgG has been of significant importance in immunological research, and is therefore well characterized. However, the IgG of other leporids has been disregarded. To evaluate the evolution of this gene in leporids, we sequenced the complete IGHG for six other genera: Bunolagus, Brachylagus, Lepus, Pentalagus, Romerolagus and Sylvilagus. The newly sequenced leporid IGHG gene has an organization and structure similar to that of the European rabbit IgG. A gradient in leporid IgG constant domain diversity was observed, with the CH1 being the most conserved and the CH3 the most variable domain. Positive selection was found to be acting on all constant domains, but with a greater incidence in the CH3 domain, where a cluster of three positively selected sites was identified. In the hinge region, only three polymorphic positions were observed. The same hinge length was observed for all leporids. Unlike the variation observed for the European rabbit, all 11 Lepus species studied share exactly the same hinge motif, suggesting its maintenance as a result of an advantageous structure or conformation.
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Affiliation(s)
- Ana Pinheiro
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto 4169-007, Portugal SaBio IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real 13071, Spain
| | - Jenny M Woof
- Division of Cancer Research, Medical Research Institute, University of Dundee Medical School, Ninewells Hospital, Dundee DD1 9SY, UK
| | - Tereza Almeida
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal
| | - Joana Abrantes
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal
| | - Paulo C Alves
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto 4169-007, Portugal Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT 59812, USA
| | - Christian Gortázar
- SaBio IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real 13071, Spain
| | - Pedro J Esteves
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos, InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto 4169-007, Portugal CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Gandra PRD, Portugal
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79
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Lefranc MP. Immunoglobulins: 25 years of immunoinformatics and IMGT-ONTOLOGY. Biomolecules 2014; 4:1102-39. [PMID: 25521638 PMCID: PMC4279172 DOI: 10.3390/biom4041102] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/02/2014] [Accepted: 12/03/2014] [Indexed: 11/17/2022] Open
Abstract
IMGT®, the international ImMunoGeneTics information system® (CNRS and Montpellier University) is the global reference in immunogenetics and immunoinformatics. By its creation in 1989, IMGT® marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT® is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH), and IgSF and MhSF superfamilies. IMGT® has been built on the IMGT-ONTOLOGY axioms and concepts, which bridged the gap between genes, sequences and three-dimensional (3D) structures. The concepts include the IMGT® standardized keywords (identification), IMGT® standardized labels (description), IMGT® standardized nomenclature (classification), IMGT unique numbering and IMGT Colliers de Perles (numerotation). IMGT® comprises seven databases, 15,000 pages of web resources and 17 tools. IMGT® tools and databases provide a high-quality analysis of the IG from fish to humans, for basic, veterinary and medical research, and for antibody engineering and humanization. They include, as examples: IMGT/V-QUEST and IMGT/JunctionAnalysis for nucleotide sequence analysis and their high-throughput version IMGT/HighV-QUEST for next generation sequencing, IMGT/DomainGapAlign for amino acid sequence analysis of IG domains, IMGT/3Dstructure-DB for 3D structures, contact analysis and paratope/epitope interactions of IG/antigen complexes, and the IMGT/mAb-DB interface for therapeutic antibodies and fusion proteins for immunological applications (FPIA).
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT®, the international ImMunoGenetics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UPR CNRS 1142, Montpellier University, 141 rue de la Cardonille, 34396 Montpellier cedex 5, France.
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80
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Pantazes RJ, Grisewood MJ, Li T, Gifford NP, Maranas CD. The Iterative Protein Redesign and Optimization (IPRO) suite of programs. J Comput Chem 2014; 36:251-63. [PMID: 25448866 DOI: 10.1002/jcc.23796] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 10/30/2014] [Accepted: 11/08/2014] [Indexed: 11/10/2022]
Abstract
Proteins are an important class of biomolecules with applications spanning across biotechnology and medicine. In many cases, native proteins must be redesigned to improve various performance metrics by changing their amino acid sequences. Algorithms can help sharpen protein library design by focusing the library on sequences that optimize computationally accessible proxies. The Iterative Protein Redesign and Optimization (IPRO) suite of programs offers an integrated environment for (1) altering protein binding affinity and specificity, (2) grafting a binding pocket into an existing protein scaffold, (3) predicting an antibody's tertiary structure based on its sequence, (4) enhancing enzymatic activity, and (5) assessing the structure and binding energetics for a specific mutant. This manuscript provides an overview of the methods involved in IPRO, input language terminology, algorithmic details, software implementation specifics and application highlights. IPRO can be downloaded at http://maranas.che.psu.edu.
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Affiliation(s)
- Robert J Pantazes
- Chemical Engineering Department, University of California, Santa Barbara, 3357 Engineering II, Santa Barbara, California, 93106
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81
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Lefranc MP, Giudicelli V, Duroux P, Jabado-Michaloud J, Folch G, Aouinti S, Carillon E, Duvergey H, Houles A, Paysan-Lafosse T, Hadi-Saljoqi S, Sasorith S, Lefranc G, Kossida S. IMGT®, the international ImMunoGeneTics information system® 25 years on. Nucleic Acids Res 2014; 43:D413-22. [PMID: 25378316 PMCID: PMC4383898 DOI: 10.1093/nar/gku1056] [Citation(s) in RCA: 389] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
IMGT®, the international ImMunoGeneTics information system®(http://www.imgt.org) is the global reference in immunogenetics and immunoinformatics. By its creation in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS), IMGT® marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT® is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) and proteins of the IgSF and MhSF superfamilies. IMGT® is built on the IMGT-ONTOLOGY axioms and concepts, which bridged the gap between genes, sequences and 3D structures. The concepts include the IMGT® standardized keywords (identification), IMGT® standardized labels (description), IMGT® standardized nomenclature (classification), IMGT unique numbering and IMGT Colliers de Perles (numerotation). IMGT® comprises 7 databases, 17 online tools and 15 000 pages of web resources, and provides a high-quality and integrated system for analysis of the genomic and expressed IG and TR repertoire of the adaptive immune responses, including NGS high-throughput data. Tools and databases are used in basic, veterinary and medical research, in clinical applications (mutation analysis in leukemia and lymphoma) and in antibody engineering and humanization. The IMGT/mAb-DB interface was developed for therapeutic antibodies and fusion proteins for immunological applications (FPIA). IMGT® is freely available at http://www.imgt.org.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT, the international ImMunoGeneTics information system, Université de Montpellier, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine IGH, 141 rue de la Cardonille, Montpellier, 34396 cedex 5, France
| | - Véronique Giudicelli
- IMGT, the international ImMunoGeneTics information system, Université de Montpellier, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine IGH, 141 rue de la Cardonille, Montpellier, 34396 cedex 5, France
| | - Patrice Duroux
- IMGT, the international ImMunoGeneTics information system, Université de Montpellier, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine IGH, 141 rue de la Cardonille, Montpellier, 34396 cedex 5, France
| | - Joumana Jabado-Michaloud
- IMGT, the international ImMunoGeneTics information system, Université de Montpellier, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine IGH, 141 rue de la Cardonille, Montpellier, 34396 cedex 5, France
| | - Géraldine Folch
- IMGT, the international ImMunoGeneTics information system, Université de Montpellier, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine IGH, 141 rue de la Cardonille, Montpellier, 34396 cedex 5, France
| | - Safa Aouinti
- IMGT, the international ImMunoGeneTics information system, Université de Montpellier, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine IGH, 141 rue de la Cardonille, Montpellier, 34396 cedex 5, France
| | - Emilie Carillon
- IMGT, the international ImMunoGeneTics information system, Université de Montpellier, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine IGH, 141 rue de la Cardonille, Montpellier, 34396 cedex 5, France
| | - Hugo Duvergey
- IMGT, the international ImMunoGeneTics information system, Université de Montpellier, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine IGH, 141 rue de la Cardonille, Montpellier, 34396 cedex 5, France
| | - Amélie Houles
- IMGT, the international ImMunoGeneTics information system, Université de Montpellier, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine IGH, 141 rue de la Cardonille, Montpellier, 34396 cedex 5, France
| | - Typhaine Paysan-Lafosse
- IMGT, the international ImMunoGeneTics information system, Université de Montpellier, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine IGH, 141 rue de la Cardonille, Montpellier, 34396 cedex 5, France
| | - Saida Hadi-Saljoqi
- IMGT, the international ImMunoGeneTics information system, Université de Montpellier, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine IGH, 141 rue de la Cardonille, Montpellier, 34396 cedex 5, France
| | - Souphatta Sasorith
- IMGT, the international ImMunoGeneTics information system, Université de Montpellier, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine IGH, 141 rue de la Cardonille, Montpellier, 34396 cedex 5, France
| | - Gérard Lefranc
- IMGT, the international ImMunoGeneTics information system, Université de Montpellier, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine IGH, 141 rue de la Cardonille, Montpellier, 34396 cedex 5, France
| | - Sofia Kossida
- IMGT, the international ImMunoGeneTics information system, Université de Montpellier, Laboratoire d'ImmunoGénétique Moléculaire LIGM, UPR CNRS 1142, Institut de Génétique Humaine IGH, 141 rue de la Cardonille, Montpellier, 34396 cedex 5, France
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Alamyar E, Giudicelli V, Duroux P, Lefranc MP. Antibody V and C domain sequence, structure, and interaction analysis with special reference to IMGT®. Methods Mol Biol 2014; 1131:337-81. [PMID: 24515476 DOI: 10.1007/978-1-62703-992-5_21] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
IMGT(®), the international ImMunoGeneTics information system(®) (http://www.imgt.org), created in 1989 (Centre National de la Recherche Scientifique, Montpellier University), is acknowledged as the global reference in immunogenetics and immunoinformatics. The accuracy and the consistency of the IMGT(®) data are based on IMGT-ONTOLOGY which bridges the gap between genes, sequences, and three-dimensional (3D) structures. Thus, receptors, chains, and domains are characterized with the same IMGT(®) rules and standards (IMGT standardized labels, IMGT gene and allele nomenclature, IMGT unique numbering, IMGT Collier de Perles), independently from the molecule type (genomic DNA, complementary DNA, transcript, or protein) or from the species. More particularly, IMGT(®) tools and databases provide a highly standardized analysis of the immunoglobulin (IG) or antibody and T cell receptor (TR) V and C domains. IMGT/V-QUEST analyzes the V domains of IG or TR rearranged nucleotide sequences, integrates the IMGT/JunctionAnalysis and IMGT/Automat tools, and provides IMGT Collier de Perles. IMGT/HighV-QUEST analyzes sequences from high-throughput sequencing (HTS) (up to 150,000 sequences per batch) and performs statistical analysis on up to 450,000 results, with the same resolution and high quality as IMGT/V-QUEST online. IMGT/DomainGapAlign analyzes amino acid sequences of V and C domains and IMGT/3Dstructure-DB and associated tools provide information on 3D structures, contact analysis, and paratope/epitope interactions. These IMGT(®) tools and databases, and the IMGT/mAb-DB interface with access to therapeutical antibody data, provide an invaluable help for antibody engineering and antibody humanization.
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Affiliation(s)
- Eltaf Alamyar
- The International ImMunoGenetics information system, Laboratoire d'ImmunoGénétique Moléculaire, Institut de Génétique Humaine IGH, Université Montpellier 2, Montpellier, France
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83
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Abbott WM, Damschroder MM, Lowe DC. Current approaches to fine mapping of antigen-antibody interactions. Immunology 2014; 142:526-35. [PMID: 24635566 DOI: 10.1111/imm.12284] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 03/10/2014] [Accepted: 03/11/2014] [Indexed: 12/23/2022] Open
Abstract
A number of different methods are commonly used to map the fine details of the interaction between an antigen and an antibody. Undoubtedly the method that is now most commonly used to give details at the level of individual amino acids and atoms is X-ray crystallography. The feasibility of undertaking crystallographic studies has increased over recent years through the introduction of automation, miniaturization and high throughput processes. However, this still requires a high level of sophistication and expense and cannot be used when the antigen is not amenable to crystallization. Nuclear magnetic resonance spectroscopy offers a similar level of detail to crystallography but the technical hurdles are even higher such that it is rarely used in this context. Mutagenesis of either antigen or antibody offers the potential to give information at the amino acid level but suffers from the uncertainty of not knowing whether an effect is direct or indirect due to an effect on the folding of a protein. Other methods such as hydrogen deuterium exchange coupled to mass spectrometry and the use of short peptides coupled with ELISA-based approaches tend to give mapping information over a peptide region rather than at the level of individual amino acids. It is quite common to use more than one method because of the limitations and even with a crystal structure it can be useful to use mutagenesis to tease apart the contribution of individual amino acids to binding affinity.
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Affiliation(s)
- W Mark Abbott
- Discovery Sciences, AstraZeneca, Macclesfield, Cheshire, UK
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84
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OptMAVEn--a new framework for the de novo design of antibody variable region models targeting specific antigen epitopes. PLoS One 2014; 9:e105954. [PMID: 25153121 PMCID: PMC4143332 DOI: 10.1371/journal.pone.0105954] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 07/29/2014] [Indexed: 01/12/2023] Open
Abstract
Antibody-based therapeutics provides novel and efficacious treatments for a number of diseases. Traditional experimental approaches for designing therapeutic antibodies rely on raising antibodies against a target antigen in an immunized animal or directed evolution of antibodies with low affinity for the desired antigen. However, these methods remain time consuming, cannot target a specific epitope and do not lead to broad design principles informing other studies. Computational design methods can overcome some of these limitations by using biophysics models to rationally select antibody parts that maximize affinity for a target antigen epitope. This has been addressed to some extend by OptCDR for the design of complementary determining regions. Here, we extend this earlier contribution by addressing the de novo design of a model of the entire antibody variable region against a given antigen epitope while safeguarding for immunogenicity (Optimal Method for Antibody Variable region Engineering, OptMAVEn). OptMAVEn simulates in silico the in vivo steps of antibody generation and evolution, and is capable of capturing the critical structural features responsible for affinity maturation of antibodies. In addition, a humanization procedure was developed and incorporated into OptMAVEn to minimize the potential immunogenicity of the designed antibody models. As case studies, OptMAVEn was applied to design models of neutralizing antibodies targeting influenza hemagglutinin and HIV gp120. For both HA and gp120, novel computational antibody models with numerous interactions with their target epitopes were generated. The observed rates of mutations and types of amino acid changes during in silico affinity maturation are consistent with what has been observed during in vivo affinity maturation. The results demonstrate that OptMAVEn can efficiently generate diverse computational antibody models with both optimized binding affinity to antigens and reduced immunogenicity.
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85
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Moulana M, Taylor EB, Edholm ES, Quiniou SMA, Wilson M, Bengtén E. Identification and characterization of TCRγ and TCRδ chains in channel catfish, Ictalurus punctatus. Immunogenetics 2014; 66:545-61. [PMID: 25129471 DOI: 10.1007/s00251-014-0793-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Accepted: 07/31/2014] [Indexed: 11/28/2022]
Abstract
Channel catfish, Ictalurus punctatus, T cell receptors (TCR) γ and δ were identified by mining of expressed sequence tag databases, and full-length sequences were obtained by 5'-RACE and RT-PCR protocols. cDNAs for each of these TCR chains encode typical variable (V), diversity (D), joining (J), and constant (C) regions. Three TCRγ V families, seven TCRγ J sequences, and three TCRγ C sequences were identified from sequencing of cDNA. Primer walking on bacterial artificial chromosomes (BACs) confirmed that the TRG locus contained seven TRGJ segments and indicated that the locus consists of (Vγ3-Jγ6-Cγ2)-(Vγ1n-Jγ7-Cγ3)-(Vγ2-Jγ5-Jγ4-Jγ3-Jγ2-Jγ1-Cγ1). In comparison for TCRδ, two V families, four TCRδ D sequences, one TCRδ J sequence, and one TCRδ C sequence were identified by cDNA sequencing. Importantly, the finding that some catfish TCRδ cDNAs contain TCR Vα-D-Jδ rearrangements and some TCRα cDNAs contain Vδ-Jα rearrangements strongly implies that the catfish TRA and TRD loci are linked. Finally, primer walking on BACs and Southern blotting suggest that catfish have four TRDD gene segments and a single TRDJ and TRDC gene. As in most vertebrates, all three reading frames of each of the catfish TRDD segments can be used in functional rearrangements, and more than one TRDD segment can be used in a single rearrangement. As expected, catfish TCRδ CDR3 regions are longer and more diverse than TCRγ CDR3 regions, and as a group they utilize more nucleotide additions and contain more nucleotide deletions than catfish TCRγ rearrangements.
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Affiliation(s)
- Mohadetheh Moulana
- Department of Microbiology, University of Mississippi Medical Center, 2500 North State Street, Jackson, MS, 39216-4505, USA
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86
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Shirai H, Prades C, Vita R, Marcatili P, Popovic B, Xu J, Overington JP, Hirayama K, Soga S, Tsunoyama K, Clark D, Lefranc MP, Ikeda K. Antibody informatics for drug discovery. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2002-2015. [PMID: 25110827 DOI: 10.1016/j.bbapap.2014.07.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 07/04/2014] [Accepted: 07/11/2014] [Indexed: 10/24/2022]
Abstract
More and more antibody therapeutics are being approved every year, mainly due to their high efficacy and antigen selectivity. However, it is still difficult to identify the antigen, and thereby the function, of an antibody if no other information is available. There are obstacles inherent to the antibody science in every project in antibody drug discovery. Recent experimental technologies allow for the rapid generation of large-scale data on antibody sequences, affinity, potency, structures, and biological functions; this should accelerate drug discovery research. Therefore, a robust bioinformatic infrastructure for these large data sets has become necessary. In this article, we first identify and discuss the typical obstacles faced during the antibody drug discovery process. We then summarize the current status of three sub-fields of antibody informatics as follows: (i) recent progress in technologies for antibody rational design using computational approaches to affinity and stability improvement, as well as ab-initio and homology-based antibody modeling; (ii) resources for antibody sequences, structures, and immune epitopes and open drug discovery resources for development of antibody drugs; and (iii) antibody numbering and IMGT. Here, we review "antibody informatics," which may integrate the above three fields so that bridging the gaps between industrial needs and academic solutions can be accelerated. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody.
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Affiliation(s)
- Hiroki Shirai
- Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi, Ibaraki 305-8585, Japan
| | - Catherine Prades
- Global Biotherapeutics, Bioinformatics, Sanofi-Aventis Recherche & Développement, Centre de recherche Vitry-sur-Seine, 13, quai Jules Guesde, BP 14, 94403 Vitry-sur-Seine Cedex, France
| | - Randi Vita
- Immune Epitope Database and Analysis Project, La Jolla Institute for Allergy & Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Paolo Marcatili
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Anker Engelunds Vej 1, 2800 Lyngby, Denmark
| | - Bojana Popovic
- MedImmune Ltd, Milstein Building, Granta Park, Cambridge CB21 6GH, UK
| | - Jianqing Xu
- MedImmune Ltd, Milstein Building, Granta Park, Cambridge CB21 6GH, UK
| | - John P Overington
- The EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kazunori Hirayama
- Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi, Ibaraki 305-8585, Japan
| | - Shinji Soga
- Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi, Ibaraki 305-8585, Japan
| | - Kazuhisa Tsunoyama
- Molecular Medicine Research Laboratories, Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba-shi, Ibaraki 305-8585, Japan
| | - Dominic Clark
- The EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marie-Paule Lefranc
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Université Montpellier 2, Institut de Génétique Humaine, UPR CNRS 1142, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France
| | - Kazuyoshi Ikeda
- The EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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Shi B, Ma L, He X, Wang X, Wang P, Zhou L, Yao X. Comparative analysis of human and mouse immunoglobulin variable heavy regions from IMGT/LIGM-DB with IMGT/HighV-QUEST. Theor Biol Med Model 2014; 11:30. [PMID: 24992938 PMCID: PMC4085081 DOI: 10.1186/1742-4682-11-30] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 06/26/2014] [Indexed: 11/18/2022] Open
Abstract
Background Immunoglobulin (IG) complementarity determining region (CDR) includes VH CDR1, VH CDR2, VH CDR3, VL CDR1, VL CDR2 and VL CDR3. Of these, VH CDR3 plays a dominant role in recognizing and binding antigens. Three major mechanisms are involved in the formation of the VH repertoire: germline gene rearrangement, junctional diversity and somatic hypermutation. Features of the generation mechanisms of VH repertoire in humans and mice share similarities while VH CDR3 amino acid (AA) composition differs. Previous studies have mainly focused on germline gene rearrangement and the composition and structure of the CDR3 AA in humans and mice. However the number of AA changes due to somatic hypermutation and analysis of the junctional mechanism have been ignored. Methods Here we analyzed 9,340 human and 6,657 murine unique productive sequences of immunoglobulin (IG) variable heavy (VH) domains derived from IMGT/LIGM-DB database to understand how VH CDR3 AA compositions significantly differed between human and mouse. These sequences were identified and analyzed by IMGT/HighV-QUEST (http://www.imgt.org), including gene usage, number of AA changes due to somatic hypermutation, AA length distribution of VH CDR3, AA composition, and junctional diversity. Results Analyses of human and murine IG repertoires showed significant differences. A higher number of AA changes due to somatic hypermutation and more abundant N-region addition were found in human compared to mouse, which might be an important factor leading to differences in VH CDR3 amino acid composition. Conclusions These findings are a benchmark for understanding VH repertoires and can be used to characterize the VH repertoire during immune responses. The study will allow standardized comparison for high throughput results obtained by IMGT/HighV-QUEST, the reference portal for NGS repertoire.
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Affiliation(s)
| | | | | | | | | | | | - Xinsheng Yao
- Department of Immunology, Research Center for Medicine & Biology, Innovation & Practice Base for Graduate Students Education, Zunyi Medical University, Zunyi 563000, China.
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Yardehnavi N, Behdani M, Bagheri KP, Mahmoodzadeh A, Khanahmad H, Shahbazzadeh D, Habibi-Anbouhi M, Hassanzadeh Ghassabeh G, Muyldermans S. A camelid antibody candidate for development of a therapeutic agent against Hemiscorpius lepturus envenomation. FASEB J 2014; 28:4004-14. [PMID: 24891523 DOI: 10.1096/fj.13-247478] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 05/19/2014] [Indexed: 11/11/2022]
Abstract
Hemiscorpius lepturus scorpionism poses one of the most dangerous health problems in many parts of the world. The common therapy consists of using antivenom antibody fragments derived from a polyclonal immune response raised in horses. However, this immunotherapy creates serious side effects, including anaphylactic shock sometimes even leading to death. Thus, many efforts have been made to introduce new replacement therapeutics that cause less adverse reactions. One of the most attractive approaches to replacing the available therapy is offered by single-domain antibody fragments, or nanobodies (Nbs). We immunized dromedaries with H. lepturus toxin and identified a functional recombinant Nb (referred to as F7Nb) against heminecrolysin (HNc), the major known hemolytic and dermonecrotic fraction of H. lepturus venom. This Nb was retrieved from the immune library by phage display selection. The in vitro neutralization tests indicated that 17.5 nmol of the F7Nb can inhibit 45% of the hemolytic activity of 1 EC100 (7.5 μg/ml) of HNc. The in vivo neutralization tests demonstrated that F7Nb had good antihemolytic and antidermonecrotic effects against HNc in all tested mice. Surprisingly, F7Nb (8.75 nmol) neutralized 1 LD100 of HNc (10 μg) via an intracerebroventricular route or 1 LD100 (80 μg) via a subcutaneous route. All of the control mice died. Hence, this Nb is a potential leading novel candidate for treating H. lepturus scorpionism in the near future.
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Affiliation(s)
- Najmeh Yardehnavi
- Biotechnology Research Center, Venom and Biotherapeutics Molecules Laboratory, and
| | - Mahdi Behdani
- Biotechnology Research Center, Venom and Biotherapeutics Molecules Laboratory, and
| | | | - Amir Mahmoodzadeh
- Biotechnology Research Center, Venom and Biotherapeutics Molecules Laboratory, and
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, Isfahan University of Medical Science, Isfahan, Iran
| | - Delavar Shahbazzadeh
- Biotechnology Research Center, Venom and Biotherapeutics Molecules Laboratory, and
| | | | - Gholamreza Hassanzadeh Ghassabeh
- Nanobody Service Facility (NSF) and Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Serge Muyldermans
- Structural Biology Research Center, Vlaams Institutuut vor Biotechnologie (VIB), Brussels, Belgium; and Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
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89
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Houimel M. The analysis of VH and VL genes repertoires of Fab library built from peripheral B cells of human rabies virus vaccinated donors. Hum Immunol 2014; 75:745-55. [PMID: 24862931 DOI: 10.1016/j.humimm.2014.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 05/13/2014] [Accepted: 05/13/2014] [Indexed: 02/04/2023]
Abstract
A human combinatorial Fab antibody library was generated from immune repertoire based on peripheral B cells of ten rabies virus vaccinated donors. The analysis of random Fab fragments from the unselected library presented some bias of V gene usage towards IGHV-genes and IGLV-gen families. The screening of the Fab library on rabies virus allowed specific human Fab antibody fragments characterized for their gene encoding sequences, binding and specificities to RV. Genetic analysis of selected Fabs indicated that the IGHV and IGLV differ from the germ-line sequence. At the level of nucleotide sequences, the IGHV and IGLV domains were found to share 74-92% and 90-96% homology with sequences encoded by the corresponding human germ-line genes respectively. IGHV domains are characterized most frequently by IGHV3 genes, and large proportions of the anti-RV heavy chain IGHV domains are obtained following a VDJ recombination process that uses IGHD3, IGHD2, IGHD1 and IGHD6 genes. IGHJ3 and IGHJ4 genes are predominantly used in RV-Fab. The IGLV domains are dominated by IGKV1, IGLV1 and IGLV3 genes. Numerous somatic hypermutations in the RV-specific IGHV are detected, but only limited amino acid replacement in most of the RV-specific IGLV particularly in those encoded by J proximal IGLV or IGKV genes are found. Furthermore, IGHV3-IGKV1, IGHV3-IGVL1, and IGHV3-IGLV3 germ-line family pairings are preferentially enriched after the screening on rabies virus.
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Affiliation(s)
- Mehdi Houimel
- Laboratoire d'Epidémiologie et de Microbiologie Vétérinaire, Institut Pasteur de Tunis, Tunisia; Université Tunis El Manar, Tunis, Tunisia.
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90
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Nguyen DC, Sanghvi R, Scinicariello F, Pulit-Penaloza J, Hill N, Attanasio R. Cynomolgus and pigtail macaque IgG subclasses: characterization of IGHG genes and computational analysis of IgG/Fc receptor binding affinity. Immunogenetics 2014; 66:361-77. [PMID: 24811270 DOI: 10.1007/s00251-014-0775-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 04/09/2014] [Indexed: 10/25/2022]
Abstract
Macaques are the most widely used experimental nonhuman primate (NHP) species. Rhesus (Macaca mulatta, Macmul), cynomolgus (Macaca fascicularis, Macfas), and pigtail (Macaca nemestrina, Macnem) macaques continue to be popular models for vaccine and infectious diseases research, especially HIV infection and AIDS, and for the development of antibody-based therapeutic strategies. Increased understanding of the immune system of these species is necessary for their optimal use as models of human infections and intervention. In the past few years, the antibody/Fc receptor system has been characterized in a stepwise manner in these species. We have continued this characterization by identifying the four IG heavy gamma (IGHG) genes of Macfas and Macnem in this study. Our results show that these genes share a high degree of similarity with those from other NHP species, while presenting consistent differences when compared to human IGHG genes. Furthermore, comparison of Macfas IGHG genes with those described in other studies suggests the existence of polymorphism. Using sequence- and structure-based computational tools, we performed in silico analysis on multiple polymorphic Macfas IgG and their interactions with human IgG Fc receptors (FcγR), thus predicting that Macfas IGHG polymorphisms influence IgG protein stability and/or binding affinity towards FcγR. The presence of macaque IGHG polymorphisms and macaque/human amino acid changes at locations potentially involved in antibody functional properties indicate the need for cautious design and data interpretation of studies in these models, possibly requiring the characterization of antibody/Fc receptor interactions at the individual level.
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Affiliation(s)
- Doan C Nguyen
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
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Abstract
ABSTRACT
Antibody informatics, a part of immunoinformatics, refers to the concepts, databases, and tools developed and used to explore and to analyze the particular properties of the immunoglobulins (IG) or antibodies, compared with conventional genes and proteins. Antibody informatics is based on a unique ontology, IMGT-ONTOLOGY, created in 1989 by IMGT, the international ImMunoGeneTics information system (
http://www.imgt.org
). IMGT-ONTOLOGY defined, for the first time, the concept of ‘genes’ for the IG and the T cell receptors (TR), which led to their gene and allele nomenclature and allowed their entry in databases and tools. A second IMGT-ONTOLOGY revolutionizing and definitive concept was the IMGT unique numbering that bridged the gap between sequences and structures for the variable (V) and constant (C) domains of the IG and TR, and for the groove (G) domains of the major histocompatibility (MH). These breakthroughs contributed to the development of IMGT databases and tools for antibody informatics and its diverse applications, such as repertoire analysis in infectious diseases, antibody engineering and humanization, and study of antibody/antigen interactions. Nucleotide sequences of antibody V domains from deep sequencing (Next Generation Sequencing or High Throughput Sequencing) are analyzed with IMGT/HighV-QUEST, the high-throughput version of IMGT/V-QUEST and IMGT/JunctionAnalysis. Amino acid sequences of V and C domains are represented with the IMGT/Collier-de-Perles tool and analyzed with IMGT/DomainGapAlign. Three-dimensional (3D) structures (including contact analysis and paratope/epitope) are described in IMGT/3Dstructure-DB. Based on a friendly interface, IMGT/mAb-DB contains therapeutic monoclonal antibodies (INN suffix–mab) that can be queried on their specificity, for example, in infectious diseases, on bacterial or viral targets.
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Antonacci R, Giannico F, Ciccarese S, Massari S. Genomic characteristics of the T cell receptor (TRB) locus in the rabbit (Oryctolagus cuniculus) revealed by comparative and phylogenetic analyses. Immunogenetics 2014; 66:255-66. [DOI: 10.1007/s00251-013-0754-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 12/20/2013] [Indexed: 02/05/2023]
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Lefranc MP. Immunoglobulin and T Cell Receptor Genes: IMGT(®) and the Birth and Rise of Immunoinformatics. Front Immunol 2014; 5:22. [PMID: 24600447 PMCID: PMC3913909 DOI: 10.3389/fimmu.2014.00022] [Citation(s) in RCA: 165] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 01/15/2014] [Indexed: 11/13/2022] Open
Abstract
IMGT(®), the international ImMunoGeneTics information system(®) (1), (CNRS and Université Montpellier 2) is the global reference in immunogenetics and immunoinformatics. By its creation in 1989, IMGT(®) marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT(®) is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH), and proteins of the IgSF and MhSF superfamilies. IMGT(®) has been built on the IMGT-ONTOLOGY axioms and concepts, which bridged the gap between genes, sequences, and three-dimensional (3D) structures. The concepts include the IMGT(®) standardized keywords (concepts of identification), IMGT(®) standardized labels (concepts of description), IMGT(®) standardized nomenclature (concepts of classification), IMGT unique numbering, and IMGT Colliers de Perles (concepts of numerotation). IMGT(®) comprises seven databases, 15,000 pages of web resources, and 17 tools, and provides a high-quality and integrated system for the analysis of the genomic and expressed IG and TR repertoire of the adaptive immune responses. Tools and databases are used in basic, veterinary, and medical research, in clinical applications (mutation analysis in leukemia and lymphoma) and in antibody engineering and humanization. They include, for example IMGT/V-QUEST and IMGT/JunctionAnalysis for nucleotide sequence analysis and their high-throughput version IMGT/HighV-QUEST for next-generation sequencing (500,000 sequences per batch), IMGT/DomainGapAlign for amino acid sequence analysis of IG and TR variable and constant domains and of MH groove domains, IMGT/3Dstructure-DB for 3D structures, contact analysis and paratope/epitope interactions of IG/antigen and TR/peptide-MH complexes and IMGT/mAb-DB interface for therapeutic antibodies and fusion proteins for immune applications (FPIA).
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Affiliation(s)
- Marie-Paule Lefranc
- The International ImMunoGenetics Information System (IMGT), Laboratoire d’ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine, UPR CNRS, Université Montpellier 2, Montpellier, France
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Pinheiro A, Woof JM, Abi-Rached L, Parham P, Esteves PJ. Computational analyses of an evolutionary arms race between mammalian immunity mediated by immunoglobulin A and its subversion by bacterial pathogens. PLoS One 2013; 8:e73934. [PMID: 24019941 PMCID: PMC3760800 DOI: 10.1371/journal.pone.0073934] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2013] [Accepted: 07/26/2013] [Indexed: 12/19/2022] Open
Abstract
IgA is the predominant immunoglobulin isotype in mucosal tissues and external secretions, playing important roles both in defense against pathogens and in maintenance of commensal microbiota. Considering the complexity of its interactions with the surrounding environment, IgA is a likely target for diversifying or positive selection. To investigate this possibility, the action of natural selection on IgA was examined in depth with six different methods: CODEML from the PAML package and the SLAC, FEL, REL, MEME and FUBAR methods implemented in the Datamonkey webserver. In considering just primate IgA, these analyses show that diversifying selection targeted five positions of the Cα1 and Cα2 domains of IgA. Extending the analysis to include other mammals identified 18 positively selected sites: ten in Cα1, five in Cα2 and three in Cα3. All but one of these positions display variation in polarity and charge. Their structural locations suggest they indirectly influence the conformation of sites on IgA that are critical for interaction with host IgA receptors and also with proteins produced by mucosal pathogens that prevent their elimination by IgA-mediated effector mechanisms. Demonstrating the plasticity of IgA in the evolution of different groups of mammals, only two of the eighteen selected positions in all mammals are included in the five selected positions in primates. That IgA residues subject to positive selection impact sites targeted both by host receptors and subversive pathogen ligands highlights the evolutionary arms race playing out between mammals and pathogens, and further emphasizes the importance of IgA in protection against mucosal pathogens.
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Affiliation(s)
- Ana Pinheiro
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos/InBio Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- SaBio - Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Jenny M. Woof
- Division of Cancer Research, Medical Research Institute, University of Dundee Medical School, Ninewells Hospital, Dundee, United Kingdom
| | - Laurent Abi-Rached
- Centre National de la Recherche Scientifique, Laboratoire d’Analyse, Topologie, Probabilités - Unité Mixte de Recherche 7353, Equipe ATIP, Aix-Marseille Université, Marseille, France
| | - Peter Parham
- Department of Structural Biology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Pedro J. Esteves
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos/InBio Laboratório Associado, Universidade do Porto, Vairão, Portugal
- CESPU, Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde, Gandra PRD, Portugal
- * E-mail:
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95
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Gong R, Wang Y, Ying T, Feng Y, Streaker E, Prabakaran P, Dimitrov DS. N-terminal truncation of an isolated human IgG1 CH2 domain significantly increases its stability and aggregation resistance. Mol Pharm 2013; 10:2642-52. [PMID: 23641816 PMCID: PMC3795862 DOI: 10.1021/mp400075f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Isolated human immunoglobulin G (IgG) CH2 domains are promising scaffolds for novel candidate therapeutics. Unlike other human IgG domains, CH2 is not involved in strong interchain interactions, and isolated CH2 is relatively stable. However, isolated single CH2 is prone to aggregation. In native IgG and Fc molecules, the N-terminal residues of CH2 from the two heavy chains interact with each other and form hinge regions. By contrast, the N-terminal residues are highly disordered in isolated CH2. We have hypothesized that the removal of the CH2 N-terminal residues may not only increase its stability but also its aggregation resistance. To test this hypothesis we constructed a shortened variant of IgG1 CH2 (CH2s) where the first seven residues of the N-terminus were deleted. We found that the thermal stability of CH2s was increased by 5 °C compared to CH2. Importantly, we demonstrated that CH2s is significantly less prone to aggregation than CH2 as measured by Thioflavin T (ThT) fluorescence, turbidity, and light scattering. We also found that the CH2s exhibited pH-dependent binding to a soluble single-chain human neonatal Fc receptor (shFcRn) which was significantly stronger than the very weak binding of CH2 to shFcRn as measured by flow cytometry. Computer modeling suggested a possible mode of CH2 aggregation involving its N-terminal residues. Therefore, deletion of the N-terminal residues could increase drugability of CH2-based therapeutic candidates. This strategy to increase stability and aggregation resistance could also be applicable to other Ig-related proteins.
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Affiliation(s)
- Rui Gong
- Antibody Engineering Group, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China
- Protein Interactions Group, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yanping Wang
- Protein Interactions Group, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
- Basic Research Program, Science Applications International Corporation-Frederick, Inc., Frederick, MD 21702, USA
| | - Tianlei Ying
- Protein Interactions Group, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yang Feng
- Protein Interactions Group, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Emily Streaker
- Protein Interactions Group, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
- Basic Research Program, Science Applications International Corporation-Frederick, Inc., Frederick, MD 21702, USA
| | - Ponraj Prabakaran
- Protein Interactions Group, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
- Basic Research Program, Science Applications International Corporation-Frederick, Inc., Frederick, MD 21702, USA
| | - Dimiter S. Dimitrov
- Protein Interactions Group, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
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96
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Pantazes RJ, Maranas CD. MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies. BMC Bioinformatics 2013; 14:168. [PMID: 23718826 PMCID: PMC3687570 DOI: 10.1186/1471-2105-14-168] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 05/24/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The de novo design of a novel protein with a particular function remains a formidable challenge with only isolated and hard-to-repeat successes to date. Due to their many structurally conserved features, antibodies are a family of proteins amenable to predictable rational design. Design algorithms must consider the structural diversity of possible naturally occurring antibodies. The human immune system samples this design space (2 1012) by randomly combining variable, diversity, and joining genes in a process known as V-(D)-J recombination. DESCRIPTION By analyzing structural features found in affinity matured antibodies, a database of Modular Antibody Parts (MAPs) analogous to the variable, diversity, and joining genes has been constructed for the prediction of antibody tertiary structures. The database contains 929 parts constructed from an analysis of 1168 human, humanized, chimeric, and mouse antibody structures and encompasses all currently observed structural diversity of antibodies. CONCLUSIONS The generation of 260 antibody structures shows that the MAPs database can be used to reliably predict antibody tertiary structures with an average all-atom RMSD of 1.9 Å. Using the broadly neutralizing anti-influenza antibody CH65 and anti-HIV antibody 4E10 as examples, promising starting antibodies for affinity maturation are identified and amino acid changes are traced as antibody affinity maturation occurs.
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97
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Haggart R, Perera J, Huang H. Cloning of a hamster anti-mouse CD79B antibody sequences and identification of a new hamster immunoglobulin lambda constant IGLC gene region. Immunogenetics 2013; 65:473-8. [PMID: 23558558 DOI: 10.1007/s00251-013-0698-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Accepted: 03/13/2013] [Indexed: 11/24/2022]
Abstract
Anti-CD79 antibodies have been effective at targeting B cell lymphoma cells and depleting B cells in animal models. In order to engineer recombinant antibodies with additional effector functions in mice, we cloned and sequenced the full-length cDNAs of the heavy and light chain of a hamster anti-mouse CD79B antibody. Although hamster antibodies represent a unique source of monoclonal antibodies against mouse, rat, and human antigens, sequence information of hamster immunoglobulins (IG) is sparse. Here, we report a new hamster (Cricetulus migratorius) IG lambda constant (IGLC) gene region that is most homologous to mouse IGLC2 and IGLC3.
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Affiliation(s)
- Ryan Haggart
- Department of Medicine, Section of Rheumatology, Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL 60637, USA
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98
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Vlachakis D, Feidakis C, Megalooikonomou V, Kossida S. IMGT/Collier-de-Perles: a two-dimensional visualization tool for amino acid domain sequences. Theor Biol Med Model 2013; 10:14. [PMID: 23432825 PMCID: PMC3621776 DOI: 10.1186/1742-4682-10-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 02/16/2013] [Indexed: 11/23/2022] Open
Abstract
IMGT/Collier-de-Perles is a tool that allows the user to analyze and draw two-dimensional graphical representations (or IMGT Collier de Perles) of protein domains (e.g., hydropathy plots). The IMGT/Collier-de-Perles specializes in the area of immunoglobulins (IG) or antibodies, T cell receptors (TR) and major histocompatibility (MH) of human and other vertebrate species as well as other proteins of the immunoglobulin superfamily (IgSF) and of the major histocompatibility superfamily (MhSF) and related proteins of the immune system of vertebrates and invertebrates.
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Affiliation(s)
- Dimitrios Vlachakis
- Bioinformatics & Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527, Greece
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99
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Use of IMGT(®) databases and tools for antibody engineering and humanization. Methods Mol Biol 2012; 907:3-37. [PMID: 22907343 DOI: 10.1007/978-1-61779-974-7_1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
IMGT(®), the international ImMunoGeneTics information system(®) (http://www.imgt.org), was created in 1989 to manage the huge diversity of the antigen receptors, immunoglobulins (IG) or antibodies, and T cell receptors (TR). Standardized sequence and structure analysis of antibody using IMGT(®) databases and tools allows one to bridge, for the first time, the gap between antibody sequences and three-dimensional (3D) structures. This is achieved through the IMGT Scientific chart rules, based on the IMGT-ONTOLOGY concepts of classification (IMGT gene and allele nomenclature), description (IMGT standardized labels), and numerotation (IMGT unique numbering and IMGT Colliers de Perles). IMGT(®) is the international reference for immunogenetics and immunoinformatics and its standards are particularly useful for antibody humanization and evaluation of immunogenicity. IMGT(®) databases for antibody nucleotide sequences and genes include IMGT/LIGM-DB and IMGT/GENE-DB, respectively, whereas nucleotide sequence analysis is performed by the IMGT/V-QUEST, IMGT/HighV-QUEST, and IMGT/JunctionAnalysis tools. In this chapter, we focus on IMGT(®) databases and tools for amino acid sequences, two-dimensional (2D) and three-dimensional (3D) structures: the IMGT/DomainGapAlign and IMGT/Collier-de-Perles tools, the IMGT/2Dstructure-DB database for amino acid sequences of monoclonal antibodies (mAb, suffix -mab) and fusion proteins for immune applications (FPIA, suffix -cept) of the World Health Organization/International Nonproprietary Name (WHO/INN) programme and other proteins of interest, and the IMGT/3Dstructure-DB database for crystallized antibodies and its associated tools (IMGT/StructuralQuery, IMGT/DomainSuperimpose).
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100
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Buonocore F, Castro R, Randelli E, Lefranc MP, Six A, Kuhl H, Reinhardt R, Facchiano A, Boudinot P, Scapigliati G. Diversity, molecular characterization and expression of T cell receptor γ in a teleost fish, the sea bass (Dicentrarchus labrax, L). PLoS One 2012; 7:e47957. [PMID: 23133531 PMCID: PMC3485050 DOI: 10.1371/journal.pone.0047957] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 09/18/2012] [Indexed: 11/19/2022] Open
Abstract
Two lineages of T cells, expressing either the αβ T cell receptor (TR) or the γδ TR, exist in Gnathostomes. The latter type of T cells account for 1–10 % of T cells in blood and up to 30 % in the small intestine. They may recognize unconventional antigens (phosphorylated microbial metabolites, lipid antigens) without the need of major histocompatibility class I (MH1) or class II (MH2) presentation. In this work we have described cloning and structural characterization of TR -chain (TRG) from the teleost Dicentrarchus labrax. Further, by means of quantitative PCR analysis, we analyzed TRG expression levels both in poly I:C stimulated leukocytes in vitro, and following infection with betanodavirus in vivo. Two full length cDNAs relative to TRG, with the highest peptide and nucleotide identity with Japanese flounder, were identified. A multiple alignment analysis showed the conservation of peptides fundamental for TRG biological functions, and of the FGXG motif in the FR4 region, typical of most TR and immunoglobulin light chains. A 3D structure consisting of two domains mainly folded as beta strands with a sandwich architecture for each domain was also reported. TRG CDR3 of 8–18 AA in length and diversity in the TRG rearrangements expressed in thymus and intestine for a given V/C combination were evidenced by junction length spectratyping. TRG mRNA expression levels were high in basal conditions both in thymus and intestine, while in kidney and gut leukocytes they were up-regulated after in vitro stimulation by poly I:C. Finally, in juveniles the TRG expression levels were up-regulated in the head kidney and down-regulated in intestine after in vivo infection with betanodavirus. Overall, in this study the involvement of TRG-bearing T cells during viral stimulation was described for the first time, leading to new insights for the identification of T cell subsets in fish.
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Affiliation(s)
- Francesco Buonocore
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università, Viterbo, Italy
| | - Rosario Castro
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires, Jouy-en-Josas, Paris, France
| | - Elisa Randelli
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università, Viterbo, Italy
| | - Marie-Paule Lefranc
- The International ImMunoGeneTics Information System®, Laboratoire d’ImmunoGénétique Moléculaire, Institut de Génétique Humaine, Centre National de la Recherche Scientifique and Université Montpellier 2, Montpellier, France
| | - Adrien Six
- Université Pierre et Marie Curie (Université Paris-06), Unité Mixte de Recherches 7211, “Integrative Immunology” Team, Paris, France
- Centre National Recherche Scientifique, Unité Mixte de Recherches, “Immunology, Immunopathology, Immunotherapy”, Paris, France
| | - Heiner Kuhl
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Richard Reinhardt
- Genome Centre at Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Angelo Facchiano
- Laboratory of Bioinformatics and Computational Biology – National Research Council, Istitute of Sciences of Alimentation, Avellino, Italy
| | - Pierre Boudinot
- Institut National de la Recherche Agronomique, Unité de Virologie et Immunologie Moléculaires, Jouy-en-Josas, Paris, France
| | - Giuseppe Scapigliati
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università, Viterbo, Italy
- * E-mail:
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