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Lefranc MP, Lefranc G. Antibody Sequence and Structure Analyses Using IMGT ®: 30 Years of Immunoinformatics. Methods Mol Biol 2023; 2552:3-59. [PMID: 36346584 DOI: 10.1007/978-1-0716-2609-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org , the global reference in immunogenetics and immunoinformatics, 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) of the adaptive immune responses. The founding of IMGT® marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. IMGT® standardized analysis of the IG, TR, and major histocompatibility (MH) genes and proteins bridges the gap between sequences and three-dimensional (3D) structures, for all jawed vertebrates from fish to humans. This is achieved through the IMGT Scientific chart rules, based on the IMGT-ONTOLOGY axioms, and primarily CLASSIFICATION (IMGT gene and allele nomenclature) and NUMEROTATION (IMGT unique numbering and IMGT Colliers de Perles). IMGT® comprises seven databases (IMGT/LIGM-DB for nucleotide sequences, IMGT/GENE-DB for genes and alleles, etc.), 17 tools (IMGT/V-QUEST, IMGT/JunctionAnalysis, IMGT/HighV-QUEST for NGS, etc.), and more than 20,000 Web resources. In this chapter, the focus is on the tools for amino acid sequences per domain (IMGT/DomainGapAlign and IMGT/Collier-de-Perles), and on the databases for receptors (IMGT/2Dstructure-DB and IMGT/3D-structure-DB) described per receptor, chain, and domain and, for 3D, with contact analysis, paratope, and epitope. The IMGT/mAb-DB is the query interface for monoclonal antibodies (mAb), fusion proteins for immune applications (FPIA), composite proteins for clinical applications (CPCA), and related proteins of interest (RPI) with links to IMGT® 2D and 3D databases and to the World Health Organization (WHO) International Nonproprietary Names (INN) program lists. The chapter includes the human IG allotypes and antibody engineered variants for effector properties used in the description of therapeutical mAb.
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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, UMR 9002 CNRS, Université de Montpellier, Montpellier cedex 5, France.
| | - Gérard Lefranc
- IMGT®, the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002 CNRS, Université de Montpellier, Montpellier cedex 5, France.
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Giudicelli V, Duroux P, Rollin M, Aouinti S, Folch G, Jabado-Michaloud J, Lefranc MP, Kossida S. IMGT ® Immunoinformatics Tools for Standardized V-DOMAIN Analysis. Methods Mol Biol 2022; 2453:477-531. [PMID: 35622340 PMCID: PMC9761511 DOI: 10.1007/978-1-0716-2115-8_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The variable domains (V-DOMAIN) of the antigen receptors, immunoglobulins (IG) or antibodies and T cell receptors (TR), which specifically recognize the antigens show a huge diversity in their sequences. This diversity results from the complex mechanisms involved in the synthesis of these domains at the DNA level (rearrangements of the variable (V), diversity (D), and joining (J) genes; N-diversity; and, for the IG, somatic hypermutations). The recognition of V, D, and J as "genes" and their entry in databases mark the creation of IMGT by Marie-Paule Lefranc, and the origin of immunoinformatics in 1989. For 30 years, IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org , has implemented databases and developed tools for IG and TR immunoinformatics, based on the IMGT Scientific chart rules and IMGT-ONTOLOGY concepts and axioms, and more particularly, the princeps ones: IMGT genes and alleles (CLASSIFICATION axiom) and the IMGT unique numbering and IMGT Collier de Perles (NUMEROTATION axiom). This chapter describes the online tools for the characterization and annotation of the expressed V-DOMAIN sequences: (a) IMGT/V-QUEST analyzes in detail IG and TR rearranged nucleotide sequences, (b) IMGT/HighV-QUEST is its high throughput version, which includes a module for the identification of IMGT clonotypes and generates immunoprofiles of expressed V, D, and J genes and alleles, (c) IMGT/StatClonotype performs the pairwise comparison of IMGT/HighV-QUEST immunoprofiles, (d) IMGT/DomainGapAlign analyzes amino acid sequences and is frequently used in antibody engineering and humanization, and (e) IMGT/Collier-de-Perles provides two-dimensional (2D) graphical representations of V-DOMAIN, bridging the gap between sequences and 3D structures. These IMGT® tools are widely used in repertoire analyses of the adaptive immune responses in normal and pathological situations and in the design of engineered IG and TR for therapeutic applications.
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Affiliation(s)
- Véronique Giudicelli
- IMGT®, the international ImMunoGenetics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine, (IGH), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Montpellier, France.
| | - Patrice Duroux
- IMGT®, the international ImMunoGenetics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine, (IGH), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Montpellier, France
| | - Maël Rollin
- IMGT®, the international ImMunoGenetics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine, (IGH), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Montpellier, France
| | - Safa Aouinti
- IMGT®, the international ImMunoGenetics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine, (IGH), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Montpellier, France
- Clinical Research and Epidemiology Unit, CHU Montpellier, Univ Montpellier, Montpellier, France
| | - Géraldine Folch
- IMGT®, the international ImMunoGenetics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine, (IGH), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Montpellier, France
| | - Joumana Jabado-Michaloud
- IMGT®, the international ImMunoGenetics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine, (IGH), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Montpellier, France
| | - Marie-Paule Lefranc
- IMGT®, the international ImMunoGenetics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine, (IGH), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Montpellier, France.
| | - Sofia Kossida
- IMGT®, the international ImMunoGenetics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine, (IGH), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Montpellier, France
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Brohl AS, Sindiri S, Wei JS, Milewski D, Chou HC, Song YK, Wen X, Kumar J, Reardon HV, Mudunuri US, Collins JR, Nagaraj S, Gangalapudi V, Tyagi M, Zhu YJ, Masih KE, Yohe ME, Shern JF, Qi Y, Guha U, Catchpoole D, Orentas RJ, Kuznetsov IB, Llosa NJ, Ligon JA, Turpin BK, Leino DG, Iwata S, Andrulis IL, Wunder JS, Toledo SRC, Meltzer PS, Lau C, Teicher BA, Magnan H, Ladanyi M, Khan J. Immuno-transcriptomic profiling of extracranial pediatric solid malignancies. Cell Rep 2021; 37:110047. [PMID: 34818552 PMCID: PMC8642810 DOI: 10.1016/j.celrep.2021.110047] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 07/20/2021] [Accepted: 11/01/2021] [Indexed: 12/13/2022] Open
Abstract
We perform an immunogenomics analysis utilizing whole-transcriptome sequencing of 657 pediatric extracranial solid cancer samples representing 14 diagnoses, and additionally utilize transcriptomes of 131 pediatric cancer cell lines and 147 normal tissue samples for comparison. We describe patterns of infiltrating immune cells, T cell receptor (TCR) clonal expansion, and translationally relevant immune checkpoints. We find that tumor-infiltrating lymphocytes and TCR counts vary widely across cancer types and within each diagnosis, and notably are significantly predictive of survival in osteosarcoma patients. We identify potential cancer-specific immunotherapeutic targets for adoptive cell therapies including cell-surface proteins, tumor germline antigens, and lineage-specific transcription factors. Using an orthogonal immunopeptidomics approach, we find several potential immunotherapeutic targets in osteosarcoma and Ewing sarcoma and validated PRAME as a bona fide multi-pediatric cancer target. Importantly, this work provides a critical framework for immune targeting of extracranial solid tumors using parallel immuno-transcriptomic and -peptidomic approaches.
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Affiliation(s)
- Andrew S Brohl
- Sarcoma Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | | | - Jun S Wei
- Genetics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | | | | | - Young K Song
- Genetics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Xinyu Wen
- Genetics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | | | - Hue V Reardon
- Advanced Biomedical Computational Science, Leidos Biomedical Research Inc., NCI Campus at Frederick, Frederick, MD 21702, USA
| | - Uma S Mudunuri
- Advanced Biomedical Computational Science, Leidos Biomedical Research Inc., NCI Campus at Frederick, Frederick, MD 21702, USA
| | - Jack R Collins
- Advanced Biomedical Computational Science, Leidos Biomedical Research Inc., NCI Campus at Frederick, Frederick, MD 21702, USA
| | - Sushma Nagaraj
- Laboratory of Pathology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | | | - Manoj Tyagi
- Laboratory of Pathology, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Yuelin J Zhu
- Genetics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Katherine E Masih
- Genetics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA; Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Marielle E Yohe
- Pediatric Oncology Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Jack F Shern
- Pediatric Oncology Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Yue Qi
- Thoracic and GI Malignancies Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Udayan Guha
- Thoracic and GI Malignancies Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA
| | - Daniel Catchpoole
- The Tumour Bank, Children's Cancer Research Unit, Kids Research Institute, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Rimas J Orentas
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA
| | - Igor B Kuznetsov
- Cancer Research Center and Department of Epidemiology and Biostatistics, School of Public Health, University at Albany, Rensselaer, NY 12144, USA
| | - Nicolas J Llosa
- Pediatric Oncology, John Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - John A Ligon
- Pediatric Oncology, John Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Brian K Turpin
- Division of Oncology, Cincinnati Children's Hospital, 3333 Burnet Avenue, Cincinnati, OH 45229-3026, USA
| | - Daniel G Leino
- Division of Oncology, Cincinnati Children's Hospital, 3333 Burnet Avenue, Cincinnati, OH 45229-3026, USA
| | | | - Irene L Andrulis
- Lunenfelf-Tanenbaum Research Institute, Sinai Health System; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Jay S Wunder
- University of Toronto Musculoskeletal Oncology Unit, Sinai Health System; Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Silvia R C Toledo
- Support Group for Children and Adolescents with Cancer (GRAACC), Pediatric Oncology Institute (IOP), Universidade Federal de Sao Paulo, Sao Paulo, Brail
| | | | - Ching Lau
- The Jackson Laboratory, Farmington, CT 06032, USA
| | - Beverly A Teicher
- Molecular Pharmacology Branch, DCTD, NCI, NIH, Bethesda, MD 20892, USA
| | - Heather Magnan
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Javed Khan
- Genetics Branch, CCR, NCI, NIH, Bethesda, MD 20892, USA.
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Littera R, Chessa L, Deidda S, Angioni G, Campagna M, Lai S, Melis M, Cipri S, Firinu D, Santus S, Lai A, Porcella R, Rassu S, Meloni F, Schirru D, Cordeddu W, Kowalik MA, Ragatzu P, Vacca M, Cannas F, Alba F, Carta MG, Del Giacco S, Restivo A, Deidda S, Palimodde A, Congera P, Perra R, Orrù G, Pes F, Loi M, Murru C, Urru E, Onali S, Coghe F, Giglio S, Perra A. Natural killer-cell immunoglobulin-like receptors trigger differences in immune response to SARS-CoV-2 infection. PLoS One 2021; 16:e0255608. [PMID: 34352002 PMCID: PMC8341547 DOI: 10.1371/journal.pone.0255608] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/20/2021] [Indexed: 12/23/2022] Open
Abstract
Background The diversity in the clinical course of COVID-19 has been related to differences in innate and adaptative immune response mechanisms. Natural killer (NK) lymphocytes are critical protagonists of human host defense against viral infections. It would seem that reduced circulating levels of these cells have an impact on COVID-19 progression and severity. Their activity is strongly regulated by killer-cell immuno-globulin-like receptors (KIRs) expressed on the NK cell surface. The present study’s focus was to investigate the impact of KIRs and their HLA Class I ligands on SARS-CoV-2 infection. Methods KIR gene frequencies, KIR haplotypes, KIR ligands and combinations of KIRs and their HLA Class I ligands were investigated in 396 Sardinian patients with SARS-CoV-2 infection. Comparisons were made between 2 groups of patients divided according to disease severity: 240 patients were symptomatic or paucisymptomatic (Group A), 156 hospitalized patients had severe disease (Group S). The immunogenetic characteristics of patients were also compared to a population group of 400 individuals from the same geographical areas. Results Substantial differences were obtained for KIR genes, KIR haplotypes and KIR-HLA ligand combinations when comparing patients of Group S to those of Group A. Patients in Group S had a statistically significant higher frequency of the KIR A/A haplotype compared to patients in Group A [34.6% vs 23.8%, OR = 1.7 (95% CI 1.1–2.6); P = 0.02, Pc = 0.04]. Moreover, the KIR2DS2/HLA C1 combination was poorly represented in the group of patients with severe symptoms compared to those of the asymptomatic-paucisymptomatic group [33.3% vs 50.0%, OR = 0.5 (95% CI 0.3–0.8), P = 0.001, Pc = 0.002]. Multivariate analysis confirmed that, regardless of the sex and age of the patients, the latter genetic variable correlated with a less severe disease course [ORM = 0.4 (95% CI 0.3–0.7), PM = 0.0005, PMC = 0.005]. Conclusions The KIR2DS2/HLA C1 functional unit resulted to have a strong protective effect against the adverse outcomes of COVID-19. Combined to other well known factors such as advanced age, male sex and concomitant autoimmune diseases, this marker could prove to be highly informative of the disease course and thus enable the timely intervention needed to reduce the mortality associated with the severe forms of SARS-CoV-2 infection. However, larger studies in other populations as well as experimental functional studies will be needed to confirm our findings and further pursue the effect of KIR receptors on NK cell immune-mediated response to SARS-Cov-2 infection.
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Affiliation(s)
- Roberto Littera
- Complex Structure of Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Sardinian Regional Company for the Protection of Health (ATS Sardegna), Cagliari, Italy
- Association for the Advancement of Research on Transplantation O.d.V., Non Profit Organisation, Cagliari, Italy
- * E-mail: (RL); (LC); (SG); (AP)
| | - Luchino Chessa
- Association for the Advancement of Research on Transplantation O.d.V., Non Profit Organisation, Cagliari, Italy
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
- Liver Unit, Department of Internal Medicine, University Hospital of Cagliari, Cagliari, Italy
- * E-mail: (RL); (LC); (SG); (AP)
| | - Silvia Deidda
- Complex Structure of Pneumology, SS Trinità Hospital, ASSL Cagliari, ATS Sardegna, Cagliari, Italy
| | - Goffredo Angioni
- Complex Structure of Infectious Diseases, SS Trinità Hospital, ASSL Cagliari, ATS Sardegna, Cagliari, Italy
| | - Marcello Campagna
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Sara Lai
- Complex Structure of Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Sardinian Regional Company for the Protection of Health (ATS Sardegna), Cagliari, Italy
| | - Maurizio Melis
- Association for the Advancement of Research on Transplantation O.d.V., Non Profit Organisation, Cagliari, Italy
| | - Selene Cipri
- Complex Structure of Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Sardinian Regional Company for the Protection of Health (ATS Sardegna), Cagliari, Italy
| | - Davide Firinu
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | | | - Alberto Lai
- Local Crisis Unit (UCL), ATS Sardegna, Cagliari, Italy
| | - Rita Porcella
- Complex Structure of Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Sardinian Regional Company for the Protection of Health (ATS Sardegna), Cagliari, Italy
| | - Stefania Rassu
- Complex Structure of Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Sardinian Regional Company for the Protection of Health (ATS Sardegna), Cagliari, Italy
| | - Federico Meloni
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Daniele Schirru
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - William Cordeddu
- Complex Structure of Infectious Diseases, SS Trinità Hospital, ASSL Cagliari, ATS Sardegna, Cagliari, Italy
| | - Marta Anna Kowalik
- Unit of Oncology and Molecular Pathology, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Paola Ragatzu
- Complex Structure of Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Sardinian Regional Company for the Protection of Health (ATS Sardegna), Cagliari, Italy
| | - Monica Vacca
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Federica Cannas
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Francesco Alba
- Complex Structure of Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Sardinian Regional Company for the Protection of Health (ATS Sardegna), Cagliari, Italy
| | - Mauro Giovanni Carta
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Stefano Del Giacco
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Angelo Restivo
- Colorectal Surgery Unit, Department of Surgical Science, University of Cagliari, Cagliari, Italy
| | - Simona Deidda
- Colorectal Surgery Unit, Department of Surgical Science, University of Cagliari, Cagliari, Italy
| | - Antonella Palimodde
- Complex Structure of Pneumology, SS Trinità Hospital, ASSL Cagliari, ATS Sardegna, Cagliari, Italy
| | - Paola Congera
- Complex Structure of Pneumology, SS Trinità Hospital, ASSL Cagliari, ATS Sardegna, Cagliari, Italy
| | - Roberto Perra
- Complex Structure of Pneumology, SS Trinità Hospital, ASSL Cagliari, ATS Sardegna, Cagliari, Italy
| | - Germano Orrù
- Molecular Biology Service Laboratory, Department of Surgical Science, University of Cagliari, Cagliari, Italy
| | - Francesco Pes
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Martina Loi
- Liver Unit, Department of Internal Medicine, University Hospital of Cagliari, Cagliari, Italy
| | - Claudia Murru
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - Enrico Urru
- Liver Unit, Department of Internal Medicine, University Hospital of Cagliari, Cagliari, Italy
| | - Simona Onali
- Unit of Oncology and Molecular Pathology, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Ferdinando Coghe
- Clinical Chemical and Microbiology Laboratory, University Hospital of Cagliari, Cagliari, Italy
| | - Sabrina Giglio
- Complex Structure of Medical Genetics, R. Binaghi Hospital, Local Public Health and Social Care Unit (ASSL) of Cagliari, Sardinian Regional Company for the Protection of Health (ATS Sardegna), Cagliari, Italy
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
- Medical Genetics, Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
- * E-mail: (RL); (LC); (SG); (AP)
| | - Andrea Perra
- Association for the Advancement of Research on Transplantation O.d.V., Non Profit Organisation, Cagliari, Italy
- Unit of Oncology and Molecular Pathology, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
- * E-mail: (RL); (LC); (SG); (AP)
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5
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Creary LE, Sacchi N, Mazzocco M, Morris GP, Montero-Martin G, Chong W, Brown CJ, Dinou A, Stavropoulos-Giokas C, Gorodezky C, Narayan S, Periathiruvadi S, Thomas R, De Santis D, Pepperall J, ElGhazali GE, Al Yafei Z, Askar M, Tyagi S, Kanga U, Marino SR, Planelles D, Chang CJ, Fernández-Viña MA. High-resolution HLA allele and haplotype frequencies in several unrelated populations determined by next generation sequencing: 17th International HLA and Immunogenetics Workshop joint report. Hum Immunol 2021; 82:505-522. [PMID: 34030896 DOI: 10.1016/j.humimm.2021.04.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 04/23/2021] [Accepted: 04/28/2021] [Indexed: 12/12/2022]
Abstract
The primary goal of the unrelated population HLA diversity (UPHD) component of the 17th International HLA and Immunogenetics Workshop was to characterize HLA alleles at maximum allelic-resolution in worldwide populations and re-evaluate patterns of HLA diversity across populations. The UPHD project included HLA genotype and sequence data, generated by various next-generation sequencing methods, from 4,240 individuals collated from 12 different countries. Population data included well-defined large datasets from the USA and smaller samples from Europe, Australia, and Western Asia. Allele and haplotype frequencies varied across populations from distant geographical regions. HLA genetic diversity estimated at 2- and 4-field allelic resolution revealed that diversity at the majority of loci, particularly for European-descent populations, was lower at the 2-field resolution. Several common alleles with identical protein sequences differing only by intronic substitutions were found in distinct haplotypes, revealing a more detailed characterization of linkage between variants within the HLA region. The examination of coding and non-coding nucleotide variation revealed many examples in which almost complete biunivocal relations between common alleles at different loci were observed resulting in higher linkage disequilibrium. Our reference data of HLA profiles characterized at maximum resolution from many populations is useful for anthropological studies, unrelated donor searches, transplantation, and disease association studies.
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Affiliation(s)
- Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto CA, USA.
| | - Nicoletta Sacchi
- Italian Bone Marrow Donor Registry Tissue Typing Laboratory, E.O. Ospedali Galliera, Genova, Italy
| | - Michela Mazzocco
- Italian Bone Marrow Donor Registry Tissue Typing Laboratory, E.O. Ospedali Galliera, Genova, Italy
| | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Gonzalo Montero-Martin
- Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto CA, USA
| | - Winnie Chong
- Histocompatibility and Immunogenetics Service Development Laboratory, NHS Blood and Transplant, London, UK
| | - Colin J Brown
- Department of Histocompatibility and Immunogenetics, NHS Blood and Transplant, London, UK; Faculty of Life Sciences and Medicine, King's College London, University of London, England, UK
| | - Amalia Dinou
- Biomedical Research Foundation Academy of Athens, Hellenic Cord Blood Bank, Athens, Greece
| | | | - Clara Gorodezky
- Laboratory of Immunology and Immunogenetics, Fundación Comparte Vida, A.C. Mexico City, Mexico
| | | | | | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, USA
| | | | - Jennifer Pepperall
- Welsh Transplant and Immunogenetics Laboratory, Welsh Blood Service, Pontyclun, United Kingdom
| | - Gehad E ElGhazali
- Sheikh Khalifa Medical City-Union 71, Abu Dhabi and the Department of Immunology, College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
| | - Zain Al Yafei
- Sheikh Khalifa Medical City-Union 71, Abu Dhabi and the Department of Immunology, College of Medicine and Health Sciences, UAE University, Al Ain, United Arab Emirates
| | - Medhat Askar
- Department of Pathology and Laboratory Medicine, Baylor University Medical center, Dallas, USA
| | - Shweta Tyagi
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Uma Kanga
- Department of Transplant Immunology and Immunogenetics, All India Institute of Medical Sciences, New Delhi, India
| | - Susana R Marino
- Department of Pathology, The University of Chicago Medicine, Chicago, IL, USA
| | - Dolores Planelles
- Histocompatibility, Centro de Transfusión de la Comunidad Valenciana, Valencia, Spain; Grupo Español de Trabajo en Histocompatibilidad e Inmunología del Trasplante (GETHIT), Spanish Society for Immunology, Madrid, Spain
| | | | - Marcelo A Fernández-Viña
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA; Histocompatibility and Immunogenetics Laboratory, Stanford Blood Center, Palo Alto CA, USA.
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Gerussi A, Natalini A, Antonangeli F, Mancuso C, Agostinetto E, Barisani D, Di Rosa F, Andrade R, Invernizzi P. Immune-Mediated Drug-Induced Liver Injury: Immunogenetics and Experimental Models. Int J Mol Sci 2021; 22:4557. [PMID: 33925355 PMCID: PMC8123708 DOI: 10.3390/ijms22094557] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 02/06/2023] Open
Abstract
Drug-induced liver injury (DILI) is a challenging clinical event in medicine, particularly because of its ability to present with a variety of phenotypes including that of autoimmune hepatitis or other immune mediated liver injuries. Limited diagnostic and therapeutic tools are available, mostly because its pathogenesis has remained poorly understood for decades. The recent scientific and technological advancements in genomics and immunology are paving the way for a better understanding of the molecular aspects of DILI. This review provides an updated overview of the genetic predisposition and immunological mechanisms behind the pathogenesis of DILI and presents the state-of-the-art experimental models to study DILI at the pre-clinical level.
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Affiliation(s)
- Alessio Gerussi
- Centre for Autoimmune Liver Diseases, Division of Gastroenterology, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (C.M.); (D.B.); (P.I.)
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, 20900 Monza, Italy
| | - Ambra Natalini
- Institute of Molecular Biology and Pathology (IBPM), National Research Council of Italy (CNR), 00185 Rome, Italy; (A.N.); (F.A.); (F.D.R.)
| | - Fabrizio Antonangeli
- Institute of Molecular Biology and Pathology (IBPM), National Research Council of Italy (CNR), 00185 Rome, Italy; (A.N.); (F.A.); (F.D.R.)
| | - Clara Mancuso
- Centre for Autoimmune Liver Diseases, Division of Gastroenterology, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (C.M.); (D.B.); (P.I.)
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, 20900 Monza, Italy
| | - Elisa Agostinetto
- Academic Trials Promoting Team, Institut Jules Bordet, L’Universite’ Libre de Bruxelles (ULB), 1050 Brussels, Belgium;
- Medical Oncology and Hematology Unit, Humanitas Clinical and Research Center—IRCCS, Humanitas Cancer Center, Rozzano, 20089 Milan, Italy
- Department of Biomedical Sciences, Humanitas University, via Rita Levi Montalcini 4, Pieve Emanuele, 20090 Milan, Italy
| | - Donatella Barisani
- Centre for Autoimmune Liver Diseases, Division of Gastroenterology, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (C.M.); (D.B.); (P.I.)
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, 20900 Monza, Italy
| | - Francesca Di Rosa
- Institute of Molecular Biology and Pathology (IBPM), National Research Council of Italy (CNR), 00185 Rome, Italy; (A.N.); (F.A.); (F.D.R.)
| | - Raul Andrade
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), UGC Aparato Digestivo, Instituto de Investigación Biomédica de Málaga-IBIMA, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, 29016 Málaga, Spain;
| | - Pietro Invernizzi
- Centre for Autoimmune Liver Diseases, Division of Gastroenterology, Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (C.M.); (D.B.); (P.I.)
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, 20900 Monza, Italy
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12th East-West Immunogenetics Conference, 8-9th March 2018, City Conference Centre, Prague, Czech Republic. HLA 2018; 92 Suppl 2:67-78. [PMID: 30575338 DOI: 10.1111/tan.13442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Sarada Nandiwada L, Ntrivalas E, O'Gorman MRG. Updates in diagnostic and clinical laboratory immunology from the 30th annual meeting of the Association of Medical Laboratory Immunologists (AMLI). J Immunol Methods 2018; 464:138-140. [PMID: 30452901 DOI: 10.1016/j.jim.2018.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 11/11/2018] [Accepted: 11/15/2018] [Indexed: 11/17/2022]
Affiliation(s)
- L Sarada Nandiwada
- Pediatrics, Section of Allergy, Immunology, Rheumatology and Retrovirology, Baylor College of Medicine, Clinical Immunology Laboratory, Texas Children's Hospital, Houston, TX, USA.
| | | | - Maurice R G O'Gorman
- Pediatrics and Pathology, Keck School of Medicine, University of Southern California, Laboratory Medicine, Children's Hospital of Los Angeles, CA, USA
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9
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Affiliation(s)
- Marcia M Miller
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA.
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10
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Nakamura Y. The current and future applications of immunopharmacogenomics. Clin Adv Hematol Oncol 2015; 13:815-817. [PMID: 27058847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
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11
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Aouinti S, Malouche D, Giudicelli V, Kossida S, Lefranc MP. IMGT/HighV-QUEST Statistical Significance of IMGT Clonotype (AA) Diversity per Gene for Standardized Comparisons of Next Generation Sequencing Immunoprofiles of Immunoglobulins and T Cell Receptors. PLoS One 2015; 10:e0142353. [PMID: 26540440 PMCID: PMC4634997 DOI: 10.1371/journal.pone.0142353] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 09/18/2015] [Indexed: 11/26/2022] Open
Abstract
The adaptive immune responses of humans and of other jawed vertebrate species (gnasthostomata) are characterized by the B and T cells and their specific antigen receptors, the immunoglobulins (IG) or antibodies and the T cell receptors (TR) (up to 2.1012 different IG and TR per individual). IMGT, the international ImMunoGeneTics information system (http://www.imgt.org), was created in 1989 by Marie-Paule Lefranc (Montpellier University and CNRS) to manage the huge and complex diversity of these antigen receptors. IMGT built on IMGT-ONTOLOGY concepts of identification (keywords), description (labels), classification (gene and allele nomenclature) and numerotation (IMGT unique numbering), is at the origin of immunoinformatics, a science at the interface between immunogenetics and bioinformatics. IMGT/HighV-QUEST, the first web portal, and so far the only one, for the next generation sequencing (NGS) analysis of IG and TR, is the paradigm for immune repertoire standardized outputs and immunoprofiles of the adaptive immune responses. It provides the identification of the variable (V), diversity (D) and joining (J) genes and alleles, analysis of the V-(D)-J junction and complementarity determining region 3 (CDR3) and the characterization of the 'IMGT clonotype (AA)' (AA for amino acid) diversity and expression. IMGT/HighV-QUEST compares outputs of different batches, up to one million nucleotide sequencesfor the statistical module. These high throughput IG and TR repertoire immunoprofiles are of prime importance in vaccination, cancer, infectious diseases, autoimmunity and lymphoproliferative disorders, however their comparative statistical analysis still remains a challenge. We present a standardized statistical procedure to analyze IMGT/HighV-QUEST outputs for the evaluation of the significance of the IMGT clonotype (AA) diversity differences in proportions, per gene of a given group, between NGS IG and TR repertoire immunoprofiles. The procedure is generic and suitable for evaluating significance of the IMGT clonotype (AA) diversity and expression per gene, and for any IG and TR immunoprofiles of any species.
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Affiliation(s)
- Safa Aouinti
- IMGT, the international ImMunoGeneTics information system, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UPR CNRS 1142, Montpellier University, Montpellier cedex 5, France
- Higher School of Statistics and Information Analysis, University of Carthage, Tunis, Tunisia
- National School of Engineers of Tunis, Information Technology and Communications Department, Laboratory U2S, University of Tunis El-Manar, Tunis, Tunisia
| | - Dhafer Malouche
- Higher School of Statistics and Information Analysis, University of Carthage, Tunis, Tunisia
- National School of Engineers of Tunis, Information Technology and Communications Department, Laboratory U2S, University of Tunis El-Manar, Tunis, Tunisia
| | - Véronique Giudicelli
- IMGT, the international ImMunoGeneTics information system, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UPR CNRS 1142, Montpellier University, Montpellier cedex 5, France
| | - Sofia Kossida
- IMGT, the international ImMunoGeneTics information system, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UPR CNRS 1142, Montpellier University, Montpellier cedex 5, France
| | - Marie-Paule Lefranc
- IMGT, the international ImMunoGeneTics information system, Laboratoire d’ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UPR CNRS 1142, Montpellier University, Montpellier cedex 5, France
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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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Guseva IA, Demidova NV, Soroka NE, Novikov AA, Luchikhina EL, Aleksandrova EN, Lukina GV, Fedorenko EV, Aronova ES, Samarkina EI, Boldyreva MN, Trofimov DI, Karateev DE, Nasonov EL. [Immunogenetic aspects of early rheumatoid arthritis]. ACTA ACUST UNITED AC 2013:36-43. [PMID: 24003720 DOI: 10.15690/vramn.v68i4.609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The study is aimed to investigate the distribution of alleles of HLA-DRB1 gene in patients with early rheumatoid arthritis and healthy individuals in Russian population, and evaluate their significance as molecular genetic markers of rheumatoid arthritis predisposition and protection. The association between alleles of HLA-DRB1 genes, antibodies to cyclic citrullinated peptides and IgM rheumatoid factor was also studied. Low and high resolution HLA-DRB1 genotyping were compared. In the cohort of patients with early rheumatoid arthritis, the alleles of HLA-DRB1 gene were found to be markers of rheumatoid arthritis protection/risk, especially in the homozygous state. They determined production of antibodies to cyclic citrullinated peptides but were not associated with rheumatoid factor IgM levels. These findings support different autoimmune mechanisms of rheumatoid arthritis pathogenesis.
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Tepper M, Schofield S. Preexposure rabies vaccination schedule. J Travel Med 2012; 19:136; author reply 136. [PMID: 22414043 DOI: 10.1111/j.1708-8305.2011.00593_1.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Abstract
In this chapter, we describe analyses commonly applied to immunogenetic population data, along with software tools that are currently available to perform those analyses. Where possible, we focus on tools that have been developed specifically for the analysis of highly polymorphic immunogenetic data. These analytical methods serve both as a means to examine the appropriateness of a dataset for testing a specific hypothesis, as well as a means of testing hypotheses. Rather than treat this chapter as a protocol for analyzing any population dataset, each researcher and analyst should first consider their data, the possible analyses, and any available tools in light of the hypothesis being tested. The extent to which the data and analyses are appropriate to each other should be determined before any analyses are performed.
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Affiliation(s)
- Steven J Mack
- Center for Genetics, Children's Hospital and Research Center Oakland, Oakland, CA, USA.
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Abstract
In this chapter, we outline some basic principles for the consistent management of immunogenetic data. These include the preparation of a single master data file that can serve as the basis for all subsequent analyses, a focus on the quality and homogeneity of the data to be analyzed, the documentation of the coding systems used to represent the data, and the application of nomenclature standards specific for each immunogenetic system being evaluated. The data management principles discussed here are intended to provide a foundation for the data analysis methods detailed in Chaps. 13 and 14 . The relationship between the data management and analysis methods covered in these three chapters is illustrated in Fig. 3.The application of these data management principles is a first step toward consistent and reproducible data analyses. While it may take extra time and effort to apply them, we feel that it is better to take this approach than to assume that low data quality can be compensated for by large sample sizes.In addition to their relevance for analytical reproducibility, it is important to consider these data management principles from an ethical perspective. The reliability of the data collected and generated as part of a research study should be as important a component of the ethical review of a research application as the security of those data. Finally, in addition to ensuring the integrity of the data from collection to publication, the application of these data management principles will provide a means to foster research integrity and to improve the potential for collaborative data sharing.
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Abstract
Recent advances in technologies for genome- and proteome-scale measurements and perturbations promise to accelerate discovery in every aspect of biology and medicine. Although such rapid technological progress provides a tremendous opportunity, it also demands that we learn how to use these tools effectively. One application with great potential to enhance our understanding of biological systems is the unbiased reconstruction of genetic and molecular networks. Cells of the immune system provide a particularly useful model for developing and applying such approaches. Here, we review approaches for the reconstruction of signalling and transcriptional networks, with a focus on applications in the mammalian innate immune system.
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Affiliation(s)
- Ido Amit
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.
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Ovsyannikova IG, Poland GA. Vaccinomics: current findings, challenges and novel approaches for vaccine development. AAPS J 2011; 13:438-44. [PMID: 21671143 PMCID: PMC3160164 DOI: 10.1208/s12248-011-9281-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Accepted: 05/05/2011] [Indexed: 02/06/2023] Open
Abstract
Recent years have witnessed a growing interest in a field of vaccinology that we have named vaccinomics. The overall idea behind vaccinomics is to identify genetic and other mechanisms and pathways that determine immune responses, and thereby provide new candidate vaccine approaches. Considerable data show that host genetic polymorphisms act as important determinants of innate and adaptive immunity to vaccines. This review highlights examples of the role of immunogenetics and immunogenomics in understanding immune responses to vaccination, which are highly variable across the population. The influence of HLA genes, non-HLA, and innate genes in inter-individual variations in immune responses to viral vaccines are examined using population-based gene/SNP association studies. The ability to understand relationships between immune response gene variants and vaccine-specific immunity may assist in designing new vaccines. At the same time, application of state-of-the-art next-generation sequencing technology (and bioinformatics) is desired to provide new genetic information and its relationship to the immune response.
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Affiliation(s)
- Inna G. Ovsyannikova
- />Vaccine Research Group, Mayo Clinic, Rochester, Minnesota USA
- />Program in Translational Immunovirology and Biodefense, Rochester, Minnesota USA
- />Department of Medicine, Mayo Clinic, Rochester, Minnesota USA
| | - Gregory A. Poland
- />Vaccine Research Group, Mayo Clinic, Rochester, Minnesota USA
- />Program in Translational Immunovirology and Biodefense, Rochester, Minnesota USA
- />Department of Medicine, Mayo Clinic, Rochester, Minnesota USA
- />Department of Pediatric and Adolescent Medicine, Mayo Clinic, Rochester, Minnesota USA
- />Mayo Clinic, 611C Guggenheim Building, 200 First Street, SW, Rochester, Minnesota 55905 USA
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Giudicelli V, Lefranc MP. IMGT/junctionanalysis: IMGT standardized analysis of the V-J and V-D-J junctions of the rearranged immunoglobulins (IG) and T cell receptors (TR). Cold Spring Harb Protoc 2011; 2011:716-725. [PMID: 21632777 DOI: 10.1101/pdb.prot5634] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
INTRODUCTIONIMGT/JunctionAnalysis is the online IMGT tool for the detailed and standardized analysis of the junctions between the variable (V), diversity (D), and joining (J) genes (V-J and V-D-J junctions) of the rearranged immunoglobulin (IG) or antibody and T cell receptor (TR) variable domains. The V-(D)-J junctions comprise the rearranged CDR3-IMGT and its anchors 2nd-CYS 104 and J-PHE or J-TRP 118. The diversity of the junctions that determines the antigen receptor specificity results from complex molecular mechanisms that occur at the DNA level during the IG and TR synthesis and create combinatorial diversity, N-diversity and, for IG, somatic hypermutations. The annotation of V-J or V-D-J junctions in rearranged IG and TR sequences represents a huge challenge due to its uniqueness and complexity. IMGT/JunctionAnalysis has been a major breakthrough by providing, for the first time, a very detailed and accurate analysis of the junctions. The tool, whose use is described here, identifies the D genes in the IGH, TRB, and TRD junctions, the trimmed nucleotides (nt) at the end of the genes which recombine, and the palindromic P regions in the absence of gene trimming. It delimits the N regions that result from the N-diversity, calculates the ratio of G+C nucleotides in the N regions, and evaluates the number of somatic hypermutations for each gene within the junction.
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Affiliation(s)
- Véronique Giudicelli
- IMGT, international ImMunoGeneTics information system, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Université Montpellier 2, Institut de Génétique Humaine IGH, UPR CNRS 1142, 34396 Montpellier cedex 5, France
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20
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Abstract
INTRODUCTIONThe “IMGT Collier de Perles” (or “IMGT_Collier_de_Perles”) concept is a major concept of numerotation (generated from the NUMEROTATION axiom) of IMGT-ONTOLOGY, the global reference in immunogenetics and immunoinformatics, built by IMGT, the international ImMunoGeneTics information system. The “IMGT Collier de Perles” concept, described here, allows standardized two-dimensional (2D) graphical representations of the domains, based on the IMGT unique numbering. Three leafconcepts (a leafconcept is a concept that corresponds to the finest level of granularity) have been defined: for the variable (V) domain and constant (C) domain of the immunoglobulin superfamily (IgSF) and for the groove (G) domain of the major histocompatibility (MH) superfamily (MhSF). IMGT Colliers de Perles are obtained, starting from V, C, or G domain amino acid sequences, using IMGT/DomainGapAlign and IMGT/Collier de Perles tools. In IMGT/3Dstructure-DB, IMGT Colliers de Perles of V and C domains are provided with hydrogen bonds and those of G domains with IMGT pMH contact analysis. IMGT Colliers de Perles allows one to bridge the gap between sequences and three-dimensional (3D) structures, whatever the species, the IgSF or MhSF protein, or the chain type. They are particularly useful for antibody engineering, sequence-structure analysis, visualization and comparison of positions for mutations, polymorphisms and contact analysis of immunoglobulins (IG), T cell receptors (TR), MH, and related proteins of the immune system (RPI) belonging to the IgSF and MhSF.
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Affiliation(s)
- Marie-Paule Lefranc
- IMGT, international ImMunoGeneTics information system, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Université Montpellier 2, Institut de Génétique Humaine IGH, UPR CNRS 1142, 34396 Montpellier cedex 5, France.
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Oksenberg JR, Klitz W. Immunogenetics in the Holy Land. Tissue Antigens 2010; 76:440-441. [PMID: 20860584 DOI: 10.1111/j.1399-0039.2010.01567.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- J R Oksenberg
- Department of Neurology, University of California, San Francisco, CA, USA.
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Carter V. My approach to cardiothoracic transplantation and the role of the histocompatibility and immunogenetics laboratory in a rapidly developing field. J Clin Pathol 2010; 63:189-93. [PMID: 20203218 DOI: 10.1136/jcp.2009.068478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Cardiothoracic transplantation presents specific challenges. The lack of long-term replacement therapy (such as dialysis for kidney patients) creates a more urgent situation than for other forms of transplantation, necessitating a different approach. This review looks at ways in which the challenges are being met and the integral role of the histocompatibility and immunogenetics laboratory.
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Tang NLS. Immunogenetic studies in SARS: developing a clinical prognostic profile for severe diseases. Hong Kong Med J 2009; 15 Suppl 8:8-10. [PMID: 20393204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023] Open
Affiliation(s)
- N L S Tang
- Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China.
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24
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Vojvodić S. [Relevance of polymerase chain reaction technique in immunogenetics and histocompatibility]. Med Pregl 2009; 62:321-326. [PMID: 19902782 DOI: 10.2298/mpns0908321v] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
INTRODUCTION During the last decade of the previous century, among many of developing sciences, molecular biology had the most important position. The greatest influence on the development of scientific knowledge had been brought by discovery of PCR technique, that showed numerous advantages in comparison to the existing techniques. PCR PROCEDURE The capability of PCR technique to amplify specific DNA sequences, in a simple, automatic procedure, accelerated the development of many fields in molecular biology researches such as cloning, identification of new genes and pathogenes, determination and quantification of nucleotide sequences, thus opening fields of experimental investigations and its clinical application. PCR technique is widely used in various investigations from anthropological researches to those in molecular biology, from basic genetic investigations to clinical diagnostics. APPLICATION OF PCR PROCEDURE IN THE FIELD OF IMMUNOGENETICS AND HISTOCOMPATIBILITY In the field of immunogenetics and histocompatibility, there are several HLA genotyping techniques: PCR-SSOP, detection by sequence specific oligonucleotide probes. PCR-SSP, detection by sequence specific primers, RSCA, detection by Reference-Strand Conformation Analysis, SBT-Sequence Based Typing. The development of these techniques has enabled the testing of the HLA alleles as well as detection of shared nucleotide sequences between alleles on the same or/and different loci and the existence of some locus-specific nucleotide sequences in coding (exon) and noncoding (intron) regions. CONCLUSION The application of PCR technique in immunogenetics made it possible to define genetic polymorphism in HLA system, which contributed to a significant progress in the field of tissue and organ transplantation, population and genetic studies as well as in studies of disease association and HLA alleles.
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Braun J, Targan SR. Multiparameter analysis of immunogenetic mechanisms in clinical diagnosis and management of inflammatory bowel disease. Adv Exp Med Biol 2009; 579:209-18. [PMID: 16620020 DOI: 10.1007/0-387-33778-4_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The integrity of the intestinal mucosa depends on a functional coordination of the epithelium, lumenal microorganisms, and the local immune system. The mammalian immune system is superbly organized for innate and adaptive recognition of microbial antigens, a defensive capacity that must be balanced against the tissue damage produced by immune activity to preserve normal intestinal function. Inflammatory bowel disease (IBD) is generally thought to reflect an impairment in this balance, due to a combination of host genetic traits that shift the balance of immune and epithelial function to commensal microbiota, and perhaps the composition or activity of certain microbial elements as well. There has been much progress defining the fundamental disorders of these host traits, immunologic processes, and microbial targets in inflammatory bowel disease. Other fields of clinical and geologic microbiology are teaching us about the dynamic interaction of commensal bacteria with their host environment. These lines of investigation have revealed not only important insights about inflammatory bowel disease (IBD) pathogenesis, but also defined technologies and tools useful for its diagnosis and clinical management. This review focuses on these advances at the translational interface. We will first consider the innate anti-microbial response, centering on the utility of NOD2 genotyping for predicting disease susceptibility, prognosis, and therapeutic response profile. We will then turn to the adaptive anti-microbial response, focusing on the application of antibodies to fungal and bacterial species and products for Crohn's disease (CD) diagnosis and prognosis, and immunogenetics of T cell immunosuppression management. Finally, we will describe autoimmune mechanisms in IBD, with particular attention to autoantibodies in IBD diagnosis and infliximab responsiveness. We will conclude with the concept of multiparameter analysis of patients, to refine patient characterization and stratification in diagnosis and clinical management.
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Affiliation(s)
- Jonathan Braun
- UCLA Hospital Center for Health Sciences, Los Angeles, CA, USA
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26
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Bondarenko AL, Ustiuzhaninov VN, Vozhegova NP, Strazhnikova GA. [Immunogenetic criteria for prediction of mixed hepatitis A + B]. Klin Lab Diagn 2009:30-32. [PMID: 19514333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The investigation has revealed that mixed hepatitis A + B is a genetically determined disease. HLA-A10, B21, Cw2, Cw5, A10-A19, B8-B13, B21-B35, A3-B21, and A9-B21 are immunogenetic markers of this disease. The carriers of HLA-B21, Cw5, A3-B21, and A9-B21 and those of HLA-A10, A10-A19, and A10-B14 are at high risk for this infection among men and women, respectively. The findings of the distribution of HLA antigens and their combinations in mixed infection with hepatitis A and B viruses allow prediction of its occurrence (including the consideration of examinees' gender) which will assist in solving the matter of timely prophylaxis of this pathology.
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Hanyu K, Iida T, Shiba H, Ohashi T, Eto Y, Yanaga K. Immunogene therapy by adenovirus vector expressing CD40 ligand for metastatic liver cancer in rats. Anticancer Res 2008; 28:2785-2789. [PMID: 19035311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
BACKGROUND We have explored a gene-therapeutic approach to stimulate antitumor immunity by adenoviral-mediated transfer of CD40 ligand (CD40L) to treat metastatic liver cancer in a rat model. MATERIALS AND METHODS Rat metastatic liver cancer cells were implanted into the back of rats bilaterally. When the larger tumor reached 8.0 mm in diameter, adenovirus vector-expressing mouse CD40L was injected intratumorally as treatment group (n=5), while LacZ was injected in the control group (n=5). RESULTS In the control group, the tumor gradually grew to be 20.7+/-1.6 (mean+/-SD) mm in intratumorally injected tumors and 21.8+/-3.7 mm in opposite tumors seven weeks after injection, respectively. In contrast, in the treatment group, the tumor was reduced to 3.6+/-8.2 mm and 3.7+/-8.2 mm. The tumor growth and survival rate were significantly different (p<0.001). CONCLUSION Adenovirus vector-mediated CD40L gene therapy is an effective therapeutic method for metastatic liver cancer.
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Affiliation(s)
- Ken Hanyu
- Department of Surgery, Institute of DNA Medicine, The Jikei University School of Medicine, Tokyo, Japan
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Affiliation(s)
- Bruce Beutler
- Department of Genetics, The Scripps Research Institute, La Jolla, California 92037, USA.
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Kim CS, Song MK, Park JS, Cho MH, Kim HJ, Nam JS, Kang ES, Ahn CW, Cha BS, Lee EG, Lim SK, Kim KR, Lee HC, Huh KB. The clinical and immunogenetic characteristics of adult-onset type 1 diabetes mellitus in Korea. Acta Diabetol 2007; 44:45-54. [PMID: 17530466 DOI: 10.1007/s00592-007-0241-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2004] [Accepted: 12/27/2006] [Indexed: 11/28/2022]
Abstract
Although the HLA class II alleles and immunological abnormalities are associated with type 1 diabetes mellitus (T1DM) in all racial groups, there are considerable variations in the genotypes and the prevalence of autoantibodies. In order to investigate the characteristics of the immunogenetic patterns and to use these as an early diagnostic tool and guideline for a therapeutic plan, we examined the clinical characteristics and the patterns of anti-GAD antibody (GADA), IA-2 antibody (IA-2A), HLA-DR and HLA-DQ in Korean adult-onset T1DM patients. Adult-onset patients had higher serum C-peptide levels than child-onset patients. In adult-onset patients, the prevalence of GADA and IA-2A were 59.5% and 15.3% respectively, and increased frequencies of HLADR4 and-DR9 were found. The frequencies of HLADQA1,-DQB1 and-DQ heterodimers were similar to those of the control, but child-onset patients had high frequencies of the HLA-DR3,-DR4,-DR9, DQA1*0301, DQA1*0501 and DQB1*0201 genotypes. In conclusion, Korean adult-onset T1DM patients had a lower prevalence of GADA, which was comparable to that found in Caucasian patients. The detection of GADA might help to predict the insulin dependency of adult-onset diabetes. Difference in the frequencies of diabetes associated with HLA type suggests that there might be a heterogeneity in the pathogenesis of diabetes according to the age of onset.
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Affiliation(s)
- C S Kim
- Department of Internal Medicine, Yonsei University College of Medicine, 134 Shinchon-Dong, Seodaemun-Ku, Seoul, Korea
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Abstract
Chloroplast structure varies depending on cell type. Currently it is difficult to obtain insight into how differences in chloroplast structure relate to function, as it is often not possible to isolate chloroplasts from specific cells. To address this, we have developed an approach that involves labelling chloroplasts from individual cell types by placing the foreign yellow fluorescent protein (YFP) on their outer surface, and then isolating those labelled chloroplasts immunogenically. Cell specificity is achieved through the use of enhancer trap lines. When whole leaves are homogenized, a mixture of labelled and unlabelled chloroplasts is released, but magnetic beads coated with antibodies to the green fluorescent protein (GFP) allow the labelled chloroplasts to be isolated. Chloroplasts from spongy mesophyll, vascular and epidermal cells of Arabidopsis thaliana were obtained in this way, and semi-quantitative RT-PCR showed that the abundance of various chloroplast transcripts differed between these three cell types. The approach is based on genetic logic, and so could be applied to the isolation of various organelles or subcellular compartments from transformable organisms other than A. thaliana.
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Affiliation(s)
- Elisabeth Truernit
- Department of Plant Sciences, Downing Street, University of Cambridge, Cambridge CB2 3EA, UK
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Xu L, Shi SQ, Yang Y, Peng JP. Immunogenicity of four complementary deoxyribonucleic acid fragments from rabbit zona pellucida 3 and their effects on fertility. Fertil Steril 2007; 87:381-90. [PMID: 17113087 DOI: 10.1016/j.fertnstert.2006.06.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2006] [Revised: 06/05/2006] [Accepted: 06/05/2006] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To evaluate the exact region in different exons of rabbit zona pellucida (ZP)3 involved in recognition and binding between sperm and the ZP. DESIGN Prospective study of a female immunocontraceptive. SETTING State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences. ANIMAL(S) BALB/C mice. INTERVENTION(S) Immunization recombinant vaccines. MAIN OUTCOME MEASURE(S) Oocyte immunofluorescence and immunohistochemistry. RESULT(S) The immunogenicity and effects on fertility of these four fragments we used were different. Except for the ZP domain, the other three fragments of rabbit ZP3 may be useful as antigen to elicit antibodies. Antiserum was specific and obvious. The fertility of mice after immunization decreased slightly compared with the control. CONCLUSION(S) The most effective fragment that is associated with the sperm binding was from sequences contained in exons 5-8 or oligosaccharide linked to this region. Exons 5-8 or oligosaccharide linked to this region may exist outside of the ZP matrix and be safe for use as the antigen. The ZP domain may be not related to the recognition and binding.
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Affiliation(s)
- Li Xu
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Sakarellos-Daitsiotis M, Krikorian D, Panou-Pomonis E, Sakarellos C. Artificial carriers: a strategy for constructing antigenic/immunogenic conjugates. Curr Top Med Chem 2006; 6:1715-35. [PMID: 17017953 DOI: 10.2174/156802606778194190] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The rational design of artificial carriers for anchoring multiple copies of B and/or T cell epitopes, built-in vaccine adjuvants and "promiscuous" T cell epitopes for the construction of conjugates as antigenic substrates or potent immunogens has been the stimulus of intensive efforts nowadays. The unambiguous composition, the reliability and the versatility of the production of reconstituted antigens or immunogens has found a great number of biochemical applications in developing immunoassays of high sensitivity, specificity and reproducibility and in generating site-specific antibodies for usage as human vaccine candidates. In this review are summarized different types of artificial carriers currently used as dendrimers bearing branching segments, multimeric core matrices and templates with built-in folding devices. Emphasis is given to the construction and application of a helicoid-type Sequential Oligopeptide Carrier (SOCn) developed in our laboratory. The beneficial structural elements of SOCn induce a favorable arrangement of the conjugated peptides, which also retain their initial "active" conformation, so that potent antigens and immunogens are generated.
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Affiliation(s)
- Maria Sakarellos-Daitsiotis
- Department of Chemistry, Section of Organic Chemistry and Biochemistry, University of Ioannina, 45110 Ioannina, Greece.
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Jennison AV, Raqib R, Verma NK. Immunoproteome analysis of soluble and membrane proteins of Shigella flexneri 2457T. World J Gastroenterol 2006; 12:6683-8. [PMID: 17075984 PMCID: PMC4125676 DOI: 10.3748/wjg.v12.i41.6683] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2006] [Revised: 08/12/2006] [Accepted: 09/21/2006] [Indexed: 02/06/2023] Open
Abstract
AIM To profile the immunogenic proteins of Shigella flexneri (S. flexneri) expressed during human infection using a proteomic approach. METHODS Soluble and membrane protein extractions of S. flexneri 2457T were separated by two-dimensional gel electrophoresis (2-DE). Proteins were transferred to PVDF membrane and immunoblotted with sera from shigellosis patients. Reactive protein spots were matched to Coomassie stained gels run in parallel, cut out and trypsin digested. Matrix-assisted laser desorption/ionization time of flight-mass spectrometry (MALDI-TOF-MS) was used to determine the peptide mass fingerprints, which were searched in the MASCOT database to identify the protein. RESULTS A total of 8 immunoreactive proteins were successfully identified from the Coomassie stained gels in three repeats. Six of these proteins have not previously been reported as immunogenic in S. flexneri. These proteins could be potential candidates for vaccine or attenuation studies. CONCLUSION Soluble and membrane proteins of S. flexneri 2457T have been screened by 2-DE and immunoblotting with sera from shigellosis patients. Eight proteins are identified as immunogenic.
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Affiliation(s)
- Amy V Jennison
- School of Biochemistry and Molecular Biology, Faculty of Science, The Australian National University, Canberra, ACT 0200, Australia
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35
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Kurbatova OL, Pobedonostseva EI, Prokhorovskaia VD, Kholod ON, Evsiukov AN, Bogomolov VV, Voronkov II, Filatova LM, Larina ON, Sidorenko LA, Morgun VV, Kasparanskiĭ RR, Altukhov IP. [Population genetic study of Russian cosmonauts and test subjects: genetic demographic parameters and immunogenetic markers]. Genetika 2006; 42:1415-25. [PMID: 17152711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Genetic demographic characteristics and immunogenetic markers (blood groups ABO, Rhesus, MNSs, P, Duffy, Kidd, and Kell) have been studied in a group of 132 Russian cosmonauts and test subjects (CTSG). Analysis of pedigrees has shown a high exogamy in the preceding generations: almost half of the subjects have mixed ethnic background. According to the results of genetic demographic analysis, a sample from the Moscow population was used as control group (CG). Comparison between the CTSG and CG has demonstrated significant differences in genotype frequencies for several blood group systems. The CTSG is characterized by a decreased proportion of rare interlocus genotypic combinations and an increased man heterozygosity. Analysis of the distributions of individual heterozygosity for loci with codominant expression of alleles has shown that highly heterozygous loci are more frequent in the CTSG. Taking into account that the CTSG has been thoroughly selected from the general population, it is concluded that heterozygosity is related to successful adaptation to a space flight.
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Wakeland EK. Modern immunogenetics: simple questions with complex answers. Curr Opin Immunol 2006; 18:605-7. [PMID: 16893634 DOI: 10.1016/j.coi.2006.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Accepted: 07/24/2006] [Indexed: 11/29/2022]
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Abstract
Similar to other classical science disciplines, immunology has been embracing novel technologies and approaches giving rise to specialised sub-disciplines such as immunogenetics and, more recently, immunogenomics, which, in many ways, is the genome-wide application of immunogenetic approaches. Here, recent progress in the understanding of the immune sub-genome will be reviewed, and the ways in which immunogenomic datasets consisting of genetic and epigenetic variation, linkage disequilibrium and recombination can be harnessed for disease association and evolutionary studies will be discussed. The discussion will focus on data available for the major histocompatibility complex and the leukocyte receptor complex, the two most polymorphic regions of the human immune sub-genome.
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Affiliation(s)
- Marcos M Miretti
- Immunogenomics Laboratory, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Stephan Beck
- Immunogenomics Laboratory, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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Parney IF, Chang LJ, Farr-Jones MA, Hao C, Smylie M, Petruk KC. Technical hurdles in a pilot clinical trial of combined B7-2 and GM-CSF immunogene therapy for glioblastomas and melanomas. J Neurooncol 2006; 78:71-80. [PMID: 16718522 DOI: 10.1007/s11060-005-9058-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2005] [Accepted: 10/12/2005] [Indexed: 10/24/2022]
Abstract
OBJECTIVE Malignant glioblastomas and melanomas continue to have a dismal prognosis despite advances in conventional therapy. This has led to investigations of novel treatment strategies including immunogene therapy. We report a pilot clinical trial of combined B7-2 and GM-CSF immunogene therapy for gliomas and melanomas and discuss technical hurdles encountered. METHODS Patients with recurrent malignant gliomas or medically refractory melanomas were vaccinated with irradiated autologous tumor cells transduced with B7-2 and GM-CSF genes using a retroviral vector. Patients were monitored for toxicity, inflammatory/immune reactions, and clinical status. RESULTS Vaccine preparation was attempted from 116 malignant glioma and 32 melanoma specimens. Adequate vaccines could only be prepared for five glioblastoma and three melanoma patients. Six patients (three recurrent glioblastomas and three melanomas) were actually vaccinated. Minor toxicities included flu-like symptoms (3/6), injection site erythema (4/6), and asymptomatic elevations in liver enzymes (3/6). Most patients showed evidence of an inflammatory response but specific anti-tumor immunity was not demonstrated. All six patients have died, although three patients with minimal residual disease at treatment had prolonged recurrence-free intervals after vaccination. CONCLUSIONS Combined B7-2 and GM-CSF immunogene therapy for glioblastomas and melanomas using autologous tumor cells has many technical pitfalls hindering large scale application and evaluation. As a result, this pilot study was too limited to draw meaningful conclusions regarding safety or anti-tumor immunity. While immunotherapy has been promising in pre-clinical studies, alternate strategies will be required to bring these benefits to patients.
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Affiliation(s)
- Ian F Parney
- Department of Clinical Neurosciences, Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada.
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Abstract
Crohn's disease (CD) and ulcerative colitis (UC) are the two most common forms of chronic inflammatory bowel disease (IBD). The etiology of IBD is still unclear and should be considered as multi-factorial according to recent studies. Genetic factors seem to play a pathogenetic role as well as environmental, infectious and immulogical factors. Substantial progress, however, has been made in the understanding of the pathogenesis of IBD during the past years persuing the view, that IBD could result from disturbances of the intestinal barrier and a pathologic activation of the intestinal immune response towards luminal, bacterial antigens. This paradigm has led to the identification of key players of the intestinal immune system, which represent promising targets for novel therapeutic approaches. The objective of this chapter is to provide an overview over recent advances in the elucidation of the intestinal immune system in IBD and novel therapeutic approaches that have been derived from these results. Molecular biological techniques have revealed, that many of the established conventional antiinflammatory drugs such as salicylic acids, steroids or immunuosuppressants act at the same molecules that are the target for modern biologicals, i.e., the cytokine TNF or the transcription factor NFkappaB. This chapter, however, focusses on novel experimental approaches such as recombinant antiinflammatory cytokines, neutralizing antibodies or antisense oligonucleotides.
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Affiliation(s)
- Martin H Holtmann
- 1st Department of Medicine, Johannes-Gutenberg-University, Mainz, Germany
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40
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Melchers I. [Immunogenetics--HLA-association, molecular chaperones and "related" diseases]. Z Rheumatol 2005; 64:402-7. [PMID: 16184348 DOI: 10.1007/s00393-005-0768-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2005] [Accepted: 07/21/2005] [Indexed: 10/25/2022]
Abstract
The association of rheumatoid arthritis (RA) with the HLA complex has been well established since 1978. But what does that mean? After reminding the reader of some existing immunological interpretations, a more recent variant is introduced. Antigens and molecular chaperones of the HSP70 family form complexes, which interact with HLA-DR beta-chains, especially of the DRB1*0401 genotype, which is the most common among patients with RA in our region. This mechanism might bring *0401(+) persons an advantage in defence against microorganisms, but a disadvantage concerning autoimmunity. Chaperone machines are upregulated in synovial tissue of RA patients. As their number and variety is huge in humans, there exist many possibilities for function, reaching from antigen presentation to immune regulation. In addition to the HLA complex, the "genetic background" plays an important role for the development of an autoimmune disease. This is demonstrated in families of patients with RA or scleroderma, where a high percentage of first degree relatives suffer from a "related" disease.
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Affiliation(s)
- I Melchers
- Klinische Forschergruppe für Rheumatologie, Universitätsklinikum Freiburg, Zentrale Klinische Forschung, Breisacher Str. 66, 79106 Freiburg, Germany.
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Abstract
Recent advances in tumor immunology have fostered the clinical implementation of different immunotherapy modalities. However, the alternate success of such regimens underscores the fact that the molecular mechanisms underlying tumor immune rejection are still poorly understood. Given the complexity of the immune system network and the multidimensionality of tumor-host interactions, the comprehension of tumor immunology might greatly benefit from high-throughput DNA array analysis, which can portray the molecular kinetics of immune response on a genome-wide scale, thus accelerating the accumulation of knowledge and ultimately catalyzing the development of new hypotheses in cell biology. Although in its infancy, the implementation of DNA array technology in tumor immunology studies has already provided investigators with novel data and intriguing hypotheses on the cascade of molecular events leading to an effective immune response against cancer. Although the principles of DNA array-based gene profiling techniques have become common knowledge, the need for mastering this technique to produce meaningful data and correctly interpret this enormous output of information is critical and represents a tremendous challenge for investigators. In the present work, we summarize the main technical features and critical issues characterizing this powerful laboratory tool and review its applications in the fascinating field of cancer immunogenomics.
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Affiliation(s)
- Simone Mocellin
- Department of Oncological and Surgical Sciences, University of Padova, Padua, Italy.
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Lefranc MP, Clement O, Kaas Q, Duprat E, Chastellan P, Coelho I, Combres K, Ginestoux C, Giudicelli V, Chaume D, Lefranc G. IMGT-Choreography for immunogenetics and immunoinformatics. In Silico Biol 2005; 5:45-60. [PMID: 15972004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
IMGT, the international ImMunoGeneTics information system (http://imgt.cines.fr), was created in 1989 at Montpellier, France. IMGT is a high quality integrated knowledge resource specialized in immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC) of human and other vertebrates, and related proteins of the immune system (RPI) which belong to the immunoglobulin superfamily (IgSF) and MHC superfamily (MhcSF). IMGT provides a common access to standardized data from genome, proteome, genetics and three-dimensional structures. The accuracy and the consistency of IMGT data are based on IMGT-ONTOLOGY, a semantic specification of terms to be used in immunogenetics and immunoinformatics. IMGT-ONTOLOGY has been formalized using XML Schema (IMGT-ML) for interoperability with other information systems. We are developing Web services to automatically query IMGT databases and tools. This is the first step towards IMGT-Choreography which will trigger and coordinate dynamic interactions between IMGT Web services to process complex significant biological and clinical requests. IMGT-Choreography will further increase the IMGT leadership in immunogenetics and immunoinformatics for medical research (repertoire analysis of the IG antibody sites and of the TR recognition sites in autoimmune and infectious diseases, AIDS, leukemias, lymphomas, myelomas), veterinary research (IG and TR repertoires in farm and wild life species), genome diversity and genome evolution studies of the adaptive immune responses, biotechnology related to antibody engineering (single chain Fragment variable (scFv), phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (detection and follow up of residual diseases) and therapeutical approaches (grafts, immunotherapy, vaccinology). IMGT is freely available at http://imgt.cines.fr.
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Affiliation(s)
- Marie-Paule Lefranc
- Universite Montpellier II, Laboratoire d'ImmunoGenetique Moleculaire LIGM, UPR CNRS 1142, Institut de Genetique Humaine IGH, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France.
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Abstract
An alloantigen is a genetically determined cell-surface molecule detected by specific antisera. An identifying letter has been assigned to each genetic locus responsible for the 12 distinct families of alloantigens: A, B, C, D, E, H, I, J, K, L, P, and R. The genes of each system segregate independently of the other systems, except that the A and E are very closely linked (0.5 centimorgans). Selection experiments over numerous generations have revealed distinct changes in gene frequency of the A-E alloantigens, suggesting immune responses associated with susceptibility to coccidiosis, response to immunizations with SRBC, and selection for size of the bursa of Fabricius. Immune response effects of the C system of alloantigen genes are indicated by distinct gene frequency changes following selection for response to SRBC, selection for size of bursa of Fabricius, and macrophage nitrite production after lipopolysaccharide (LPS) stimulation. Immune response effects of the D system of antigens are indicated by data from genetic selection for response to immunization with SRBC, selection for bursa size, and macrophage nitrite and cytokine interleukin (IL)-6 production following LPS stimulation. Immune response effects of the I system genes are indicated by distinct gene frequency changes in lines selected for bursa size and within family comparisons for macrophage nitrite and cytokine IL-6 production following LPS stimulation. Effects of the L system, consisting of only 2 alleles, are indicated by the gene frequency changes following selection for bursa size, direct comparison of genotypes within families for monocyte phagocytosis, susceptibility to coccidiosis, outcome of Rous sarcomas, and immune responses to SRBC and Brucella abortus. Genotypes of the P alloantigen system were directly compared within families of fully pedigreed chicks with significant differences for monocyte phagocytosis. An experimental procedure for simultaneously testing for immune responses of genotypes of 9 of the alloantigen systems (A, B, C, D, E, H, I, L, and P) has been established by producing test progeny from a single cross of parent lines segregating for genes of each of the systems.
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Affiliation(s)
- W E Briles
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois 60115, USA.
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Su HB, Zhang YG, He JT, Mo W, Zhang YL, Tao XM, Song HY. Construction and characterization of novel staphylokinase variants with antiplatelet aggregation activity and reduced immunogenecity. Acta Biochim Biophys Sin (Shanghai) 2004; 36:336-42. [PMID: 15156275 DOI: 10.1093/abbs/36.5.336] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To develop target thrombolytic agents with fibrinolytic activity, antiplatelet aggregation activity and reduced immunogenicity, two staphylokinase variants containing Arg-Gly-Asp (RGD) motif were constructed. Gene expression was induced in E. coli JF1125 and the variants, designated DGR and RL1, were purified with gel filtration and ion-exchange chromatography and the purity was over 95%. The fibrinolytic activity and kinetic constants of the two variants were comparable to those of recombinant wild-type staphylokinase. Both the variants can inhibit the platelet aggregation at a final concentration of 2 microM. The titers of antibodies against variants were much lower than those against recombinant staphylokinase in guinea pigs, which indicated that the immunogenicity of the variants was greatly reduced. These results confirm that it is possible to design and produce a bifunctional protein that possesses fibrinolytic and antiplatelet aggregation activities.
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Affiliation(s)
- Hua-Bo Su
- Department of Molecular Genetics, Shanghai Medical School, Fudan University, Key Laboratory of Molecular Medicine, Ministry of Education, Shanghai 200032, China
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Mohabatkar H, Kar SK. Prediction of exposed domains of envelope glycoprotein in Indian HIV-1 isolates and experimental confirmation of their immunogenicity in humans. Braz J Med Biol Res 2004; 37:675-81. [PMID: 15107929 DOI: 10.1590/s0100-879x2004000500008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We describe the impact of subtype differences on the seroreactivity of linear antigenic epitopes in envelope glycoprotein of HIV-1 isolates from different geographical locations. By computer analysis, we predicted potential antigenic sites of envelope glycoprotein (gp120 and gp4l) of this virus. For this purpose, after fetching sequences of proteins of interest from data banks, values of hydrophilicity, flexibility, accessibility, inverted hydrophobicity, and secondary structure were considered. We identified several potential antigenic epitopes in a B subtype strain of envelope glycoprotein of HIV-1 (IIIB). Solid- phase peptide synthesis methods of Merrifield and Fmoc chemistry were used for synthesizing peptides. These synthetic peptides corresponded mainly to the C2, V3 and CD4 binding sites of gp120 and some parts of the ectodomain of gp41. The reactivity of these peptides was tested by ELISA against different HIV-1-positive sera from different locations in India. For two of these predicted epitopes, the corresponding Indian consensus sequences (LAIERYLKQQLLGWG and DIIGDIRQAHCNISEDKWNET) (subtype C) were also synthesized and their reactivity was tested by ELISA. These peptides also distinguished HIV-1-positive sera of Indians with C subtype infections from sera from HIV-negative subjects.
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Affiliation(s)
- H Mohabatkar
- Centre for Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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Armandola E. Conference report--adjuvants and delivery: improving on vaccine immunogenicity highlights from the viral vaccine meeting; October 25-28, 2003; Barcelona, Spain. MedGenMed 2004; 6:46. [PMID: 15208557 PMCID: PMC1140700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
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Cordwell SJ. Exploring and exploiting bacterial proteomes. Methods Mol Biol 2004; 266:115-35. [PMID: 15148417 DOI: 10.1385/1-59259-763-7:115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
The plethora of data now available from bacterial genome sequencing has opened a wealth of new research opportunities. Many of these have been reviewed in preceding chapters. Genomics alone, however, cannot capture a biological snapshot from an organism at a given point in time. The genome itself is static, and it is the changes in expression of genes, leading to the production of functional proteins, which allows an organism to survive and adapt to a constantly changing environment. Proteomics is the term used to describe the global analysis of proteins involved in a particular biological process. Such processes may be analyzed via comparative studies that examine bacterial strain differences, both phenotypic and genetic, bacteria grown under nutrient limiting conditions, growth phase, temperature, or in the presence of chemical compounds, such as antibiotics. Proteomics also provides the researcher with a tool to begin characterizing the functions of the vast proportion of "hypothetical" or "unknown" proteins elucidated from genome sequencing and database comparisons. For example, study of protein-protein, protein-ligand, protein-substrate, and protein-nucleic acid interactions for a given target protein may all help to define the functions of previously unknown proteins. Furthermore, genetic manipulation combined with proteomics technologies can provide an understanding of how gene expression is regulated. This chapter examines the technologies used in proteome analysis and the applications of proteomics to microbiological research, with an emphasis on clinically-relevant bacteria.
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Affiliation(s)
- Stuart J Cordwell
- Australian Proteome Analysis Facility, Macquarie University, Sydney, Australia
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Yamanaka R, Tsuchiya N, Yajima N, Honma J, Hasegawa H, Tanaka R, Ramsey J, Blaese RM, Xanthopoulos KG. Induction of an antitumor immunological response by an intratumoral injection of dendritic cells pulsed with genetically engineered Semliki Forest virus to produce interleukin-18 combined with the systemic administration of interleukin-12. J Neurosurg 2003; 99:746-53. [PMID: 14567611 DOI: 10.3171/jns.2003.99.4.0746] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECT The aim of this study was to investigate further immunogene treatment of malignant brain tumor to improve its therapeutic efficacy. METHODS Intratumoral dendritic cells pulsed with Semliki Forest virus (SFV)-interleukin-18 (IL-18) and/or systemic IL-12 were injected into mice bearing the B16 brain tumor. To study the immune mechanisms involved in tumor regression, we monitored the growth of implanted B16 brain tumor cells in T cell-depleted mice and IFNgamma-neutralized mice. To analyze the protective immunity created by tumor inoculation, B16 cells were injected into the left thighs of mice that had received an inoculation, and tumor growth was monitored. The local delivery of dendritic cells pulsed with IL-18 bound by SFV combined with the systemic administration of IL-12 enhanced the induction of the T helper type 1 response from tumor-specific CD4+ and CD8+ T cells and natural killer cells as well as antitumor immunity. Interferon-gamma is partly responsible for this IL-18-mediated antitumor immunity. Furthermore, the protective immunity is mediated mainly by CD8+ T cells. CONCLUSIONS Immunogene therapy that combines the local administration of dendritic cells pulsed with IL-18 bound by SFV and the systemic administration of IL-12 may be an excellent candidate for the development of a new treatment protocol. A self-replicating SFV system may therefore open a novel approach for the treatment of malignant brain tumor.
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MESH Headings
- Animals
- Antibody Formation
- Antigens, CD/genetics
- Antigens, CD/immunology
- Brain Neoplasms/immunology
- Brain Neoplasms/therapy
- Brain Neoplasms/virology
- Cricetinae
- DNA Primers/genetics
- DNA Primers/immunology
- DNA, Complementary/genetics
- DNA, Complementary/immunology
- Dendritic Cells/immunology
- Dendritic Cells/virology
- Genetic Engineering/methods
- Genetic Therapy/methods
- Glioma/immunology
- Glioma/therapy
- Glioma/virology
- Immunogenetics/methods
- Immunotherapy, Active/methods
- Interleukin-12/biosynthesis
- Interleukin-12/immunology
- Interleukin-12/therapeutic use
- Interleukin-18/biosynthesis
- Interleukin-18/immunology
- Interleukin-18/therapeutic use
- Killer Cells, Natural/immunology
- Male
- Mice
- Mice, Inbred C57BL
- Reverse Transcriptase Polymerase Chain Reaction
- Semliki forest virus/immunology
- T-Lymphocytes, Helper-Inducer/immunology
- Transduction, Genetic
- Tumor Cells, Cultured/transplantation
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Affiliation(s)
- Ryuya Yamanaka
- Clinical Gene Therapy Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA.
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Abstract
A better description of the immune system can be afforded if the latest developments in bioinformatics are applied to integrate sequence with structure and function. Clear guidelines for the upgrade of the bioinformatic capability of the immunogenetics laboratory are discussed in the light of more powerful methods to detect homology, combined approaches to predict the three dimensional properties of a protein and a robust strategy to represent the biological role of a gene.
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Affiliation(s)
- Bernard de Bono
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
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